---
OA_place: repository
OA_type: green
_id: '21039'
abstract:
- lang: eng
text: Cellular plasticity, the ability of a differentiated cell to adopt another
phenotypic identity, is restricted under basal conditions, but can be elicited
upon damage. However, the molecular mechanism enabling such plasticity remains
largely unexplored. Here, we report damage-induced cellular plasticity of secretory
enteroendocrine cells (EEs) in the adult Drosophila midgut. Ionizing radiation
induces EE fate conversion and activates stress-responsive programs in EE lineages,
accompanied by the induction of the stress-inducible transcription factor Xrp1
and the cytokine gene upd3. Xrp1 and upd3 are both necessary for radiation-induced
EE plasticity. Under basal conditions, EE-specific Xrp1 overexpression triggers
ectopic expression of progenitor-specific genes, which is necessary for Xrp1 to
drive EE plasticity. Our work identifies Xrp1 as a crucial regulator that coordinates
damage-induced signaling and transcriptional reprogramming, enabling the reactivation
of cellular plasticity in differentiated cells.
acknowledgement: We thank Pierre Léopold, Tatsushi Igaki, Erik Storkebaum, Tobias
Reiff, Masayuki Miura, Xiaohang Yang, Mikio Furuse, Bloomington Drosophila Stock
Center and Developmental Studies Hybridoma Bank for providing us with fly stocks
and reagents. We are also grateful to Hiromi Yanagisawa, Satoru Kobayashi, Md Al
Amin Sheikh and Yaxuan Cui for allowing us to use their equipment, and to Allison
Bardin, Pierre Léopold and Tadashi Uemura for helpful discussions.
article_number: dev205225
article_processing_charge: No
article_type: original
author:
- first_name: Qingyin
full_name: Qian, Qingyin
last_name: Qian
- first_name: Hiroki
full_name: Nagai, Hiroki
id: 608df3e6-e2ab-11ed-8890-c9318cec7da4
last_name: Nagai
orcid: 0000-0003-1671-9434
- first_name: Yuya
full_name: Sanaki, Yuya
last_name: Sanaki
- first_name: Makoto
full_name: Hayashi, Makoto
last_name: Hayashi
- first_name: Kenichi
full_name: Kimura, Kenichi
last_name: Kimura
- first_name: Yu Ichiro
full_name: Nakajima, Yu Ichiro
last_name: Nakajima
- first_name: Ryusuke
full_name: Niwa, Ryusuke
last_name: Niwa
citation:
ama: Qian Q, NAGAI H, Sanaki Y, et al. Xrp1 drives damage-induced cellular plasticity
of enteroendocrine cells in the adult Drosophila midgut. Development. 2026;153(2).
doi:10.1242/dev.205225
apa: Qian, Q., NAGAI, H., Sanaki, Y., Hayashi, M., Kimura, K., Nakajima, Y. I.,
& Niwa, R. (2026). Xrp1 drives damage-induced cellular plasticity of enteroendocrine
cells in the adult Drosophila midgut. Development. The Company of Biologists.
https://doi.org/10.1242/dev.205225
chicago: Qian, Qingyin, HIROKI NAGAI, Yuya Sanaki, Makoto Hayashi, Kenichi Kimura,
Yu Ichiro Nakajima, and Ryusuke Niwa. “Xrp1 Drives Damage-Induced Cellular Plasticity
of Enteroendocrine Cells in the Adult Drosophila Midgut.” Development.
The Company of Biologists, 2026. https://doi.org/10.1242/dev.205225.
ieee: Q. Qian et al., “Xrp1 drives damage-induced cellular plasticity of
enteroendocrine cells in the adult Drosophila midgut,” Development, vol.
153, no. 2. The Company of Biologists, 2026.
ista: Qian Q, NAGAI H, Sanaki Y, Hayashi M, Kimura K, Nakajima YI, Niwa R. 2026.
Xrp1 drives damage-induced cellular plasticity of enteroendocrine cells in the
adult Drosophila midgut. Development. 153(2), dev205225.
mla: Qian, Qingyin, et al. “Xrp1 Drives Damage-Induced Cellular Plasticity of Enteroendocrine
Cells in the Adult Drosophila Midgut.” Development, vol. 153, no. 2, dev205225,
The Company of Biologists, 2026, doi:10.1242/dev.205225.
short: Q. Qian, H. NAGAI, Y. Sanaki, M. Hayashi, K. Kimura, Y.I. Nakajima, R. Niwa,
Development 153 (2026).
date_created: 2026-01-25T23:01:39Z
date_published: 2026-01-15T00:00:00Z
date_updated: 2026-02-12T12:41:18Z
day: '15'
department:
- _id: XiFe
doi: 10.1242/dev.205225
external_id:
pmid:
- '41392708'
intvolume: ' 153'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2025.07.05.662934
month: '01'
oa: 1
oa_version: Preprint
pmid: 1
publication: Development
publication_identifier:
eissn:
- 1477-9129
issn:
- 0950-1991
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
scopus_import: '1'
status: public
title: Xrp1 drives damage-induced cellular plasticity of enteroendocrine cells in
the adult Drosophila midgut
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 153
year: '2026'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '21158'
abstract:
- lang: eng
text: Vernalization-regulated flowering is vital for wheat yield and geographical
distribution, and the diversity of flowering time genes is essential for the breeding
of climate-resilient varieties. Sugars have long been recognized in regulating
flowering; however, the intrinsic connection between carbohydrate metabolism and
vernalization response remains largely unexplored. Here, we identify a fructose
1,6-bisphosphate aldolase (FBA) encoding gene, HtL1/FBA10, as a modulator of heading
time variation based on a genome-wide association study utilizing wheat core germplasm
collections. Evolutionary analysis shows a decrease in the proportion of haplotype-2
of HtL1, which is linked to delayed flowering, in Chinese and American wheat varieties
compared to landraces. Vernalization reduces HtL1/FBA10 phosphorylation levels
and increases its O-GlcNAcylation, which in turn enhances its enzymatic activity
and facilitates VERNALIZATION 1 (VRN1) transcription by regulating histone acetylation
at the VRN1 locus. Our findings provide mechanistic insights into the interplay
between glucose metabolism and the epigenetic regulation of vernalization in winter
wheat.
acknowledgement: This work was supported by the Basic Science Center Project of National
Natural Science Foundation of China (32388201) to K.C and the National Natural Science
Foundation of China (31970331) to L.X. We thank Dr. Zhuang Lu, Dr. Bin Han and Ms.
Jingquan Li (Plant Science Facility of the Institute of Botany, Chinese Academy
of Sciences) for their technical assistance in LC-MS/MS assay, small molecule compound
analysis and the subcellular localization assay, respectively. We thank Dr. Wei
Luo and Dr. Dongfeng Liu for helpful discussions.
article_number: '999'
article_processing_charge: Yes
article_type: original
author:
- first_name: Pengfang
full_name: Yang, Pengfang
last_name: Yang
- first_name: Yangyang
full_name: Liu, Yangyang
last_name: Liu
- first_name: Qi
full_name: Dong, Qi
last_name: Dong
- first_name: Yuting
full_name: Miao, Yuting
last_name: Miao
- first_name: Jianlong
full_name: Zhang, Jianlong
last_name: Zhang
- first_name: Shujuan
full_name: Xu, Shujuan
id: 9724dd9d-f591-11ee-bd51-e97ed0652286
last_name: Xu
- first_name: Hong
full_name: Zhao, Hong
last_name: Zhao
- first_name: Yuda
full_name: Niu, Yuda
last_name: Niu
- first_name: Xueyong
full_name: Zhang, Xueyong
last_name: Zhang
- first_name: Yunyuan
full_name: Xu, Yunyuan
last_name: Xu
- first_name: Zifeng
full_name: Guo, Zifeng
last_name: Guo
- first_name: Lijing
full_name: Xing, Lijing
last_name: Xing
- first_name: Kang
full_name: Chong, Kang
last_name: Chong
citation:
ama: Yang P, Liu Y, Dong Q, et al. O-GlcNAc and phosphorylation modifications on
HtL1/FBA10 regulate wheat vernalization for flowering. Nature Communications.
2026;17. doi:10.1038/s41467-025-67734-0
apa: Yang, P., Liu, Y., Dong, Q., Miao, Y., Zhang, J., Xu, S., … Chong, K. (2026).
O-GlcNAc and phosphorylation modifications on HtL1/FBA10 regulate wheat vernalization
for flowering. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-025-67734-0
chicago: Yang, Pengfang, Yangyang Liu, Qi Dong, Yuting Miao, Jianlong Zhang, Shujuan
Xu, Hong Zhao, et al. “O-GlcNAc and Phosphorylation Modifications on HtL1/FBA10
Regulate Wheat Vernalization for Flowering.” Nature Communications. Springer
Nature, 2026. https://doi.org/10.1038/s41467-025-67734-0.
ieee: P. Yang et al., “O-GlcNAc and phosphorylation modifications on HtL1/FBA10
regulate wheat vernalization for flowering,” Nature Communications, vol.
17. Springer Nature, 2026.
ista: Yang P, Liu Y, Dong Q, Miao Y, Zhang J, Xu S, Zhao H, Niu Y, Zhang X, Xu Y,
Guo Z, Xing L, Chong K. 2026. O-GlcNAc and phosphorylation modifications on HtL1/FBA10
regulate wheat vernalization for flowering. Nature Communications. 17, 999.
mla: Yang, Pengfang, et al. “O-GlcNAc and Phosphorylation Modifications on HtL1/FBA10
Regulate Wheat Vernalization for Flowering.” Nature Communications, vol.
17, 999, Springer Nature, 2026, doi:10.1038/s41467-025-67734-0.
short: P. Yang, Y. Liu, Q. Dong, Y. Miao, J. Zhang, S. Xu, H. Zhao, Y. Niu, X. Zhang,
Y. Xu, Z. Guo, L. Xing, K. Chong, Nature Communications 17 (2026).
date_created: 2026-02-08T23:02:48Z
date_published: 2026-01-27T00:00:00Z
date_updated: 2026-02-12T14:34:24Z
day: '27'
ddc:
- '580'
department:
- _id: XiFe
doi: 10.1038/s41467-025-67734-0
external_id:
pmid:
- '41455723'
file:
- access_level: open_access
checksum: 9ae170ec70ba1ab56b6f1ffe67d1de7f
content_type: application/pdf
creator: dernst
date_created: 2026-02-12T14:33:14Z
date_updated: 2026-02-12T14:33:14Z
file_id: '21223'
file_name: 2026_NatureComm_Yang.pdf
file_size: 4685882
relation: main_file
success: 1
file_date_updated: 2026-02-12T14:33:14Z
has_accepted_license: '1'
intvolume: ' 17'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: O-GlcNAc and phosphorylation modifications on HtL1/FBA10 regulate wheat vernalization
for flowering
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '21752'
abstract:
- lang: eng
text: Epithelial tissues function as multicellular communities that preserve tissue
integrity while adapting to diverse environmental stresses by altering cell behaviors.
A striking manifestation of such adaptability is cell plasticity, the ability
of differentiated cells to revert to stem-like states or adopt alternative fates.
Once considered rare and confined to highly regenerative species, cell plasticity
is now recognized across the metazoan tree. In early-branching animals such as
sponges and cnidarians, transdifferentiation and dedifferentiation are integral
to life-cycle transitions and regeneration, whereas in more complex organisms,
these processes typically emerge under stress, including stem cell loss or environmental
perturbations. Here, we examine epithelial cell plasticity through evolutionary,
cellular, and molecular perspectives. Focusing on the intestinal epithelium, we
explore findings from mammalian and Drosophila models showing that progenitors
and even terminally differentiated cells can dedifferentiate in response to external
stimuli that disrupt homeostasis, such as pathogen infection and nutrient fluctuations.
We further discuss conserved mechanisms involving intercellular signaling (e.g.,
Notch, EGFR, and JAK-STAT) and chromatin states primed for reprogramming, modulated
by metabolic cues. Together, these insights position cell plasticity as an ancient
environmental adaptation strategy, shaped by conserved molecular toolkits and
refined by species- and cell lineage-specific innovations.
acknowledgement: This work was supported by JSPS/MEXT KAKENHI (grant numbers JP22J01430
to H.N., JP23H04696, JP23K24025, JP25H02543, JP25K02406 to Y.N.), JST FOREST Program
JPMJFR233E (Y.N.), The Cell Science Research Foundation (Y.N.), and Takeda Science
Foundation (Y.N.).
article_number: '103670'
article_processing_charge: Yes (in subscription journal)
article_type: review
author:
- first_name: Hiroki
full_name: Nagai, Hiroki
id: 608df3e6-e2ab-11ed-8890-c9318cec7da4
last_name: Nagai
orcid: 0000-0003-1671-9434
- first_name: Yu Ichiro
full_name: Nakajima, Yu Ichiro
last_name: Nakajima
citation:
ama: 'NAGAI H, Nakajima YI. Epithelial cell plasticity in metazoans: Evolutionary
insights into roles and mechanisms. Seminars in Cell and Developmental Biology.
2026;179-180. doi:10.1016/j.semcdb.2026.103670'
apa: 'NAGAI, H., & Nakajima, Y. I. (2026). Epithelial cell plasticity in metazoans:
Evolutionary insights into roles and mechanisms. Seminars in Cell and Developmental
Biology. Elsevier. https://doi.org/10.1016/j.semcdb.2026.103670'
chicago: 'NAGAI, HIROKI, and Yu Ichiro Nakajima. “Epithelial Cell Plasticity in
Metazoans: Evolutionary Insights into Roles and Mechanisms.” Seminars in Cell
and Developmental Biology. Elsevier, 2026. https://doi.org/10.1016/j.semcdb.2026.103670.'
ieee: 'H. NAGAI and Y. I. Nakajima, “Epithelial cell plasticity in metazoans: Evolutionary
insights into roles and mechanisms,” Seminars in Cell and Developmental Biology,
vol. 179–180. Elsevier, 2026.'
ista: 'NAGAI H, Nakajima YI. 2026. Epithelial cell plasticity in metazoans: Evolutionary
insights into roles and mechanisms. Seminars in Cell and Developmental Biology.
179–180, 103670.'
mla: 'NAGAI, HIROKI, and Yu Ichiro Nakajima. “Epithelial Cell Plasticity in Metazoans:
Evolutionary Insights into Roles and Mechanisms.” Seminars in Cell and Developmental
Biology, vol. 179–180, 103670, Elsevier, 2026, doi:10.1016/j.semcdb.2026.103670.'
short: H. NAGAI, Y.I. Nakajima, Seminars in Cell and Developmental Biology 179–180
(2026).
corr_author: '1'
date_created: 2026-04-19T22:07:49Z
date_published: 2026-05-01T00:00:00Z
date_updated: 2026-04-28T14:11:13Z
day: '01'
ddc:
- '570'
department:
- _id: XiFe
doi: 10.1016/j.semcdb.2026.103670
file:
- access_level: open_access
checksum: 0a0929a045d0cbd964297768833c14ae
content_type: application/pdf
creator: dernst
date_created: 2026-04-28T13:58:47Z
date_updated: 2026-04-28T13:58:47Z
file_id: '21775'
file_name: 2026_SeminarsCellDevBiology_Nagai.pdf
file_size: 1306613
relation: main_file
success: 1
file_date_updated: 2026-04-28T13:58:47Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
publication: Seminars in Cell and Developmental Biology
publication_identifier:
eissn:
- 1096-3634
issn:
- 1084-9521
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Epithelial cell plasticity in metazoans: Evolutionary insights into roles
and mechanisms'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 179-180
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '21716'
abstract:
- lang: eng
text: Male germline development in plants is highly sensitive to heat stress, with
elevated temperatures frequently impairing male fertility and consequently reducing
seed production. Indeed, recent global warming has decreased major crop yields,
emphasizing the urgent need to elucidate the molecular and cellular mechanisms
underlying heat-induced male sterility. This review synthesizes current knowledge
on how heat stress disrupts microsporogenesis and microgametogenesis, and how
plants counteract these stresses through diverse thermotolerance mechanisms. We
emphasize temperature-sensitive processes, including meiotic progression in male
germ cells, programmed cell death of somatic tapetal nurse cells, and post-meiotic
pollen tube development. We further discuss how epigenetic regulators enhance
thermotolerance by reprogramming DNA methylation landscapes and modulating histone
variant distribution. Finally, we propose future directions aimed at understanding
the mechanisms of reproductive thermotolerance from the epigenetic perspective.
acknowledgement: This work was supported by JSPS KAKENHI (grant number JP22J01430)
and the Osamu Hayaishi Memorial Scholarship for Study Abroad for H.N.
article_number: '102881'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Hiroki
full_name: Nagai, Hiroki
id: 608df3e6-e2ab-11ed-8890-c9318cec7da4
last_name: Nagai
orcid: 0000-0003-1671-9434
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
citation:
ama: NAGAI H, Feng X. Genetic and epigenetic mechanisms underlying male reproductive
thermotolerance. Current Opinion in Plant Biology. 2026;91(6). doi:10.1016/j.pbi.2026.102881
apa: NAGAI, H., & Feng, X. (2026). Genetic and epigenetic mechanisms underlying
male reproductive thermotolerance. Current Opinion in Plant Biology. Elsevier.
https://doi.org/10.1016/j.pbi.2026.102881
chicago: NAGAI, HIROKI, and Xiaoqi Feng. “Genetic and Epigenetic Mechanisms Underlying
Male Reproductive Thermotolerance.” Current Opinion in Plant Biology. Elsevier,
2026. https://doi.org/10.1016/j.pbi.2026.102881.
ieee: H. NAGAI and X. Feng, “Genetic and epigenetic mechanisms underlying male reproductive
thermotolerance,” Current Opinion in Plant Biology, vol. 91, no. 6. Elsevier,
2026.
ista: NAGAI H, Feng X. 2026. Genetic and epigenetic mechanisms underlying male reproductive
thermotolerance. Current Opinion in Plant Biology. 91(6), 102881.
mla: NAGAI, HIROKI, and Xiaoqi Feng. “Genetic and Epigenetic Mechanisms Underlying
Male Reproductive Thermotolerance.” Current Opinion in Plant Biology, vol.
91, no. 6, 102881, Elsevier, 2026, doi:10.1016/j.pbi.2026.102881.
short: H. NAGAI, X. Feng, Current Opinion in Plant Biology 91 (2026).
corr_author: '1'
date_created: 2026-04-12T22:01:50Z
date_published: 2026-04-01T00:00:00Z
date_updated: 2026-05-04T11:15:57Z
day: '01'
ddc:
- '580'
department:
- _id: XiFe
doi: 10.1016/j.pbi.2026.102881
has_accepted_license: '1'
intvolume: ' 91'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.pbi.2026.102881
month: '04'
oa: 1
oa_version: Published Version
publication: Current Opinion in Plant Biology
publication_identifier:
eissn:
- 1879-0356
issn:
- 1369-5266
publication_status: epub_ahead
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genetic and epigenetic mechanisms underlying male reproductive thermotolerance
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 91
year: '2026'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '20220'
abstract:
- lang: eng
text: Stress granules (SG) are biomolecular condensates that represent an adaptive
response of cells to various stresses, including heat. However, the cell type–specific
function and relevance of SG formation, especially during reproductive development,
are largely not understood. Here, we show that the meiotic A-type cyclin TARDY
ASYNCHRONOUS MEIOSIS (TAM) is recruited to SGs in male meiocytes of Arabidopsis
after exposure to heat. We find that the amino terminus of TAM is necessary and
sufficient for the localization of proteins to meiotic SGs. Swapping the amino
terminus of TAM with the one of its sister protein CYCA1;1 resulted in a separation-of-function
allele of TAM, which prevents the partitioning of TAM to SGs while restoring a
wild-type phenotype in a tam mutant background under nonheat stress conditions.
Notably, plants expressing this TAM version prematurely terminate meiosis under
heat resulting in unreduced gametes. Thus, the formation of TAM-containing SGs
is necessary for genome stability under heat stress.
acknowledged_ssus:
- _id: Bio
acknowledgement: "We thank L. Strader (Duke University, Durham) and A. Holehouse (Washington
University, Saint Louis) for discussion and input in LLPS. We thank T. Nakagawa
(Shimane University, Matsue) for providing the pGWB604 Gateway vector containing
bar gene identified by Meiji Seika Kaisha Ltd. We thank M. Heese (Hamburg University)
for the critical reading and comments on this manuscript. We further thank J. Mehrmann
(Hamburg University) for technical assistance. We thank the ISTA imaging facility
for assistance for microscopy.\r\nThis project has received funding from JST-PRESTO
(JPMJPR18H7), JST-CREST (JPMJCR18H4), European Union’s Horizon 2020 under MSCA grant
101034413, and a federal grant from the state of Hamburg (LFF-BiCon)."
article_processing_charge: Yes
article_type: original
author:
- first_name: Joke G
full_name: De Jaeger-Braet, Joke G
id: 26bd38d3-c59a-11ee-a1af-d7a988cafcc5
last_name: De Jaeger-Braet
- first_name: Merle
full_name: Hartmann, Merle
last_name: Hartmann
- first_name: Lev
full_name: Böttger, Lev
last_name: Böttger
- first_name: Chao
full_name: Yang, Chao
id: 082e3e6e-8069-11ed-8390-c8cce7b1aaca
last_name: Yang
- first_name: Takahiro
full_name: Hamada, Takahiro
last_name: Hamada
- first_name: Stefan
full_name: Hoth, Stefan
last_name: Hoth
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Magdalena
full_name: Weingartner, Magdalena
last_name: Weingartner
- first_name: Arp
full_name: Schnittger, Arp
last_name: Schnittger
citation:
ama: De Jaeger-Braet JG, Hartmann M, Böttger L, et al. The recruitment of the A-type
cyclin TAM to stress granules is crucial for meiotic fidelity under heat. Science
Advances. 2025;11(32):eadr5694. doi:10.1126/sciadv.adr5694
apa: De Jaeger-Braet, J. G., Hartmann, M., Böttger, L., Yang, C., Hamada, T., Hoth,
S., … Schnittger, A. (2025). The recruitment of the A-type cyclin TAM to stress
granules is crucial for meiotic fidelity under heat. Science Advances.
AAAS. https://doi.org/10.1126/sciadv.adr5694
chicago: De Jaeger-Braet, Joke G, Merle Hartmann, Lev Böttger, Chao Yang, Takahiro
Hamada, Stefan Hoth, Xiaoqi Feng, Magdalena Weingartner, and Arp Schnittger. “The
Recruitment of the A-Type Cyclin TAM to Stress Granules Is Crucial for Meiotic
Fidelity under Heat.” Science Advances. AAAS, 2025. https://doi.org/10.1126/sciadv.adr5694.
ieee: J. G. De Jaeger-Braet et al., “The recruitment of the A-type cyclin
TAM to stress granules is crucial for meiotic fidelity under heat,” Science
Advances, vol. 11, no. 32. AAAS, p. eadr5694, 2025.
ista: De Jaeger-Braet JG, Hartmann M, Böttger L, Yang C, Hamada T, Hoth S, Feng
X, Weingartner M, Schnittger A. 2025. The recruitment of the A-type cyclin TAM
to stress granules is crucial for meiotic fidelity under heat. Science Advances.
11(32), eadr5694.
mla: De Jaeger-Braet, Joke G., et al. “The Recruitment of the A-Type Cyclin TAM
to Stress Granules Is Crucial for Meiotic Fidelity under Heat.” Science Advances,
vol. 11, no. 32, AAAS, 2025, p. eadr5694, doi:10.1126/sciadv.adr5694.
short: J.G. De Jaeger-Braet, M. Hartmann, L. Böttger, C. Yang, T. Hamada, S. Hoth,
X. Feng, M. Weingartner, A. Schnittger, Science Advances 11 (2025) eadr5694.
date_created: 2025-08-24T22:01:30Z
date_published: 2025-08-08T00:00:00Z
date_updated: 2025-09-30T14:24:10Z
day: '08'
ddc:
- '580'
department:
- _id: XiFe
doi: 10.1126/sciadv.adr5694
ec_funded: 1
external_id:
isi:
- '001549102600016'
file:
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checksum: 0f1ae246acc9b075f01bf4afe382c8ba
content_type: application/pdf
creator: dernst
date_created: 2025-09-02T07:05:37Z
date_updated: 2025-09-02T07:05:37Z
file_id: '20270'
file_name: 2025_ScienceAdvance_DeJaegerBraet.pdf
file_size: 10876817
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success: 1
file_date_updated: 2025-09-02T07:05:37Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '32'
language:
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month: '08'
oa: 1
oa_version: Published Version
page: eadr5694
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Science Advances
publication_identifier:
eissn:
- 2375-2548
publication_status: published
publisher: AAAS
quality_controlled: '1'
scopus_import: '1'
status: public
title: The recruitment of the A-type cyclin TAM to stress granules is crucial for
meiotic fidelity under heat
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 11
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20656'
abstract:
- lang: eng
text: Phytohormone auxin and its directional transport mediate much of the remarkably
plastic development of higher plants. Positive feedback between auxin signaling
and transport is a prerequisite for (1) self-organizing processes, including vascular
tissue formation, and (2) directional growth responses such as gravitropism. Here,
we identify a mechanism by which auxin signaling directly targets PIN auxin transporters.
Via the cell-surface AUXIN-BINDING PROTEIN1 (ABP1)-TRANSMEMBRANE KINASE 1 (TMK1)
receptor module, auxin rapidly induces phosphorylation and thus stabilization
of PIN2. Following gravistimulation, initial auxin asymmetry activates autophosphorylation
of the TMK1 kinase. This induces TMK1 interaction with and phosphorylation of
PIN2, stabilizing PIN2 at the lower root side, thus reinforcing asymmetric auxin
flow for root bending. Upstream of TMK1 in this regulation, ABP1 acts redundantly
with the root-expressed ABP1-LIKE 3 (ABL3) auxin receptor. Such positive feedback
between cell-surface auxin signaling and PIN-mediated polar auxin transport is
fundamental for robust root gravitropism and presumably for other self-organizing
developmental phenomena.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: We gratefully acknowledge Tongda Xu for experimental, material, and
conceptual support. We thank William Gray for providing material, Nataliia Gnyliukh
and Ema Cervenova for help with manuscript preparation, and Julia Schmid for help
with cloning. We thank Dolf Weijers, Mark Roosjen, and Andre Kuhn for discussions
and support with phospho-proteomic analyses. We thank the Bioimaging and Life Science
facilities at the Institute of Science and Technology Austria (ISTA) for their excellent
service and assistance. The research leading to these results has received funding
from the European Union (ERC, CYNIPS, 101142681) and Austrian Science Fund (FWF;
I 6123-B) to J.F., and Y.J. was funded by ERC no. 3363360-APPL under FP/2007-2013.
L.R. was supported by the FP7-PEOPLE-2011-COFUND ISTFELLOW program (IC1023FELL01)
and the European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship
(ALTF 985-2016). S.T. was supported by the National Natural Science Foundation of
China (32321001, 32570366). The work of J.H. was supported by the project JG_2024_003
implemented within the Palacký University Young Researcher Grant.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Lesia
full_name: Rodriguez Solovey, Lesia
id: 3922B506-F248-11E8-B48F-1D18A9856A87
last_name: Rodriguez Solovey
orcid: 0000-0002-7244-7237
- first_name: Lukas
full_name: Fiedler, Lukas
id: 7c417475-8972-11ed-ae7b-8b674ca26986
last_name: Fiedler
- first_name: Minxia
full_name: Zou, Minxia
id: 5c243f41-03f3-11ec-841c-96faf48a7ef9
last_name: Zou
- first_name: Caterina
full_name: Giannini, Caterina
id: e3fdddd5-f6e0-11ea-865d-ca99ee6367f4
last_name: Giannini
- first_name: Aline
full_name: Monzer, Aline
id: 2DB5D88C-D7B3-11E9-B8FD-7907E6697425
last_name: Monzer
- first_name: Dmitrii
full_name: Vladimirtsev, Dmitrii
id: 60466724-5355-11ee-ae5a-fa55e8f99c3d
last_name: Vladimirtsev
- first_name: Marek
full_name: Randuch, Marek
id: 6ac4636d-15b2-11ec-abd3-fb8df79972ae
last_name: Randuch
- first_name: Yongfan
full_name: Yu, Yongfan
last_name: Yu
- first_name: Zuzana
full_name: Gelová, Zuzana
id: 0AE74790-0E0B-11E9-ABC7-1ACFE5697425
last_name: Gelová
orcid: 0000-0003-4783-1752
- first_name: Inge
full_name: Verstraeten, Inge
id: 362BF7FE-F248-11E8-B48F-1D18A9856A87
last_name: Verstraeten
orcid: 0000-0001-7241-2328
- first_name: Jakub
full_name: Hajny, Jakub
id: 4800CC20-F248-11E8-B48F-1D18A9856A87
last_name: Hajny
orcid: 0000-0003-2140-7195
- first_name: Meng
full_name: Chen, Meng
last_name: Chen
- first_name: Shutang
full_name: Tan, Shutang
id: 2DE75584-F248-11E8-B48F-1D18A9856A87
last_name: Tan
orcid: 0000-0002-0471-8285
- first_name: Lukas
full_name: Hörmayer, Lukas
id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87
last_name: Hörmayer
orcid: 0000-0001-8295-2926
- first_name: Lanxin
full_name: Li, Lanxin
id: 367EF8FA-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0002-5607-272X
- first_name: Maria Mar
full_name: Marques-Bueno, Maria Mar
last_name: Marques-Bueno
- first_name: Zainab
full_name: Quddoos, Zainab
id: 32ff3c64-04a0-11f0-a50f-d0c45bfac466
last_name: Quddoos
- first_name: Gergely
full_name: Molnar, Gergely
id: 34F1AF46-F248-11E8-B48F-1D18A9856A87
last_name: Molnar
- first_name: Ivan
full_name: Kulich, Ivan
id: 57a1567c-8314-11eb-9063-c9ddc3451a54
last_name: Kulich
- first_name: Yvon
full_name: Jaillais, Yvon
last_name: Jaillais
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Rodriguez Solovey L, Fiedler L, Zou M, et al. ABP1/ABL3-TMK1 cell-surface auxin
signaling targets PIN2-mediated auxin fluxes for root gravitropism. Cell.
2025;188(22):6138-6150.e17. doi:10.1016/j.cell.2025.08.026
apa: Rodriguez Solovey, L., Fiedler, L., Zou, M., Giannini, C., Monzer, A., Vladimirtsev,
D., … Friml, J. (2025). ABP1/ABL3-TMK1 cell-surface auxin signaling targets PIN2-mediated
auxin fluxes for root gravitropism. Cell. Elsevier. https://doi.org/10.1016/j.cell.2025.08.026
chicago: Rodriguez Solovey, Lesia, Lukas Fiedler, Minxia Zou, Caterina Giannini,
Aline Monzer, Dmitrii Vladimirtsev, Marek Randuch, et al. “ABP1/ABL3-TMK1 Cell-Surface
Auxin Signaling Targets PIN2-Mediated Auxin Fluxes for Root Gravitropism.” Cell.
Elsevier, 2025. https://doi.org/10.1016/j.cell.2025.08.026.
ieee: L. Rodriguez Solovey et al., “ABP1/ABL3-TMK1 cell-surface auxin signaling
targets PIN2-mediated auxin fluxes for root gravitropism,” Cell, vol. 188,
no. 22. Elsevier, p. 6138–6150.e17, 2025.
ista: Rodriguez Solovey L, Fiedler L, Zou M, Giannini C, Monzer A, Vladimirtsev
D, Randuch M, Yu Y, Gelová Z, Verstraeten I, Hajny J, Chen M, Tan S, Hörmayer
L, Li L, Marques-Bueno MM, Quddoos Z, Molnar G, Kulich I, Jaillais Y, Friml J.
2025. ABP1/ABL3-TMK1 cell-surface auxin signaling targets PIN2-mediated auxin
fluxes for root gravitropism. Cell. 188(22), 6138–6150.e17.
mla: Rodriguez Solovey, Lesia, et al. “ABP1/ABL3-TMK1 Cell-Surface Auxin Signaling
Targets PIN2-Mediated Auxin Fluxes for Root Gravitropism.” Cell, vol. 188,
no. 22, Elsevier, 2025, p. 6138–6150.e17, doi:10.1016/j.cell.2025.08.026.
short: L. Rodriguez Solovey, L. Fiedler, M. Zou, C. Giannini, A. Monzer, D. Vladimirtsev,
M. Randuch, Y. Yu, Z. Gelová, I. Verstraeten, J. Hajny, M. Chen, S. Tan, L. Hörmayer,
L. Li, M.M. Marques-Bueno, Z. Quddoos, G. Molnar, I. Kulich, Y. Jaillais, J. Friml,
Cell 188 (2025) 6138–6150.e17.
corr_author: '1'
date_created: 2025-11-19T09:44:31Z
date_published: 2025-10-30T00:00:00Z
date_updated: 2025-12-01T15:27:22Z
day: '30'
ddc:
- '580'
department:
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- _id: XiFe
doi: 10.1016/j.cell.2025.08.026
ec_funded: 1
external_id:
isi:
- '001616077900005'
pmid:
- '41043433'
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oa_version: Published Version
page: 6138-6150.e17
pmid: 1
project:
- _id: 8f347782-16d5-11f0-9cad-8c19706ee739
grant_number: '101142681'
name: Cyclic nucleotides as second messengers in plants
- _id: bd76d395-d553-11ed-ba76-f678c14f9033
grant_number: I06123
name: Peptide receptors for auxin canalization in Arabidopsis
- _id: 26060676-B435-11E9-9278-68D0E5697425
grant_number: ALTF 985-2016
name: Cell surface receptor complexes for auxin signaling in plants
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Cell
publication_identifier:
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
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title: ABP1/ABL3-TMK1 cell-surface auxin signaling targets PIN2-mediated auxin fluxes
for root gravitropism
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 188
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18823'
article_number: kiae651
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
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full_name: Cao, Dechang
last_name: Cao
- first_name: Joke G
full_name: De Jaeger-Braet, Joke G
id: 26bd38d3-c59a-11ee-a1af-d7a988cafcc5
last_name: De Jaeger-Braet
citation:
ama: 'Cao D, De Jaeger-Braet JG. Memory of maternal temperatures: DNA methylation
alterations across generations. Plant Physiology. 2025;197(1). doi:10.1093/plphys/kiae651'
apa: 'Cao, D., & De Jaeger-Braet, J. G. (2025). Memory of maternal temperatures:
DNA methylation alterations across generations. Plant Physiology. Oxford
University Press. https://doi.org/10.1093/plphys/kiae651'
chicago: 'Cao, Dechang, and Joke G De Jaeger-Braet. “Memory of Maternal Temperatures:
DNA Methylation Alterations across Generations.” Plant Physiology. Oxford
University Press, 2025. https://doi.org/10.1093/plphys/kiae651.'
ieee: 'D. Cao and J. G. De Jaeger-Braet, “Memory of maternal temperatures: DNA methylation
alterations across generations,” Plant Physiology, vol. 197, no. 1. Oxford
University Press, 2025.'
ista: 'Cao D, De Jaeger-Braet JG. 2025. Memory of maternal temperatures: DNA methylation
alterations across generations. Plant Physiology. 197(1), kiae651.'
mla: 'Cao, Dechang, and Joke G. De Jaeger-Braet. “Memory of Maternal Temperatures:
DNA Methylation Alterations across Generations.” Plant Physiology, vol.
197, no. 1, kiae651, Oxford University Press, 2025, doi:10.1093/plphys/kiae651.'
short: D. Cao, J.G. De Jaeger-Braet, Plant Physiology 197 (2025).
corr_author: '1'
date_created: 2025-01-12T23:04:02Z
date_published: 2025-01-01T00:00:00Z
date_updated: 2025-07-15T08:18:19Z
day: '01'
ddc:
- '580'
department:
- _id: XiFe
doi: 10.1093/plphys/kiae651
external_id:
isi:
- '001382979900001'
pmid:
- '39691053'
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checksum: a9b2a12d7bc6174f27e28413e9c77a9c
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oa_version: Published Version
pmid: 1
publication: Plant Physiology
publication_identifier:
eissn:
- 1532-2548
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Memory of maternal temperatures: DNA methylation alterations across generations'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 197
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '19367'
article_number: kiaf055
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Joke G
full_name: De Jaeger-Braet, Joke G
id: 26bd38d3-c59a-11ee-a1af-d7a988cafcc5
last_name: De Jaeger-Braet
citation:
ama: De Jaeger-Braet JG. Arabidopsis accessions and their difference in heat tolerance
during meiosis. Plant Physiology. 2025;197(2). doi:10.1093/plphys/kiaf055
apa: De Jaeger-Braet, J. G. (2025). Arabidopsis accessions and their difference
in heat tolerance during meiosis. Plant Physiology. Oxford University Press.
https://doi.org/10.1093/plphys/kiaf055
chicago: De Jaeger-Braet, Joke G. “Arabidopsis Accessions and Their Difference in
Heat Tolerance during Meiosis.” Plant Physiology. Oxford University Press,
2025. https://doi.org/10.1093/plphys/kiaf055.
ieee: J. G. De Jaeger-Braet, “Arabidopsis accessions and their difference in heat
tolerance during meiosis,” Plant Physiology, vol. 197, no. 2. Oxford University
Press, 2025.
ista: De Jaeger-Braet JG. 2025. Arabidopsis accessions and their difference in heat
tolerance during meiosis. Plant Physiology. 197(2), kiaf055.
mla: De Jaeger-Braet, Joke G. “Arabidopsis Accessions and Their Difference in Heat
Tolerance during Meiosis.” Plant Physiology, vol. 197, no. 2, kiaf055,
Oxford University Press, 2025, doi:10.1093/plphys/kiaf055.
short: J.G. De Jaeger-Braet, Plant Physiology 197 (2025).
corr_author: '1'
date_created: 2025-03-09T23:01:27Z
date_published: 2025-02-07T00:00:00Z
date_updated: 2025-09-30T10:48:08Z
day: '07'
ddc:
- '580'
department:
- _id: XiFe
doi: 10.1093/plphys/kiaf055
external_id:
isi:
- '001427994500001'
pmid:
- '39938057'
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checksum: 28e18fd7d00c74782f4f42501ecd4aae
content_type: application/pdf
creator: dernst
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date_updated: 2025-04-16T07:25:21Z
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language:
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oa_version: Published Version
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publication: Plant Physiology
publication_identifier:
eissn:
- 1532-2548
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Arabidopsis accessions and their difference in heat tolerance during meiosis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
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type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
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year: '2025'
...
---
OA_type: closed access
_id: '19406'
abstract:
- lang: eng
text: "Polyploidization is a common occurrence in the evolutionary history of flowering
plants, significantly contributing to their adaptability and diversity. However,
the molecular mechanisms behind these adaptive advantages are not well understood.\r\nThrough
comprehensive phenotyping of diploid and tetraploid clones from Citrus and Poncirus
genera, we discovered that genome doubling significantly enhances salt stress
resilience. Epigenetic and transcriptomic analyses revealed that increased ethylene
production in the roots of tetraploid plants was associated with hypomethylation
and enhanced chromatin accessibility of the ACO1 gene. This increased ethylene
production activates the transcription of reactive oxygen species scavenging genes
and stress-related hormone biosynthesis genes. Consequently, tetraploid plants
exhibited superior root functionality under salt stress, maintaining improved
cytosolic K+/Na+ homeostasis.\r\nTo genetically validate the link between salt
stress resilience and ACO1 expression, we generated overexpression and knockout
lines, confirming the central role of ACO1 expression regulation following genome
doubling in salt stress resilience.\r\nOur work elucidates the molecular mechanisms
underlying the role of genome doubling in stress resilience. We also highlight
the importance of chromatin dynamics in fine-tuning ethylene gene expression and
activating salt stress resilience pathways, offering valuable insights into plant
adaptation and crop genome evolution."
acknowledgement: We thank Prof. Qi Xie from the Institute of Genetics and Development,
Chinese Academy of Sciences, for providing the YAO promoter-driven CRISPR/Cas9 vector,
our colleague Dr Robert M. Larkin from Huazhong Agricultural University, and Dr
Olivier Martin from IPS2 (INRAE, France) for critical reading of the manuscript.
This research was financially supported by grants from the National Key Research
& Development Program of China (2024YFD1200501), the National Natural Science Foundation
of China (32172525 and 32202432), the Foundation of Hubei Hongshan laboratory (2021hszd009),
the China Agricultural Research System (CARS-26) and the Department of Science and
Technology of Hubei Province (2022BBA0019). A. Bendahmane is funded by the ANR BioAdapt
(ANR-21-LCV3-0003), LabEx Saclay Plant Sciences (SPS) (ANR-10-LABX-40-SPS), and
the NectarGland ERC Project (101095736).
article_processing_charge: No
article_type: original
author:
- first_name: Xin
full_name: Song, Xin
last_name: Song
- first_name: Miao
full_name: Zhang, Miao
last_name: Zhang
- first_name: Ting Ting
full_name: Wang, Ting Ting
last_name: Wang
- first_name: Yao Yuan
full_name: Duan, Yao Yuan
last_name: Duan
- first_name: Jie
full_name: Ren, Jie
last_name: Ren
- first_name: Hu
full_name: Gao, Hu
last_name: Gao
- first_name: Yan Jie
full_name: Fan, Yan Jie
last_name: Fan
- first_name: Qiang Ming
full_name: Xia, Qiang Ming
last_name: Xia
- first_name: Hui Xiang
full_name: Cao, Hui Xiang
last_name: Cao
- first_name: Kai Dong
full_name: Xie, Kai Dong
last_name: Xie
- first_name: Xiao Meng
full_name: Wu, Xiao Meng
last_name: Wu
- first_name: Fei
full_name: Zhang, Fei
last_name: Zhang
- first_name: Si Qi
full_name: Zhang, Si Qi
last_name: Zhang
- first_name: Ying
full_name: Huang, Ying
id: 11b5bbff-8b61-11ed-b69e-d8ddd6bce951
last_name: Huang
- first_name: Adnane
full_name: Boualem, Adnane
last_name: Boualem
- first_name: Abdelhafid
full_name: Bendahmane, Abdelhafid
last_name: Bendahmane
- first_name: Feng Quan
full_name: Tan, Feng Quan
last_name: Tan
- first_name: Wen Wu
full_name: Guo, Wen Wu
last_name: Guo
citation:
ama: Song X, Zhang M, Wang TT, et al. Polyploidization leads to salt stress resilience
via ethylene signaling in citrus plants. New Phytologist. 2025;246(1):176-191.
doi:10.1111/nph.20428
apa: Song, X., Zhang, M., Wang, T. T., Duan, Y. Y., Ren, J., Gao, H., … Guo, W.
W. (2025). Polyploidization leads to salt stress resilience via ethylene signaling
in citrus plants. New Phytologist. Wiley. https://doi.org/10.1111/nph.20428
chicago: Song, Xin, Miao Zhang, Ting Ting Wang, Yao Yuan Duan, Jie Ren, Hu Gao,
Yan Jie Fan, et al. “Polyploidization Leads to Salt Stress Resilience via Ethylene
Signaling in Citrus Plants.” New Phytologist. Wiley, 2025. https://doi.org/10.1111/nph.20428.
ieee: X. Song et al., “Polyploidization leads to salt stress resilience via
ethylene signaling in citrus plants,” New Phytologist, vol. 246, no. 1.
Wiley, pp. 176–191, 2025.
ista: Song X, Zhang M, Wang TT, Duan YY, Ren J, Gao H, Fan YJ, Xia QM, Cao HX, Xie
KD, Wu XM, Zhang F, Zhang SQ, Huang Y, Boualem A, Bendahmane A, Tan FQ, Guo WW.
2025. Polyploidization leads to salt stress resilience via ethylene signaling
in citrus plants. New Phytologist. 246(1), 176–191.
mla: Song, Xin, et al. “Polyploidization Leads to Salt Stress Resilience via Ethylene
Signaling in Citrus Plants.” New Phytologist, vol. 246, no. 1, Wiley, 2025,
pp. 176–91, doi:10.1111/nph.20428.
short: X. Song, M. Zhang, T.T. Wang, Y.Y. Duan, J. Ren, H. Gao, Y.J. Fan, Q.M. Xia,
H.X. Cao, K.D. Xie, X.M. Wu, F. Zhang, S.Q. Zhang, Y. Huang, A. Boualem, A. Bendahmane,
F.Q. Tan, W.W. Guo, New Phytologist 246 (2025) 176–191.
date_created: 2025-03-16T23:01:25Z
date_published: 2025-04-01T00:00:00Z
date_updated: 2025-09-30T11:00:06Z
day: '01'
department:
- _id: XiFe
doi: 10.1111/nph.20428
external_id:
isi:
- '001424915600001'
pmid:
- '39969116'
intvolume: ' 246'
isi: 1
issue: '1'
language:
- iso: eng
month: '04'
oa_version: None
page: 176-191
pmid: 1
publication: New Phytologist
publication_identifier:
eissn:
- 1469-8137
issn:
- 0028-646X
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Polyploidization leads to salt stress resilience via ethylene signaling in
citrus plants
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 246
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '19436'
abstract:
- lang: eng
text: Dynamic DNA methylation represses transposable elements (TEs) and regulates
gene activity, playing a pivotal role in plant development. Although substantial
progress has been made in understanding DNA methylation reprogramming during germline
development in Arabidopsis thaliana, whether similar mechanisms exist in other
dicot plants remains unclear. Here, we analyzed DNA methylation levels in meiocytes,
microspores, and pollens of Brassica Rapa using whole-genome bisulfite sequencing
(WGBS). Global DNA methylation analysis revealed similar CHH methylation reprogramming
compared to Arabidopsis, while distinct patterns were observed in the dynamics
of global CG and CHG methylation in B. rapa. Differentially methylated region
(DMR) analysis identified specifically methylated loci in the male sex cells of
B. Rapa with a stronger tendency to target genes, similar to observations in Arabidopsis.
Additionally, we found that the activity and genomic targeting preference of the
small RNA-directed DNA methylation (RdDM) were altered during B. Rapa male germline
development. A subset of long terminal repeat (LTR) TEs were activated, possibly
due to the dynamic regulation of DNA methylation during male sexual development
in B. Rapa. These findings provided new insights into the evolution of epigenetic
reprogramming mechanisms in plants.
acknowledgement: We thank Prof. Ying Li of Nanjing Agricultural University for her
help in providing seeds of K2 materials. This work was carried out with the support
of National Natural Science Foundation of China (Grant No. 32070608).
article_number: '16'
article_processing_charge: Yes
article_type: original
author:
- first_name: Jun
full_name: Zhang, Jun
last_name: Zhang
- first_name: Di
full_name: Wu, Di
last_name: Wu
- first_name: Yating
full_name: Zhang, Yating
last_name: Zhang
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Hongbo
full_name: Gao, Hongbo
id: 77c2e73a-eabd-11ef-aee9-8093a2ba7a93
last_name: Gao
citation:
ama: Zhang J, Wu D, Zhang Y, Feng X, Gao H. DNA methylation dynamics in male germline
development in Brassica Rapa. Molecular Horticulture. 2025;5. doi:10.1186/s43897-024-00137-9
apa: Zhang, J., Wu, D., Zhang, Y., Feng, X., & Gao, H. (2025). DNA methylation
dynamics in male germline development in Brassica Rapa. Molecular Horticulture.
Springer Nature. https://doi.org/10.1186/s43897-024-00137-9
chicago: Zhang, Jun, Di Wu, Yating Zhang, Xiaoqi Feng, and Hongbo Gao. “DNA Methylation
Dynamics in Male Germline Development in Brassica Rapa.” Molecular Horticulture.
Springer Nature, 2025. https://doi.org/10.1186/s43897-024-00137-9.
ieee: J. Zhang, D. Wu, Y. Zhang, X. Feng, and H. Gao, “DNA methylation dynamics
in male germline development in Brassica Rapa,” Molecular Horticulture,
vol. 5. Springer Nature, 2025.
ista: Zhang J, Wu D, Zhang Y, Feng X, Gao H. 2025. DNA methylation dynamics in male
germline development in Brassica Rapa. Molecular Horticulture. 5, 16.
mla: Zhang, Jun, et al. “DNA Methylation Dynamics in Male Germline Development in
Brassica Rapa.” Molecular Horticulture, vol. 5, 16, Springer Nature, 2025,
doi:10.1186/s43897-024-00137-9.
short: J. Zhang, D. Wu, Y. Zhang, X. Feng, H. Gao, Molecular Horticulture 5 (2025).
corr_author: '1'
date_created: 2025-03-23T23:01:25Z
date_published: 2025-03-04T00:00:00Z
date_updated: 2025-09-30T11:17:08Z
day: '04'
ddc:
- '580'
department:
- _id: XiFe
doi: 10.1186/s43897-024-00137-9
external_id:
isi:
- '001436233900001'
pmid:
- '40033451'
file:
- access_level: open_access
checksum: 6d1e0e9b0e1902e4a711f81c5c17a070
content_type: application/pdf
creator: dernst
date_created: 2025-03-25T12:15:32Z
date_updated: 2025-03-25T12:15:32Z
file_id: '19460'
file_name: 2025_MolecularHorticulture_Zhang.pdf
file_size: 3014980
relation: main_file
success: 1
file_date_updated: 2025-03-25T12:15:32Z
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: Molecular Horticulture
publication_identifier:
eissn:
- 2730-9401
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA methylation dynamics in male germline development in Brassica Rapa
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 5
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '19399'
abstract:
- lang: eng
text: Phytohormone auxin and its directional transport mediate much of the remarkably
plastic development of higher plants. Positive feedback between auxin signaling
and transport is a key prerequisite for (i) self-organizing processes including
vascular tissue formation and (ii) directional growth responses such as gravitropism.
Here we identify a mechanism, by which auxin signaling directly targets PIN auxin
transporters. Via the cell-surface ABP1-TMK1 receptor module, auxin rapidly induces
phosphorylation and thus stabilization of PIN2. Following gravistimulation, initial
auxin asymmetry activates autophosphorylation of the TMK1 kinase. This induces
TMK1 interaction with and phosphorylation of PIN2, stabilizing PIN2 at the lower
root side, thus reinforcing asymmetric auxin flow for root bending. Upstream of
TMK1 in this regulation, ABP1 acts redundantly with the root-expressed ABP1-LIKE
auxin receptor ABL3. Such positive feedback between cell-surface auxin signaling
and PIN-mediated polar auxin transport is fundamental for robust root gravitropism
and presumably also for other self-organizing developmental phenomena.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: 'We thank W. Gray for providing material; N. Gnyliukh and E. Cervenova
for help with manuscript preparation; J. Schmid for help with cloning. We thank
Dolf Weijers, Mark Roosjen, and Andre Kuhn for discussions and support with phospho-proteomic
analyses. We thank the Bioimaging and Life Science facilities at ISTA for their
excellent service and assistance. The research leading to these results has received
funding from the European Research Council (ERC) under the European Union’s Horizon
2020 research and innovation program grant agreement No 742985 and Austrian Science
Fund (FWF): I3630-775 B25 to J.F; National Natural Science Foundation of China (Grant
32130010, 31422008), start-up funds from FAFU to T.X., Y.J. was funded by ERC no.
3363360-APPL under FP/2007-2013. L.R. was supported by FP7-PEOPLE-2011-COFUND ISTFELLOW
program (IC1023FELL01) and the European Molecular Biology Organization (EMBO) long-term
postdoctoral fellowship (ALTF 985- 2016). S.T. was supported by the National Natural
Science Foundation of China (32321001).'
article_processing_charge: No
author:
- first_name: Lesia
full_name: Rodriguez Solovey, Lesia
id: 3922B506-F248-11E8-B48F-1D18A9856A87
last_name: Rodriguez Solovey
orcid: 0000-0002-7244-7237
- first_name: Lukas
full_name: Fiedler, Lukas
id: 7c417475-8972-11ed-ae7b-8b674ca26986
last_name: Fiedler
- first_name: Minxia
full_name: Zou, Minxia
id: 5c243f41-03f3-11ec-841c-96faf48a7ef9
last_name: Zou
- first_name: Caterina
full_name: Giannini, Caterina
id: e3fdddd5-f6e0-11ea-865d-ca99ee6367f4
last_name: Giannini
- first_name: Aline
full_name: Monzer, Aline
id: 2DB5D88C-D7B3-11E9-B8FD-7907E6697425
last_name: Monzer
- first_name: Dmitrii
full_name: Vladimirtsev, Dmitrii
id: 60466724-5355-11ee-ae5a-fa55e8f99c3d
last_name: Vladimirtsev
- first_name: Marek
full_name: Randuch, Marek
id: 6ac4636d-15b2-11ec-abd3-fb8df79972ae
last_name: Randuch
- first_name: Yongfan
full_name: Yu, Yongfan
last_name: Yu
- first_name: Zuzana
full_name: Gelová, Zuzana
id: 0AE74790-0E0B-11E9-ABC7-1ACFE5697425
last_name: Gelová
orcid: 0000-0003-4783-1752
- first_name: Inge
full_name: Verstraeten, Inge
id: 362BF7FE-F248-11E8-B48F-1D18A9856A87
last_name: Verstraeten
orcid: 0000-0001-7241-2328
- first_name: Jakub
full_name: Hajny, Jakub
id: 4800CC20-F248-11E8-B48F-1D18A9856A87
last_name: Hajny
orcid: 0000-0003-2140-7195
- first_name: Meng
full_name: Chen, Meng
last_name: Chen
- first_name: Shutang
full_name: Tan, Shutang
id: 2DE75584-F248-11E8-B48F-1D18A9856A87
last_name: Tan
orcid: 0000-0002-0471-8285
- first_name: Lukas
full_name: Hörmayer, Lukas
id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87
last_name: Hörmayer
orcid: 0000-0001-8295-2926
- first_name: Lanxin
full_name: Li, Lanxin
id: 367EF8FA-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0002-5607-272X
- first_name: Maria Mar
full_name: Marques-Bueno, Maria Mar
last_name: Marques-Bueno
- first_name: Zainab
full_name: Quddoos, Zainab
id: 32ff3c64-04a0-11f0-a50f-d0c45bfac466
last_name: Quddoos
- first_name: Gergely
full_name: Molnar, Gergely
id: 34F1AF46-F248-11E8-B48F-1D18A9856A87
last_name: Molnar
- first_name: Tongda
full_name: Xu, Tongda
last_name: Xu
- first_name: Ivan
full_name: Kulich, Ivan
id: 57a1567c-8314-11eb-9063-c9ddc3451a54
last_name: Kulich
- first_name: Yvon
full_name: Jaillais, Yvon
last_name: Jaillais
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Rodriguez Solovey L, Fiedler L, Zou M, et al. ABP1/ABL3-TMK1 cell-surface auxin
signaling directly targets PIN2-mediated auxin fluxes for root gravitropism. bioRxiv.
doi:10.1101/2022.11.30.518503
apa: Rodriguez Solovey, L., Fiedler, L., Zou, M., Giannini, C., Monzer, A., Vladimirtsev,
D., … Friml, J. (n.d.). ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets
PIN2-mediated auxin fluxes for root gravitropism. bioRxiv. Cold Spring
Harbor Laboratory. https://doi.org/10.1101/2022.11.30.518503
chicago: Rodriguez Solovey, Lesia, Lukas Fiedler, Minxia Zou, Caterina Giannini,
Aline Monzer, Dmitrii Vladimirtsev, Marek Randuch, et al. “ABP1/ABL3-TMK1 Cell-Surface
Auxin Signaling Directly Targets PIN2-Mediated Auxin Fluxes for Root Gravitropism.”
BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2022.11.30.518503.
ieee: L. Rodriguez Solovey et al., “ABP1/ABL3-TMK1 cell-surface auxin signaling
directly targets PIN2-mediated auxin fluxes for root gravitropism,” bioRxiv.
Cold Spring Harbor Laboratory.
ista: Rodriguez Solovey L, Fiedler L, Zou M, Giannini C, Monzer A, Vladimirtsev
D, Randuch M, Yu Y, Gelová Z, Verstraeten I, Hajny J, Chen M, Tan S, Hörmayer
L, Li L, Marques-Bueno MM, Quddoos Z, Molnar G, Xu T, Kulich I, Jaillais Y, Friml
J. ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated
auxin fluxes for root gravitropism. bioRxiv, 10.1101/2022.11.30.518503.
mla: Rodriguez Solovey, Lesia, et al. “ABP1/ABL3-TMK1 Cell-Surface Auxin Signaling
Directly Targets PIN2-Mediated Auxin Fluxes for Root Gravitropism.” BioRxiv,
Cold Spring Harbor Laboratory, doi:10.1101/2022.11.30.518503.
short: L. Rodriguez Solovey, L. Fiedler, M. Zou, C. Giannini, A. Monzer, D. Vladimirtsev,
M. Randuch, Y. Yu, Z. Gelová, I. Verstraeten, J. Hajny, M. Chen, S. Tan, L. Hörmayer,
L. Li, M.M. Marques-Bueno, Z. Quddoos, G. Molnar, T. Xu, I. Kulich, Y. Jaillais,
J. Friml, BioRxiv (n.d.).
corr_author: '1'
date_created: 2025-03-13T08:36:48Z
date_published: 2025-02-20T00:00:00Z
date_updated: 2026-04-07T11:52:15Z
day: '20'
department:
- _id: JiFr
- _id: XiFe
doi: 10.1101/2022.11.30.518503
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2022.11.30.518503
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 26060676-B435-11E9-9278-68D0E5697425
grant_number: ALTF 985-2016
name: Cell surface receptor complexes for auxin signaling in plants
publication: bioRxiv
publication_status: draft
publisher: Cold Spring Harbor Laboratory
related_material:
record:
- id: '20656'
relation: later_version
status: public
- id: '19395'
relation: dissertation_contains
status: public
- id: '20364'
relation: dissertation_contains
status: public
status: public
title: ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated
auxin fluxes for root gravitropism
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '19602'
abstract:
- lang: eng
text: N4-methylcytosine (4mC) is an important DNA modification in prokaryotes, but
its relevance and even its presence in eukaryotes have been mysterious. Here we
show that spermatogenesis in the liverwort Marchantia polymorpha involves two
waves of extensive DNA methylation reprogramming. First, 5-methylcytosine (5mC)
expands from transposons to the entire genome. Notably, the second wave installs
4mC throughout genic regions, covering over 50% of CG sites in sperm. 4mC requires
a methyltransferase (MpDN4MT1a) that is specifically expressed during late spermiogenesis.
Deletion of MpDN4MT1a alters the sperm transcriptome, causes sperm swimming and
fertility defects, and impairs post-fertilization development. Our results reveal
extensive 4mC in a eukaryote, identify a family of eukaryotic methyltransferases,
and elucidate the biological functions of 4mC in reproductive development, thereby
expanding the repertoire of functional eukaryotic DNA modifications.
acknowledged_ssus:
- _id: Bio
- _id: ScienComp
acknowledgement: We thank Sir Richard Roberts (NEB) for the kind gift of anti-4mC
antibodies. We are also grateful to the JIC Small Molecule Mass Spectrometry (Lionel
Hill) and Chemistry (Martin Rejzek) platforms as well as the High Resolution Metabolomics
Laboratory (Manfred Beckmann, Aberystwyth University) for their assistance with
LC-MS. Additionally, we acknowledge the assistance of the JIC Bioimaging Facility
and ISTA Imaging and Optics Facility for microscopy. Finally, we appreciate the
High Performance Computing resources provided by the ISTA Scientific Computing Facility
and Norwich BioScience Institute Partnership Computing Infrastructure. This work
was funded by a Sainsbury Charitable Foundation studentship (J.W.), a UKRI-BBSRC
Doctoral Training Partnerships studentship (BBT0087171 to J.T.), a European Research
Council Starting Grant (“SexMeth” 804981 to J.W., S.X., and X.F.), two Biotechnology
and Biological Sciences Research Council (BBSRC) grants (BBS0096201 and BBP0135111
to J.Z., M.V., and X.F.), an EMBO Long Term Fellowship (Y.L.), an ISTA Bridge Fellowship
(S.X.), and ISTA core funding (Y.Y. and X.F.).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: James
full_name: Walker, James
last_name: Walker
- first_name: Jingyi
full_name: Zhang, Jingyi
last_name: Zhang
- first_name: Yalin
full_name: Liu, Yalin
last_name: Liu
- first_name: Shujuan
full_name: Xu, Shujuan
id: 9724dd9d-f591-11ee-bd51-e97ed0652286
last_name: Xu
- first_name: Yiming
full_name: Yu, Yiming
id: 318e643b-8b61-11ed-b69e-aafa103ec8dd
last_name: Yu
orcid: 0000-0002-9919-7282
- first_name: Martin
full_name: Vickers, Martin
last_name: Vickers
- first_name: Weizhi
full_name: Ouyang, Weizhi
id: fec73395-8b60-11ed-b69e-927fda99c743
last_name: Ouyang
- first_name: Judit
full_name: Tálas, Judit
last_name: Tálas
- first_name: Liam
full_name: Dolan, Liam
last_name: Dolan
- first_name: Keiji
full_name: Nakajima, Keiji
last_name: Nakajima
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
citation:
ama: Walker J, Zhang J, Liu Y, et al. Extensive N4 cytosine methylation is essential
for Marchantia sperm function. Cell. 2025;188(11):2890-2906.e14. doi:10.1016/j.cell.2025.03.014
apa: Walker, J., Zhang, J., Liu, Y., Xu, S., Yu, Y., Vickers, M., … Feng, X. (2025).
Extensive N4 cytosine methylation is essential for Marchantia sperm function.
Cell. Elsevier. https://doi.org/10.1016/j.cell.2025.03.014
chicago: Walker, James, Jingyi Zhang, Yalin Liu, Shujuan Xu, Yiming Yu, Martin Vickers,
Weizhi Ouyang, et al. “Extensive N4 Cytosine Methylation Is Essential for Marchantia
Sperm Function.” Cell. Elsevier, 2025. https://doi.org/10.1016/j.cell.2025.03.014.
ieee: J. Walker et al., “Extensive N4 cytosine methylation is essential for
Marchantia sperm function,” Cell, vol. 188, no. 11. Elsevier, p. 2890–2906.e14,
2025.
ista: Walker J, Zhang J, Liu Y, Xu S, Yu Y, Vickers M, Ouyang W, Tálas J, Dolan
L, Nakajima K, Feng X. 2025. Extensive N4 cytosine methylation is essential for
Marchantia sperm function. Cell. 188(11), 2890–2906.e14.
mla: Walker, James, et al. “Extensive N4 Cytosine Methylation Is Essential for Marchantia
Sperm Function.” Cell, vol. 188, no. 11, Elsevier, 2025, p. 2890–2906.e14,
doi:10.1016/j.cell.2025.03.014.
short: J. Walker, J. Zhang, Y. Liu, S. Xu, Y. Yu, M. Vickers, W. Ouyang, J. Tálas,
L. Dolan, K. Nakajima, X. Feng, Cell 188 (2025) 2890–2906.e14.
corr_author: '1'
date_created: 2025-04-20T22:01:28Z
date_published: 2025-05-29T00:00:00Z
date_updated: 2026-04-28T13:36:51Z
day: '29'
ddc:
- '570'
department:
- _id: XiFe
doi: 10.1016/j.cell.2025.03.014
ec_funded: 1
external_id:
isi:
- '001504744800006'
pmid:
- '40209706'
file:
- access_level: open_access
checksum: 0dcc2feb368dfe7c4890093366b2dacb
content_type: application/pdf
creator: dernst
date_created: 2025-12-29T13:40:32Z
date_updated: 2025-12-29T13:40:32Z
file_id: '20871'
file_name: 2025_Cell_Walker.pdf
file_size: 11622960
relation: main_file
success: 1
file_date_updated: 2025-12-29T13:40:32Z
has_accepted_license: '1'
intvolume: ' 188'
isi: 1
issue: '11'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 2890-2906.e14
pmid: 1
project:
- _id: bdb51a6e-d553-11ed-ba76-c2025f3d5725
call_identifier: H2020
grant_number: '804981'
name: Establishment, modulation and inheritance of sexual lineage specific DNA methylation
in plants
publication: Cell
publication_identifier:
eissn:
- 1097-4172
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/from-bacterial-immunity-to-plant-sex/
scopus_import: '1'
status: public
title: Extensive N4 cytosine methylation is essential for Marchantia sperm function
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 188
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '15375'
abstract:
- lang: eng
text: In the eukaryotic nucleus, heterochromatin forms highly condensed, visible
foci known as heterochromatin foci (HF). These HF are enriched with linker histone
H1, a key player in heterochromatin condensation and silencing. However, it is
unknown how H1 aggregates HF and condenses heterochromatin. In this study, we
established that H1 facilitates heterochromatin condensation by enhancing inter-
and intrachromosomal interactions between and within heterochromatic regions of
the Arabidopsis (Arabidopsis thaliana) genome. We demonstrated that H1 drives
HF formation via phase separation, which requires its C-terminal intrinsically
disordered region (C-IDR). A truncated H1 lacking the C-IDR fails to form foci
or recover HF in the h1 mutant background, whereas C-IDR with a short stretch
of the globular domain (18 out of 71 amino acids) is sufficient to rescue both
defects. In addition, C-IDR is essential for H1's roles in regulating nucleosome
repeat length and DNA methylation in Arabidopsis, indicating that phase separation
capability is required for chromatin functions of H1. Our data suggest that bacterial
H1-like proteins, which have been shown to condense DNA, are intrinsically disordered
and capable of mediating phase separation. Therefore, we propose that phase separation
mediated by H1 or H1-like proteins may represent an ancient mechanism for condensing
chromatin and DNA.
acknowledged_ssus:
- _id: Bio
- _id: ScienComp
acknowledgement: "This work was funded by ISTA core support (Y.Y. and X.F.) and grants
from the National Natural Science Foundation of China (31871443 to L.W. and P.L.;
32100417 to L.W.).\r\nWe thank the ISTA Imaging and Optics Facility for assistance
with microscopy and the ISTA Scientific Computing Facility for high-performance
computing resources."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Shengbo
full_name: He, Shengbo
last_name: He
- first_name: Yiming
full_name: Yu, Yiming
id: 318e643b-8b61-11ed-b69e-aafa103ec8dd
last_name: Yu
- first_name: Liang
full_name: Wang, Liang
last_name: Wang
- first_name: Jingyi
full_name: Zhang, Jingyi
last_name: Zhang
- first_name: Zhengyong
full_name: Bai, Zhengyong
last_name: Bai
- first_name: Guohong
full_name: Li, Guohong
last_name: Li
- first_name: Pilong
full_name: Li, Pilong
last_name: Li
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
citation:
ama: He S, Yu Y, Wang L, et al. Linker histone H1 drives heterochromatin condensation
via phase separation in Arabidopsis. The Plant Cell. 2024;36(5):1829-1843.
doi:10.1093/plcell/koae034
apa: He, S., Yu, Y., Wang, L., Zhang, J., Bai, Z., Li, G., … Feng, X. (2024). Linker
histone H1 drives heterochromatin condensation via phase separation in Arabidopsis.
The Plant Cell. Oxford University Press. https://doi.org/10.1093/plcell/koae034
chicago: He, Shengbo, Yiming Yu, Liang Wang, Jingyi Zhang, Zhengyong Bai, Guohong
Li, Pilong Li, and Xiaoqi Feng. “Linker Histone H1 Drives Heterochromatin Condensation
via Phase Separation in Arabidopsis.” The Plant Cell. Oxford University
Press, 2024. https://doi.org/10.1093/plcell/koae034.
ieee: S. He et al., “Linker histone H1 drives heterochromatin condensation
via phase separation in Arabidopsis,” The Plant Cell, vol. 36, no. 5. Oxford
University Press, pp. 1829–1843, 2024.
ista: He S, Yu Y, Wang L, Zhang J, Bai Z, Li G, Li P, Feng X. 2024. Linker histone
H1 drives heterochromatin condensation via phase separation in Arabidopsis. The
Plant Cell. 36(5), 1829–1843.
mla: He, Shengbo, et al. “Linker Histone H1 Drives Heterochromatin Condensation
via Phase Separation in Arabidopsis.” The Plant Cell, vol. 36, no. 5, Oxford
University Press, 2024, pp. 1829–43, doi:10.1093/plcell/koae034.
short: S. He, Y. Yu, L. Wang, J. Zhang, Z. Bai, G. Li, P. Li, X. Feng, The Plant
Cell 36 (2024) 1829–1843.
corr_author: '1'
date_created: 2024-05-12T22:01:01Z
date_published: 2024-05-01T00:00:00Z
date_updated: 2025-09-08T07:21:17Z
day: '01'
ddc:
- '580'
department:
- _id: XiFe
doi: 10.1093/plcell/koae034
external_id:
isi:
- '001180817000001'
pmid:
- '38309957'
file:
- access_level: open_access
checksum: eed76c848fe3d8fe9a53943181aaa53c
content_type: application/pdf
creator: dernst
date_created: 2025-04-23T07:43:12Z
date_updated: 2025-04-23T07:43:12Z
file_id: '19611'
file_name: 2024_PlantCell_He.pdf
file_size: 50791962
relation: main_file
success: 1
file_date_updated: 2025-04-23T07:43:12Z
has_accepted_license: '1'
intvolume: ' 36'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 1829-1843
pmid: 1
publication: The Plant Cell
publication_identifier:
eissn:
- 1532-298X
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Linker histone H1 drives heterochromatin condensation via phase separation
in Arabidopsis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 36
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '17285'
abstract:
- lang: eng
text: Winter plants rely on vernalization, a crucial process for adapting to cold
conditions and ensuring successful reproduction. However, understanding the role
of histone modifications in guiding the vernalization process in winter wheat
remains limited. In this study, we investigated the transcriptome and chromatin
dynamics in the shoot apex throughout the life cycle of winter wheat in the field.
Two core histone modifications, H3K27me3 and H3K36me3, exhibited opposite patterns
on the key vernalization gene VERNALIZATION1 (VRN1), correlating with its induction
during cold exposure. Moreover, the H3K36me3 level remained high at VRN1 after
cold exposure, which may maintain its active state. Mutations in FERTILIZATION-INDEPENDENT
ENDOSPERM (TaFIE) and SET DOMAIN GROUP 8/EARLY FLOWERING IN SHORT DAYS (TaSDG8/TaEFS),
components of the writer complex for H3K27me3 and H3K36me3, respectively, affected
flowering time. Intriguingly, VRN1 lost its high expression after the cold exposure
memory in the absence of H3K36me3. During embryo development, VRN1 was silenced
with the removal of active histone modifications in both winter and spring wheat,
with selective restoration of H3K27me3 in winter wheat. The mutant of Tafie-cr-87,
a component of H3K27me3 “writer” complex, did not influence the silence of VRN1
during embryo development, but rather attenuated the cold exposure requirement
of winter wheat. Integrating gene expression with H3K27me3 and H3K36me3 patterns
identified potential regulators of flowering. This study unveils distinct roles
of H3K27me3 and H3K36me3 in controlling vernalization response, maintenance, and
resetting in winter wheat.
acknowledgement: We thank Prof. Kang Chong from Institute of Botany, the Chinese Academy
of Science for valuable comments, Dr. Haoran Li for the help with western blot of
H3K36me3 in Tasdg8-cr lines. This research was supported by National Natural Science
Foundation (31970529), Beijing Natural Science Foundation Outstanding Youth Project
(JQ23026), National Key Research and Development Program of China (2021YFD1201500),
and the Major Basic Research Program of Shandong Natural Science Foundation (ZR2019ZD15).
article_processing_charge: No
article_type: original
author:
- first_name: Xuemei
full_name: Liu, Xuemei
last_name: Liu
- first_name: Min
full_name: Deng, Min
last_name: Deng
- first_name: Bingxin
full_name: Shi, Bingxin
last_name: Shi
- first_name: Kehui
full_name: Zhu, Kehui
last_name: Zhu
- first_name: Jinchao
full_name: Chen, Jinchao
last_name: Chen
- first_name: Shujuan
full_name: Xu, Shujuan
id: 9724dd9d-f591-11ee-bd51-e97ed0652286
last_name: Xu
- first_name: Xiaomin
full_name: Bie, Xiaomin
last_name: Bie
- first_name: Xiansheng
full_name: Zhang, Xiansheng
last_name: Zhang
- first_name: Xuelei
full_name: Lin, Xuelei
last_name: Lin
- first_name: Jun
full_name: Xiao, Jun
last_name: Xiao
citation:
ama: Liu X, Deng M, Shi B, et al. Distinct roles of H3K27me3 and H3K36me3 in vernalization
response, maintenance, and resetting in winter wheat. Science China Life Sciences.
2024;67:2251-2266. doi:10.1007/s11427-024-2664-0
apa: Liu, X., Deng, M., Shi, B., Zhu, K., Chen, J., Xu, S., … Xiao, J. (2024). Distinct
roles of H3K27me3 and H3K36me3 in vernalization response, maintenance, and resetting
in winter wheat. Science China Life Sciences. Springer Nature. https://doi.org/10.1007/s11427-024-2664-0
chicago: Liu, Xuemei, Min Deng, Bingxin Shi, Kehui Zhu, Jinchao Chen, Shujuan Xu,
Xiaomin Bie, Xiansheng Zhang, Xuelei Lin, and Jun Xiao. “Distinct Roles of H3K27me3
and H3K36me3 in Vernalization Response, Maintenance, and Resetting in Winter Wheat.”
Science China Life Sciences. Springer Nature, 2024. https://doi.org/10.1007/s11427-024-2664-0.
ieee: X. Liu et al., “Distinct roles of H3K27me3 and H3K36me3 in vernalization
response, maintenance, and resetting in winter wheat,” Science China Life Sciences,
vol. 67. Springer Nature, pp. 2251–2266, 2024.
ista: Liu X, Deng M, Shi B, Zhu K, Chen J, Xu S, Bie X, Zhang X, Lin X, Xiao J.
2024. Distinct roles of H3K27me3 and H3K36me3 in vernalization response, maintenance,
and resetting in winter wheat. Science China Life Sciences. 67, 2251–2266.
mla: Liu, Xuemei, et al. “Distinct Roles of H3K27me3 and H3K36me3 in Vernalization
Response, Maintenance, and Resetting in Winter Wheat.” Science China Life Sciences,
vol. 67, Springer Nature, 2024, pp. 2251–66, doi:10.1007/s11427-024-2664-0.
short: X. Liu, M. Deng, B. Shi, K. Zhu, J. Chen, S. Xu, X. Bie, X. Zhang, X. Lin,
J. Xiao, Science China Life Sciences 67 (2024) 2251–2266.
date_created: 2024-07-21T22:01:02Z
date_published: 2024-10-01T00:00:00Z
date_updated: 2025-09-08T08:15:08Z
day: '01'
department:
- _id: XiFe
doi: 10.1007/s11427-024-2664-0
external_id:
isi:
- '001268807700002'
pmid:
- '38987431'
intvolume: ' 67'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2023.12.19.572364
month: '10'
oa: 1
oa_version: Preprint
page: 2251-2266
pmid: 1
publication: Science China Life Sciences
publication_identifier:
eissn:
- 1869-1889
issn:
- 1674-7305
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Distinct roles of H3K27me3 and H3K36me3 in vernalization response, maintenance,
and resetting in winter wheat
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 67
year: '2024'
...
---
_id: '17408'
abstract:
- lang: eng
text: "Background: The remarkable regenerative abilities observed in planarians
and cnidarians are closely linked to the active proliferation of adult stem cells
and the precise differentiation of their progeny, both of which typically deteriorate
during aging in low regenerative animals. While regeneration-specific genes conserved
in highly regenerative organisms may confer regenerative abilities and long-term
maintenance of tissue homeostasis, it remains unclear whether introducing these
regenerative genes into low regenerative animals can improve their regeneration
and aging processes.\r\n\r\nResults: Here, we ectopically express highly regenerative
species-specific JmjC domain-encoding genes (HRJDs) in Drosophila, a widely used
low regenerative model organism. Surprisingly, HRJD expression impedes tissue
regeneration in the developing wing disc but extends organismal lifespan when
expressed in the intestinal stem cell lineages of the adult midgut under non-regenerative
conditions. Notably, HRJDs enhance the proliferative activity of intestinal stem
cells while maintaining their differentiation fidelity, ameliorating age-related
decline in gut barrier functions.\r\n\r\nConclusions: These findings together
suggest that the introduction of highly regenerative species-specific genes can
improve stem cell functions and promote a healthy lifespan when expressed in aging
animals."
acknowledgement: "We thank I. Miguel-Aliaga, N. Shinoda, M. Furuse, Y. Izumi, BDSC,
Kyoto Stock Center, Drosophila Genomics Resource Center (DGRC), and Developmental
Studies Hybridoma Bank (DSHB) for fly stocks and reagents.\r\nThis work was supported
by JSPS/MEXT KAKENHI (grant numbers JP22J01430 to H.N., JP21H04774, JP23H04766,
JP24H00567 to M.M., and JP17H06332, JP22H02762, JP23K18134, JP23H04696 to Y.N.),
AMED-Aging (JP21gm5010001 to M.M.), AMED-PRIME (JP22gm6110025 to Y.N.), and Sadako
O. Hirai Ban Award for Young Researchers (H.N.)"
article_number: '157'
article_processing_charge: Yes
article_type: original
author:
- first_name: Hiroki
full_name: Nagai, Hiroki
id: 608df3e6-e2ab-11ed-8890-c9318cec7da4
last_name: Nagai
orcid: 0000-0003-1671-9434
- first_name: Yuya
full_name: Adachi, Yuya
last_name: Adachi
- first_name: Tenki
full_name: Nakasugi, Tenki
last_name: Nakasugi
- first_name: Ema
full_name: Takigawa, Ema
last_name: Takigawa
- first_name: Junichiro
full_name: Ui, Junichiro
last_name: Ui
- first_name: Takashi
full_name: Makino, Takashi
last_name: Makino
- first_name: Masayuki
full_name: Miura, Masayuki
last_name: Miura
- first_name: Yu Ichiro
full_name: Nakajima, Yu Ichiro
last_name: Nakajima
citation:
ama: NAGAI H, Adachi Y, Nakasugi T, et al. Highly regenerative species-specific
genes improve age-associated features in the adult Drosophila midgut. BMC Biology.
2024;22. doi:10.1186/s12915-024-01956-4
apa: NAGAI, H., Adachi, Y., Nakasugi, T., Takigawa, E., Ui, J., Makino, T., … Nakajima,
Y. I. (2024). Highly regenerative species-specific genes improve age-associated
features in the adult Drosophila midgut. BMC Biology. Springer Nature.
https://doi.org/10.1186/s12915-024-01956-4
chicago: NAGAI, HIROKI, Yuya Adachi, Tenki Nakasugi, Ema Takigawa, Junichiro Ui,
Takashi Makino, Masayuki Miura, and Yu Ichiro Nakajima. “Highly Regenerative Species-Specific
Genes Improve Age-Associated Features in the Adult Drosophila Midgut.” BMC
Biology. Springer Nature, 2024. https://doi.org/10.1186/s12915-024-01956-4.
ieee: H. NAGAI et al., “Highly regenerative species-specific genes improve
age-associated features in the adult Drosophila midgut,” BMC Biology, vol.
22. Springer Nature, 2024.
ista: NAGAI H, Adachi Y, Nakasugi T, Takigawa E, Ui J, Makino T, Miura M, Nakajima
YI. 2024. Highly regenerative species-specific genes improve age-associated features
in the adult Drosophila midgut. BMC Biology. 22, 157.
mla: NAGAI, HIROKI, et al. “Highly Regenerative Species-Specific Genes Improve Age-Associated
Features in the Adult Drosophila Midgut.” BMC Biology, vol. 22, 157, Springer
Nature, 2024, doi:10.1186/s12915-024-01956-4.
short: H. NAGAI, Y. Adachi, T. Nakasugi, E. Takigawa, J. Ui, T. Makino, M. Miura,
Y.I. Nakajima, BMC Biology 22 (2024).
date_created: 2024-08-11T22:01:11Z
date_published: 2024-08-02T00:00:00Z
date_updated: 2025-09-08T08:51:29Z
day: '02'
ddc:
- '570'
department:
- _id: XiFe
doi: 10.1186/s12915-024-01956-4
external_id:
isi:
- '001282893200001'
pmid:
- '39090637'
file:
- access_level: open_access
checksum: 318759626ec83b13f909c82904393ef1
content_type: application/pdf
creator: dernst
date_created: 2024-08-12T08:14:44Z
date_updated: 2024-08-12T08:14:44Z
file_id: '17417'
file_name: 2024_BMCBio_Nagai.pdf
file_size: 3345718
relation: main_file
success: 1
file_date_updated: 2024-08-12T08:14:44Z
has_accepted_license: '1'
intvolume: ' 22'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: BMC Biology
publication_identifier:
eissn:
- 1741-7007
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Highly regenerative species-specific genes improve age-associated features
in the adult Drosophila midgut
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 22
year: '2024'
...
---
_id: '12668'
abstract:
- lang: eng
text: "Background: Plant and animal embryogenesis have conserved and distinct features.
Cell fate transitions occur during embryogenesis in both plants and animals. The
epigenomic processes regulating plant embryogenesis remain largely elusive.\r\n\r\nResults:
Here, we elucidate chromatin and transcriptomic dynamics during embryogenesis
of the most cultivated crop, hexaploid wheat. Time-series analysis reveals stage-specific
and proximal–distal distinct chromatin accessibility and dynamics concordant with
transcriptome changes. Following fertilization, the remodeling kinetics of H3K4me3,
H3K27ac, and H3K27me3 differ from that in mammals, highlighting considerable species-specific
epigenomic dynamics during zygotic genome activation. Polycomb repressive complex
2 (PRC2)-mediated H3K27me3 deposition is important for embryo establishment. Later
H3K27ac, H3K27me3, and chromatin accessibility undergo dramatic remodeling to
establish a permissive chromatin environment facilitating the access of transcription
factors to cis-elements for fate patterning. Embryonic maturation is characterized
by increasing H3K27me3 and decreasing chromatin accessibility, which likely participates
in restricting totipotency while preventing extensive organogenesis. Finally,
epigenomic signatures are correlated with biased expression among homeolog triads
and divergent expression after polyploidization, revealing an epigenomic contributor
to subgenome diversification in an allohexaploid genome.\r\n\r\nConclusions: Collectively,
we present an invaluable resource for comparative and mechanistic analysis of
the epigenomic regulation of crop embryogenesis."
article_number: '7'
article_processing_charge: No
article_type: original
author:
- first_name: Long
full_name: Zhao, Long
last_name: Zhao
- first_name: Yiman
full_name: Yang, Yiman
last_name: Yang
- first_name: Jinchao
full_name: Chen, Jinchao
last_name: Chen
- first_name: Xuelei
full_name: Lin, Xuelei
last_name: Lin
- first_name: Hao
full_name: Zhang, Hao
last_name: Zhang
- first_name: Hao
full_name: Wang, Hao
last_name: Wang
- first_name: Hongzhe
full_name: Wang, Hongzhe
last_name: Wang
- first_name: Xiaomin
full_name: Bie, Xiaomin
last_name: Bie
- first_name: Jiafu
full_name: Jiang, Jiafu
last_name: Jiang
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Xiangdong
full_name: Fu, Xiangdong
last_name: Fu
- first_name: Xiansheng
full_name: Zhang, Xiansheng
last_name: Zhang
- first_name: Zhuo
full_name: Du, Zhuo
last_name: Du
- first_name: Jun
full_name: Xiao, Jun
last_name: Xiao
citation:
ama: Zhao L, Yang Y, Chen J, et al. Dynamic chromatin regulatory programs during
embryogenesis of hexaploid wheat. Genome Biology. 2023;24. doi:10.1186/s13059-022-02844-2
apa: Zhao, L., Yang, Y., Chen, J., Lin, X., Zhang, H., Wang, H., … Xiao, J. (2023).
Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat.
Genome Biology. Springer Nature. https://doi.org/10.1186/s13059-022-02844-2
chicago: Zhao, Long, Yiman Yang, Jinchao Chen, Xuelei Lin, Hao Zhang, Hao Wang,
Hongzhe Wang, et al. “Dynamic Chromatin Regulatory Programs during Embryogenesis
of Hexaploid Wheat.” Genome Biology. Springer Nature, 2023. https://doi.org/10.1186/s13059-022-02844-2.
ieee: L. Zhao et al., “Dynamic chromatin regulatory programs during embryogenesis
of hexaploid wheat,” Genome Biology, vol. 24. Springer Nature, 2023.
ista: Zhao L, Yang Y, Chen J, Lin X, Zhang H, Wang H, Wang H, Bie X, Jiang J, Feng
X, Fu X, Zhang X, Du Z, Xiao J. 2023. Dynamic chromatin regulatory programs during
embryogenesis of hexaploid wheat. Genome Biology. 24, 7.
mla: Zhao, Long, et al. “Dynamic Chromatin Regulatory Programs during Embryogenesis
of Hexaploid Wheat.” Genome Biology, vol. 24, 7, Springer Nature, 2023,
doi:10.1186/s13059-022-02844-2.
short: L. Zhao, Y. Yang, J. Chen, X. Lin, H. Zhang, H. Wang, H. Wang, X. Bie, J.
Jiang, X. Feng, X. Fu, X. Zhang, Z. Du, J. Xiao, Genome Biology 24 (2023).
date_created: 2023-02-23T09:13:49Z
date_published: 2023-01-13T00:00:00Z
date_updated: 2023-05-08T10:52:49Z
day: '13'
department:
- _id: XiFe
doi: 10.1186/s13059-022-02844-2
extern: '1'
external_id:
pmid:
- '36639687'
intvolume: ' 24'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1186/s13059-022-02844-2
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genome Biology
publication_identifier:
issn:
- 1474-760X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2023'
...
---
_id: '12669'
abstract:
- lang: eng
text: The study of RNAs has become one of the most influential research fields in
contemporary biology and biomedicine. In the last few years, new sequencing technologies
have produced an explosion of new and exciting discoveries in the field but have
also given rise to many open questions. Defining these questions, together with
old, long-standing gaps in our knowledge, is the spirit of this article. The breadth
of topics within RNA biology research is vast, and every aspect of the biology
of these molecules contains countless exciting open questions. Here, we asked
12 groups to discuss their most compelling question among some plant RNA biology
topics. The following vignettes cover RNA alternative splicing; RNA dynamics;
RNA translation; RNA structures; R-loops; epitranscriptomics; long non-coding
RNAs; small RNA production and their functions in crops; small RNAs during gametogenesis
and in cross-kingdom RNA interference; and RNA-directed DNA methylation. In each
section, we will present the current state-of-the-art in plant RNA biology research
before asking the questions that will surely motivate future discoveries in the
field. We hope this article will spark a debate about the future perspective on
RNA biology and provoke novel reflections in the reader.
article_number: koac346
article_processing_charge: No
article_type: original
author:
- first_name: Pablo A
full_name: Manavella, Pablo A
last_name: Manavella
- first_name: Micaela A
full_name: Godoy Herz, Micaela A
last_name: Godoy Herz
- first_name: Alberto R
full_name: Kornblihtt, Alberto R
last_name: Kornblihtt
- first_name: Reed
full_name: Sorenson, Reed
last_name: Sorenson
- first_name: Leslie E
full_name: Sieburth, Leslie E
last_name: Sieburth
- first_name: Kentaro
full_name: Nakaminami, Kentaro
last_name: Nakaminami
- first_name: Motoaki
full_name: Seki, Motoaki
last_name: Seki
- first_name: Yiliang
full_name: Ding, Yiliang
last_name: Ding
- first_name: Qianwen
full_name: Sun, Qianwen
last_name: Sun
- first_name: Hunseung
full_name: Kang, Hunseung
last_name: Kang
- first_name: Federico D
full_name: Ariel, Federico D
last_name: Ariel
- first_name: Martin
full_name: Crespi, Martin
last_name: Crespi
- first_name: Axel J
full_name: Giudicatti, Axel J
last_name: Giudicatti
- first_name: Qiang
full_name: Cai, Qiang
last_name: Cai
- first_name: Hailing
full_name: Jin, Hailing
last_name: Jin
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Yijun
full_name: Qi, Yijun
last_name: Qi
- first_name: Craig S
full_name: Pikaard, Craig S
last_name: Pikaard
citation:
ama: 'Manavella PA, Godoy Herz MA, Kornblihtt AR, et al. Beyond transcription: compelling
open questions in plant RNA biology. The Plant Cell. 2023;35(6). doi:10.1093/plcell/koac346'
apa: 'Manavella, P. A., Godoy Herz, M. A., Kornblihtt, A. R., Sorenson, R., Sieburth,
L. E., Nakaminami, K., … Pikaard, C. S. (2023). Beyond transcription: compelling
open questions in plant RNA biology. The Plant Cell. Oxford University
Press. https://doi.org/10.1093/plcell/koac346'
chicago: 'Manavella, Pablo A, Micaela A Godoy Herz, Alberto R Kornblihtt, Reed Sorenson,
Leslie E Sieburth, Kentaro Nakaminami, Motoaki Seki, et al. “Beyond Transcription:
Compelling Open Questions in Plant RNA Biology.” The Plant Cell. Oxford
University Press, 2023. https://doi.org/10.1093/plcell/koac346.'
ieee: 'P. A. Manavella et al., “Beyond transcription: compelling open questions
in plant RNA biology,” The Plant Cell, vol. 35, no. 6. Oxford University
Press, 2023.'
ista: 'Manavella PA, Godoy Herz MA, Kornblihtt AR, Sorenson R, Sieburth LE, Nakaminami
K, Seki M, Ding Y, Sun Q, Kang H, Ariel FD, Crespi M, Giudicatti AJ, Cai Q, Jin
H, Feng X, Qi Y, Pikaard CS. 2023. Beyond transcription: compelling open questions
in plant RNA biology. The Plant Cell. 35(6), koac346.'
mla: 'Manavella, Pablo A., et al. “Beyond Transcription: Compelling Open Questions
in Plant RNA Biology.” The Plant Cell, vol. 35, no. 6, koac346, Oxford
University Press, 2023, doi:10.1093/plcell/koac346.'
short: P.A. Manavella, M.A. Godoy Herz, A.R. Kornblihtt, R. Sorenson, L.E. Sieburth,
K. Nakaminami, M. Seki, Y. Ding, Q. Sun, H. Kang, F.D. Ariel, M. Crespi, A.J.
Giudicatti, Q. Cai, H. Jin, X. Feng, Y. Qi, C.S. Pikaard, The Plant Cell 35 (2023).
date_created: 2023-02-23T09:14:59Z
date_published: 2023-06-01T00:00:00Z
date_updated: 2023-10-04T09:48:43Z
day: '01'
department:
- _id: XiFe
doi: 10.1093/plcell/koac346
extern: '1'
external_id:
pmid:
- '36477566'
intvolume: ' 35'
issue: '6'
keyword:
- Cell Biology
- Plant Science
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1093/plcell/koac346
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: The Plant Cell
publication_identifier:
eissn:
- 1532-298X
issn:
- 1040-4651
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Beyond transcription: compelling open questions in plant RNA biology'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2023'
...
---
_id: '12672'
abstract:
- lang: eng
text: Cytosine methylation within CG dinucleotides (mCG) can be epigenetically inherited
over many generations. Such inheritance is thought to be mediated by a semiconservative
mechanism that produces binary present/absent methylation patterns. However, we
show here that in Arabidopsis thaliana h1ddm1 mutants, intermediate heterochromatic
mCG is stably inherited across many generations and is quantitatively associated
with transposon expression. We develop a mathematical model that estimates the
rates of semiconservative maintenance failure and de novo methylation at each
transposon, demonstrating that mCG can be stably inherited at any level via a
dynamic balance of these activities. We find that DRM2 – the core methyltransferase
of the RNA-directed DNA methylation pathway – catalyzes most of the heterochromatic
de novo mCG, with de novo rates orders of magnitude higher than previously thought,
whereas chromomethylases make smaller contributions. Our results demonstrate that
stable epigenetic inheritance of mCG in plant heterochromatin is enabled by extensive
de novo methylation.
acknowledgement: The authors would like to thank Jasper Rine for advice and mentorship
to D.B.L., Lesley Philips, Timothy Wells, Sophie Able, and Christina Wistrom for
support with plant growth, and Bhagyshree Jamge and Frédéric Berger for help with
analysis of ddm1 × WT RNA-sequencing data. This work was supported by BBSRC Institute
Strategic Program GEN (BB/P013511/1) to X.F., M.H., and D.Z., a European Research
Council grant MaintainMeth (725746) to D.Z., and a postdoctoral fellowship from
the Helen Hay Whitney Foundation to D.B.L.
article_number: '112132'
article_processing_charge: Yes
article_type: original
author:
- first_name: David B.
full_name: Lyons, David B.
last_name: Lyons
- first_name: Amy
full_name: Briffa, Amy
last_name: Briffa
- first_name: Shengbo
full_name: He, Shengbo
last_name: He
- first_name: Jaemyung
full_name: Choi, Jaemyung
last_name: Choi
- first_name: Elizabeth
full_name: Hollwey, Elizabeth
id: b8c4f54b-e484-11eb-8fdc-a54df64ef6dd
last_name: Hollwey
- first_name: Jack
full_name: Colicchio, Jack
last_name: Colicchio
- first_name: Ian
full_name: Anderson, Ian
last_name: Anderson
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Martin
full_name: Howard, Martin
last_name: Howard
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Lyons DB, Briffa A, He S, et al. Extensive de novo activity stabilizes epigenetic
inheritance of CG methylation in Arabidopsis transposons. Cell Reports.
2023;42(3). doi:10.1016/j.celrep.2023.112132
apa: Lyons, D. B., Briffa, A., He, S., Choi, J., Hollwey, E., Colicchio, J., … Zilberman,
D. (2023). Extensive de novo activity stabilizes epigenetic inheritance of CG
methylation in Arabidopsis transposons. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2023.112132
chicago: Lyons, David B., Amy Briffa, Shengbo He, Jaemyung Choi, Elizabeth Hollwey,
Jack Colicchio, Ian Anderson, Xiaoqi Feng, Martin Howard, and Daniel Zilberman.
“Extensive de Novo Activity Stabilizes Epigenetic Inheritance of CG Methylation
in Arabidopsis Transposons.” Cell Reports. Elsevier, 2023. https://doi.org/10.1016/j.celrep.2023.112132.
ieee: D. B. Lyons et al., “Extensive de novo activity stabilizes epigenetic
inheritance of CG methylation in Arabidopsis transposons,” Cell Reports,
vol. 42, no. 3. Elsevier, 2023.
ista: Lyons DB, Briffa A, He S, Choi J, Hollwey E, Colicchio J, Anderson I, Feng
X, Howard M, Zilberman D. 2023. Extensive de novo activity stabilizes epigenetic
inheritance of CG methylation in Arabidopsis transposons. Cell Reports. 42(3),
112132.
mla: Lyons, David B., et al. “Extensive de Novo Activity Stabilizes Epigenetic Inheritance
of CG Methylation in Arabidopsis Transposons.” Cell Reports, vol. 42, no.
3, 112132, Elsevier, 2023, doi:10.1016/j.celrep.2023.112132.
short: D.B. Lyons, A. Briffa, S. He, J. Choi, E. Hollwey, J. Colicchio, I. Anderson,
X. Feng, M. Howard, D. Zilberman, Cell Reports 42 (2023).
corr_author: '1'
date_created: 2023-02-23T09:17:44Z
date_published: 2023-03-28T00:00:00Z
date_updated: 2025-04-14T07:57:43Z
day: '28'
ddc:
- '580'
department:
- _id: DaZi
- _id: XiFe
doi: 10.1016/j.celrep.2023.112132
ec_funded: 1
external_id:
isi:
- '000944921600001'
file:
- access_level: open_access
checksum: 6cbc44fdb18bf18834c9e2a5b9c67123
content_type: application/pdf
creator: kschuh
date_created: 2023-05-11T10:41:42Z
date_updated: 2023-05-11T10:41:42Z
file_id: '12941'
file_name: 2023_CellReports_Lyons.pdf
file_size: 8401261
relation: main_file
success: 1
file_date_updated: 2023-05-11T10:41:42Z
has_accepted_license: '1'
intvolume: ' 42'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 62935a00-2b32-11ec-9570-eff30fa39068
call_identifier: H2020
grant_number: '725746'
name: Quantitative analysis of DNA methylation maintenance with chromatin
publication: Cell Reports
publication_identifier:
eissn:
- 2211-1247
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Extensive de novo activity stabilizes epigenetic inheritance of CG methylation
in Arabidopsis transposons
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 42
year: '2023'
...
---
_id: '12670'
abstract:
- lang: eng
text: DNA methylation plays essential homeostatic functions in eukaryotic genomes.
In animals, DNA methylation is also developmentally regulated and, in turn, regulates
development. In the past two decades, huge research effort has endorsed the understanding
that DNA methylation plays a similar role in plant development, especially during
sexual reproduction. The power of whole-genome sequencing and cell isolation techniques,
as well as bioinformatics tools, have enabled recent studies to reveal dynamic
changes in DNA methylation during germline development. Furthermore, the combination
of these technological advances with genetics, developmental biology and cell
biology tools has revealed functional methylation reprogramming events that control
gene and transposon activities in flowering plant germlines. In this review, we
discuss the major advances in our knowledge of DNA methylation dynamics during
male and female germline development in flowering plants.
article_processing_charge: No
article_type: review
author:
- first_name: Shengbo
full_name: He, Shengbo
last_name: He
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
citation:
ama: He S, Feng X. DNA methylation dynamics during germline development. Journal
of Integrative Plant Biology. 2022;64(12):2240-2251. doi:10.1111/jipb.13422
apa: He, S., & Feng, X. (2022). DNA methylation dynamics during germline development.
Journal of Integrative Plant Biology. Wiley. https://doi.org/10.1111/jipb.13422
chicago: He, Shengbo, and Xiaoqi Feng. “DNA Methylation Dynamics during Germline
Development.” Journal of Integrative Plant Biology. Wiley, 2022. https://doi.org/10.1111/jipb.13422.
ieee: S. He and X. Feng, “DNA methylation dynamics during germline development,”
Journal of Integrative Plant Biology, vol. 64, no. 12. Wiley, pp. 2240–2251,
2022.
ista: He S, Feng X. 2022. DNA methylation dynamics during germline development.
Journal of Integrative Plant Biology. 64(12), 2240–2251.
mla: He, Shengbo, and Xiaoqi Feng. “DNA Methylation Dynamics during Germline Development.”
Journal of Integrative Plant Biology, vol. 64, no. 12, Wiley, 2022, pp.
2240–51, doi:10.1111/jipb.13422.
short: S. He, X. Feng, Journal of Integrative Plant Biology 64 (2022) 2240–2251.
date_created: 2023-02-23T09:15:57Z
date_published: 2022-12-07T00:00:00Z
date_updated: 2024-10-14T12:03:14Z
day: '07'
department:
- _id: XiFe
doi: 10.1111/jipb.13422
extern: '1'
external_id:
pmid:
- '36478632'
intvolume: ' 64'
issue: '12'
keyword:
- Plant Science
- General Biochemistry
- Genetics and Molecular Biology
- Biochemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/jipb.13422
month: '12'
oa: 1
oa_version: Published Version
page: 2240-2251
pmid: 1
publication: Journal of Integrative Plant Biology
publication_identifier:
eissn:
- 1744-7909
issn:
- 1672-9072
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA methylation dynamics during germline development
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 64
year: '2022'
...
---
_id: '12671'
abstract:
- lang: eng
text: Sperm chromatin is typically transformed by protamines into a compact and
transcriptionally inactive state1,2. Sperm cells of flowering plants lack protamines,
yet they have small, transcriptionally active nuclei with chromatin condensed
through an unknown mechanism3,4. Here we show that a histone variant, H2B.8, mediates
sperm chromatin and nuclear condensation in Arabidopsis thaliana. Loss of H2B.8
causes enlarged sperm nuclei with dispersed chromatin, whereas ectopic expression
in somatic cells produces smaller nuclei with aggregated chromatin. This result
demonstrates that H2B.8 is sufficient for chromatin condensation. H2B.8 aggregates
transcriptionally inactive AT-rich chromatin into phase-separated condensates,
which facilitates nuclear compaction without reducing transcription. Reciprocal
crosses show that mutation of h2b.8 reduces male transmission, which suggests
that H2B.8-mediated sperm compaction is important for fertility. Altogether, our
results reveal a new mechanism of nuclear compaction through global aggregation
of unexpressed chromatin. We propose that H2B.8 is an evolutionary innovation
of flowering plants that achieves nuclear condensation compatible with active
transcription.
article_processing_charge: No
article_type: original
author:
- first_name: Toby
full_name: Buttress, Toby
last_name: Buttress
- first_name: Shengbo
full_name: He, Shengbo
last_name: He
- first_name: Liang
full_name: Wang, Liang
last_name: Wang
- first_name: Shaoli
full_name: Zhou, Shaoli
last_name: Zhou
- first_name: Gerhard
full_name: Saalbach, Gerhard
last_name: Saalbach
- first_name: Martin
full_name: Vickers, Martin
last_name: Vickers
- first_name: Guohong
full_name: Li, Guohong
last_name: Li
- first_name: Pilong
full_name: Li, Pilong
last_name: Li
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
citation:
ama: Buttress T, He S, Wang L, et al. Histone H2B.8 compacts flowering plant sperm
through chromatin phase separation. Nature. 2022;611(7936):614-622. doi:10.1038/s41586-022-05386-6
apa: Buttress, T., He, S., Wang, L., Zhou, S., Saalbach, G., Vickers, M., … Feng,
X. (2022). Histone H2B.8 compacts flowering plant sperm through chromatin phase
separation. Nature. Springer Nature. https://doi.org/10.1038/s41586-022-05386-6
chicago: Buttress, Toby, Shengbo He, Liang Wang, Shaoli Zhou, Gerhard Saalbach,
Martin Vickers, Guohong Li, Pilong Li, and Xiaoqi Feng. “Histone H2B.8 Compacts
Flowering Plant Sperm through Chromatin Phase Separation.” Nature. Springer
Nature, 2022. https://doi.org/10.1038/s41586-022-05386-6.
ieee: T. Buttress et al., “Histone H2B.8 compacts flowering plant sperm through
chromatin phase separation,” Nature, vol. 611, no. 7936. Springer Nature,
pp. 614–622, 2022.
ista: Buttress T, He S, Wang L, Zhou S, Saalbach G, Vickers M, Li G, Li P, Feng
X. 2022. Histone H2B.8 compacts flowering plant sperm through chromatin phase
separation. Nature. 611(7936), 614–622.
mla: Buttress, Toby, et al. “Histone H2B.8 Compacts Flowering Plant Sperm through
Chromatin Phase Separation.” Nature, vol. 611, no. 7936, Springer Nature,
2022, pp. 614–22, doi:10.1038/s41586-022-05386-6.
short: T. Buttress, S. He, L. Wang, S. Zhou, G. Saalbach, M. Vickers, G. Li, P.
Li, X. Feng, Nature 611 (2022) 614–622.
date_created: 2023-02-23T09:17:05Z
date_published: 2022-11-17T00:00:00Z
date_updated: 2024-10-14T12:03:36Z
day: '17'
department:
- _id: XiFe
doi: 10.1038/s41586-022-05386-6
extern: '1'
external_id:
pmid:
- '36323776'
intvolume: ' 611'
issue: '7936'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41586-022-05386-6
month: '11'
oa: 1
oa_version: Published Version
page: 614-622
pmid: 1
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Histone H2B.8 compacts flowering plant sperm through chromatin phase separation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 611
year: '2022'
...