@article{21039,
  abstract     = {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.},
  author       = {Qian, Qingyin and Nagai, Hiroki and Sanaki, Yuya and Hayashi, Makoto and Kimura, Kenichi and Nakajima, Yu Ichiro and Niwa, Ryusuke},
  issn         = {1477-9129},
  journal      = {Development},
  number       = {2},
  publisher    = {The Company of Biologists},
  title        = {{Xrp1 drives damage-induced cellular plasticity of enteroendocrine cells in the adult Drosophila midgut}},
  doi          = {10.1242/dev.205225},
  volume       = {153},
  year         = {2026},
}

@article{21158,
  abstract     = {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.},
  author       = {Yang, Pengfang and Liu, Yangyang and Dong, Qi and Miao, Yuting and Zhang, Jianlong and Xu, Shujuan and Zhao, Hong and Niu, Yuda and Zhang, Xueyong and Xu, Yunyuan and Guo, Zifeng and Xing, Lijing and Chong, Kang},
  issn         = {2041-1723},
  journal      = {Nature Communications},
  publisher    = {Springer Nature},
  title        = {{O-GlcNAc and phosphorylation modifications on HtL1/FBA10 regulate wheat vernalization for flowering}},
  doi          = {10.1038/s41467-025-67734-0},
  volume       = {17},
  year         = {2026},
}

@article{21752,
  abstract     = {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.},
  author       = {Nagai, Hiroki and Nakajima, Yu Ichiro},
  issn         = {1096-3634},
  journal      = {Seminars in Cell and Developmental Biology},
  publisher    = {Elsevier},
  title        = {{Epithelial cell plasticity in metazoans: Evolutionary insights into roles and mechanisms}},
  doi          = {10.1016/j.semcdb.2026.103670},
  volume       = {179-180},
  year         = {2026},
}

@article{21716,
  abstract     = {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.},
  author       = {Nagai, Hiroki and Feng, Xiaoqi},
  issn         = {1879-0356},
  journal      = {Current Opinion in Plant Biology},
  number       = {6},
  publisher    = {Elsevier},
  title        = {{Genetic and epigenetic mechanisms underlying male reproductive thermotolerance}},
  doi          = {10.1016/j.pbi.2026.102881},
  volume       = {91},
  year         = {2026},
}

@article{20220,
  abstract     = {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.},
  author       = {De Jaeger-Braet, Joke G and Hartmann, Merle and Böttger, Lev and Yang, Chao and Hamada, Takahiro and Hoth, Stefan and Feng, Xiaoqi and Weingartner, Magdalena and Schnittger, Arp},
  issn         = {2375-2548},
  journal      = {Science Advances},
  number       = {32},
  pages        = {eadr5694},
  publisher    = {AAAS},
  title        = {{The recruitment of the A-type cyclin TAM to stress granules is crucial for meiotic fidelity under heat}},
  doi          = {10.1126/sciadv.adr5694},
  volume       = {11},
  year         = {2025},
}

@article{20656,
  abstract     = {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.},
  author       = {Rodriguez Solovey, Lesia and Fiedler, Lukas and Zou, Minxia and Giannini, Caterina and Monzer, Aline and Vladimirtsev, Dmitrii and Randuch, Marek and Yu, Yongfan and Gelová, Zuzana and Verstraeten, Inge and Hajny, Jakub and Chen, Meng and Tan, Shutang and Hörmayer, Lukas and Li, Lanxin and Marques-Bueno, Maria Mar and Quddoos, Zainab and Molnar, Gergely and Kulich, Ivan and Jaillais, Yvon and Friml, Jiří},
  issn         = {0092-8674},
  journal      = {Cell},
  number       = {22},
  pages        = {6138--6150.e17},
  publisher    = {Elsevier},
  title        = {{ABP1/ABL3-TMK1 cell-surface auxin signaling targets PIN2-mediated auxin fluxes for root gravitropism}},
  doi          = {10.1016/j.cell.2025.08.026},
  volume       = {188},
  year         = {2025},
}

@article{18823,
  author       = {Cao, Dechang and De Jaeger-Braet, Joke G},
  issn         = {1532-2548},
  journal      = {Plant Physiology},
  number       = {1},
  publisher    = {Oxford University Press},
  title        = {{Memory of maternal temperatures: DNA methylation alterations across generations}},
  doi          = {10.1093/plphys/kiae651},
  volume       = {197},
  year         = {2025},
}

@article{19367,
  author       = {De Jaeger-Braet, Joke G},
  issn         = {1532-2548},
  journal      = {Plant Physiology},
  number       = {2},
  publisher    = {Oxford University Press},
  title        = {{Arabidopsis accessions and their difference in heat tolerance during meiosis}},
  doi          = {10.1093/plphys/kiaf055},
  volume       = {197},
  year         = {2025},
}

@article{19406,
  abstract     = {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.
Through 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.
To 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.
Our 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.},
  author       = {Song, Xin and Zhang, Miao and Wang, Ting Ting and Duan, Yao Yuan and Ren, Jie and Gao, Hu and Fan, Yan Jie and Xia, Qiang Ming and Cao, Hui Xiang and Xie, Kai Dong and Wu, Xiao Meng and Zhang, Fei and Zhang, Si Qi and Huang, Ying and Boualem, Adnane and Bendahmane, Abdelhafid and Tan, Feng Quan and Guo, Wen Wu},
  issn         = {1469-8137},
  journal      = {New Phytologist},
  number       = {1},
  pages        = {176--191},
  publisher    = {Wiley},
  title        = {{Polyploidization leads to salt stress resilience via ethylene signaling in citrus plants}},
  doi          = {10.1111/nph.20428},
  volume       = {246},
  year         = {2025},
}

@article{19436,
  abstract     = {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.},
  author       = {Zhang, Jun and Wu, Di and Zhang, Yating and Feng, Xiaoqi and Gao, Hongbo},
  issn         = {2730-9401},
  journal      = {Molecular Horticulture},
  publisher    = {Springer Nature},
  title        = {{DNA methylation dynamics in male germline development in Brassica Rapa}},
  doi          = {10.1186/s43897-024-00137-9},
  volume       = {5},
  year         = {2025},
}

@unpublished{19399,
  abstract     = {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.},
  author       = {Rodriguez Solovey, Lesia and Fiedler, Lukas and Zou, Minxia and Giannini, Caterina and Monzer, Aline and Vladimirtsev, Dmitrii and Randuch, Marek and Yu, Yongfan and Gelová, Zuzana and Verstraeten, Inge and Hajny, Jakub and Chen, Meng and Tan, Shutang and Hörmayer, Lukas and Li, Lanxin and Marques-Bueno, Maria Mar and Quddoos, Zainab and Molnar, Gergely and Xu, Tongda and Kulich, Ivan and Jaillais, Yvon and Friml, Jiří},
  booktitle    = {bioRxiv},
  publisher    = {Cold Spring Harbor Laboratory},
  title        = {{ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated auxin fluxes for root gravitropism}},
  doi          = {10.1101/2022.11.30.518503},
  year         = {2025},
}

@article{19602,
  abstract     = {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.},
  author       = {Walker, James and Zhang, Jingyi and Liu, Yalin and Xu, Shujuan and Yu, Yiming and Vickers, Martin and Ouyang, Weizhi and Tálas, Judit and Dolan, Liam and Nakajima, Keiji and Feng, Xiaoqi},
  issn         = {1097-4172},
  journal      = {Cell},
  number       = {11},
  pages        = {2890--2906.e14},
  publisher    = {Elsevier},
  title        = {{Extensive N4 cytosine methylation is essential for Marchantia sperm function}},
  doi          = {10.1016/j.cell.2025.03.014},
  volume       = {188},
  year         = {2025},
}

@article{15375,
  abstract     = {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.},
  author       = {He, Shengbo and Yu, Yiming and Wang, Liang and Zhang, Jingyi and Bai, Zhengyong and Li, Guohong and Li, Pilong and Feng, Xiaoqi},
  issn         = {1532-298X},
  journal      = {The Plant Cell},
  number       = {5},
  pages        = {1829--1843},
  publisher    = {Oxford University Press},
  title        = {{Linker histone H1 drives heterochromatin condensation via phase separation in Arabidopsis}},
  doi          = {10.1093/plcell/koae034},
  volume       = {36},
  year         = {2024},
}

@article{17285,
  abstract     = {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.},
  author       = {Liu, Xuemei and Deng, Min and Shi, Bingxin and Zhu, Kehui and Chen, Jinchao and Xu, Shujuan and Bie, Xiaomin and Zhang, Xiansheng and Lin, Xuelei and Xiao, Jun},
  issn         = {1869-1889},
  journal      = {Science China Life Sciences},
  pages        = {2251--2266},
  publisher    = {Springer Nature},
  title        = {{Distinct roles of H3K27me3 and H3K36me3 in vernalization response, maintenance, and resetting in winter wheat}},
  doi          = {10.1007/s11427-024-2664-0},
  volume       = {67},
  year         = {2024},
}

@article{17408,
  abstract     = {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.

Results: 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.

Conclusions: 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.},
  author       = {Nagai, Hiroki and Adachi, Yuya and Nakasugi, Tenki and Takigawa, Ema and Ui, Junichiro and Makino, Takashi and Miura, Masayuki and Nakajima, Yu Ichiro},
  issn         = {1741-7007},
  journal      = {BMC Biology},
  publisher    = {Springer Nature},
  title        = {{Highly regenerative species-specific genes improve age-associated features in the adult Drosophila midgut}},
  doi          = {10.1186/s12915-024-01956-4},
  volume       = {22},
  year         = {2024},
}

@article{12668,
  abstract     = {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.

Results: 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.

Conclusions: Collectively, we present an invaluable resource for comparative and mechanistic analysis of the epigenomic regulation of crop embryogenesis.},
  author       = {Zhao, Long and Yang, Yiman and Chen, Jinchao and Lin, Xuelei and Zhang, Hao and Wang, Hao and Wang, Hongzhe and Bie, Xiaomin and Jiang, Jiafu and Feng, Xiaoqi and Fu, Xiangdong and Zhang, Xiansheng and Du, Zhuo and Xiao, Jun},
  issn         = {1474-760X},
  journal      = {Genome Biology},
  publisher    = {Springer Nature},
  title        = {{Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat}},
  doi          = {10.1186/s13059-022-02844-2},
  volume       = {24},
  year         = {2023},
}

@article{12669,
  abstract     = {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.},
  author       = {Manavella, Pablo A and Godoy Herz, Micaela A and Kornblihtt, Alberto R and Sorenson, Reed and Sieburth, Leslie E and Nakaminami, Kentaro and Seki, Motoaki and Ding, Yiliang and Sun, Qianwen and Kang, Hunseung and Ariel, Federico D and Crespi, Martin and Giudicatti, Axel J and Cai, Qiang and Jin, Hailing and Feng, Xiaoqi and Qi, Yijun and Pikaard, Craig S},
  issn         = {1532-298X},
  journal      = {The Plant Cell},
  keywords     = {Cell Biology, Plant Science},
  number       = {6},
  publisher    = {Oxford University Press},
  title        = {{Beyond transcription: compelling open questions in plant RNA biology}},
  doi          = {10.1093/plcell/koac346},
  volume       = {35},
  year         = {2023},
}

@article{12672,
  abstract     = {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.},
  author       = {Lyons, David B. and Briffa, Amy and He, Shengbo and Choi, Jaemyung and Hollwey, Elizabeth and Colicchio, Jack and Anderson, Ian and Feng, Xiaoqi and Howard, Martin and Zilberman, Daniel},
  issn         = {2211-1247},
  journal      = {Cell Reports},
  number       = {3},
  publisher    = {Elsevier},
  title        = {{Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons}},
  doi          = {10.1016/j.celrep.2023.112132},
  volume       = {42},
  year         = {2023},
}

@article{12670,
  abstract     = {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.},
  author       = {He, Shengbo and Feng, Xiaoqi},
  issn         = {1744-7909},
  journal      = {Journal of Integrative Plant Biology},
  keywords     = {Plant Science, General Biochemistry, Genetics and Molecular Biology, Biochemistry},
  number       = {12},
  pages        = {2240--2251},
  publisher    = {Wiley},
  title        = {{DNA methylation dynamics during germline development}},
  doi          = {10.1111/jipb.13422},
  volume       = {64},
  year         = {2022},
}

@article{12671,
  abstract     = {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.},
  author       = {Buttress, Toby and He, Shengbo and Wang, Liang and Zhou, Shaoli and Saalbach, Gerhard and Vickers, Martin and Li, Guohong and Li, Pilong and Feng, Xiaoqi},
  issn         = {1476-4687},
  journal      = {Nature},
  number       = {7936},
  pages        = {614--622},
  publisher    = {Springer Nature},
  title        = {{Histone H2B.8 compacts flowering plant sperm through chromatin phase separation}},
  doi          = {10.1038/s41586-022-05386-6},
  volume       = {611},
  year         = {2022},
}