---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '21509'
abstract:
- lang: eng
text: Chromatin remodeling complexes mobilize nucleosomes and promote transcription
factor (TF) binding. Using ensemble and single-molecule assays combined with cryo-electron
microscopy (cryo-EM), we studied the interaction between pioneer TFs OCT4–SOX2
and the human BRG1/BRM-associated factor (BAF) complex on nucleosomes. BAF engages
TF-bound substrates in two orientations, placing OCT4–SOX2 at either the remodeler
ENTRY or EXIT site. At the ENTRY site, OCT4–SOX2 initially coexists with BAF without
structural interference. However, continued DNA translocation is expected to cause
collisions with bound TFs, which can trigger remodeling direction reversals or
may induce TF dissociation. To accommodate TFs at the EXIT site, BAF undergoes
structural rearrangements, and ensemble assays reveal a nucleosome subpopulation
translocating away from TF-binding sites. Moreover, single-molecule experiments
show that nucleosome-bound BAF frequently changes remodeling direction, and we
identify an ADP-bound remodeler conformation as a potential intermediate. Together,
these findings reveal key aspects of the conformational dynamics and remodeling
outcomes underlying BAF processing of TF-bound nucleosomes.
acknowledgement: We thank D. Hess, V. Iesmantavicius, and J. Seebacher (FMI Proteomics
and Protein Analysis Facility) for mass spectrometry support; S. Smallwood, K. Shimada,
D. Klein, and M. Schütz-Stoffregen for technical assistance; J. Côté and C. Lachance
for critical discussions; and members of the Thomä lab for helpful feedback. Support
for this work was provided to N.H.T. by the European Research Council under the
European Union’s Horizon 2020 research program (NucEM, no. 884331), the Novartis
Research Foundation, the Swiss National Science Foundation (SNF 31003A_179541, 310030_214852,
and Sinergia CRSII5_186230), and the Swiss Cancer Research (KFS-4980-02-2020 and
KFS-5933-08-2023). S.D. was supported by the European Research Council (DONUTS,
no. 101092623), the Knut and Alice Wallenberg Foundation (2024.0012), the Cancerfonden
(25 4453 Pj), and the Swedish Research Council (VR 03255). A.K.M. was supported
by a Human Frontier Science Program Long-Term Fellowship, and L.V. was supported
by an EMBO fellowship (ALTF 549-2021).
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Joscha
full_name: Weiss, Joscha
last_name: Weiss
- first_name: Luca
full_name: Vecchia, Luca
last_name: Vecchia
- first_name: David
full_name: Domjan, David
last_name: Domjan
- first_name: Simone
full_name: Cavadini, Simone
last_name: Cavadini
- first_name: Anton
full_name: Sabantsev, Anton
last_name: Sabantsev
- first_name: Georg
full_name: Kempf, Georg
last_name: Kempf
- first_name: Ganesh R.
full_name: Pathare, Ganesh R.
last_name: Pathare
- first_name: Klaus
full_name: Brackmann, Klaus
last_name: Brackmann
- first_name: Alicia
full_name: Michael, Alicia
id: 6437c950-2a03-11ee-914d-d6476dd7b75c
last_name: Michael
orcid: 0000-0002-6080-839X
- first_name: Lukas
full_name: Kater, Lukas
last_name: Kater
- first_name: Eric
full_name: Hietter-Pfeiffer, Eric
last_name: Hietter-Pfeiffer
- first_name: Mina
full_name: Haddawi, Mina
last_name: Haddawi
- first_name: Urja P.
full_name: Kuber, Urja P.
last_name: Kuber
- first_name: Sandra
full_name: Mühlhäusser, Sandra
last_name: Mühlhäusser
- first_name: Ralph S.
full_name: Grand, Ralph S.
last_name: Grand
- first_name: Michael B.
full_name: Stadler, Michael B.
last_name: Stadler
- first_name: Sebastian
full_name: Deindl, Sebastian
last_name: Deindl
- first_name: Nicolas H.
full_name: Thomä, Nicolas H.
last_name: Thomä
citation:
ama: Weiss J, Vecchia L, Domjan D, et al. The human BAF chromatin remodeler processes
nucleosomes bound by pioneer transcription factors OCT4–SOX2. Molecular Cell.
2026;86(4):625-639.e8. doi:10.1016/j.molcel.2026.01.021
apa: Weiss, J., Vecchia, L., Domjan, D., Cavadini, S., Sabantsev, A., Kempf, G.,
… Thomä, N. H. (2026). The human BAF chromatin remodeler processes nucleosomes
bound by pioneer transcription factors OCT4–SOX2. Molecular Cell. Elsevier.
https://doi.org/10.1016/j.molcel.2026.01.021
chicago: Weiss, Joscha, Luca Vecchia, David Domjan, Simone Cavadini, Anton Sabantsev,
Georg Kempf, Ganesh R. Pathare, et al. “The Human BAF Chromatin Remodeler Processes
Nucleosomes Bound by Pioneer Transcription Factors OCT4–SOX2.” Molecular Cell.
Elsevier, 2026. https://doi.org/10.1016/j.molcel.2026.01.021.
ieee: J. Weiss et al., “The human BAF chromatin remodeler processes nucleosomes
bound by pioneer transcription factors OCT4–SOX2,” Molecular Cell, vol.
86, no. 4. Elsevier, p. 625–639.e8, 2026.
ista: Weiss J, Vecchia L, Domjan D, Cavadini S, Sabantsev A, Kempf G, Pathare GR,
Brackmann K, Michael AK, Kater L, Hietter-Pfeiffer E, Haddawi M, Kuber UP, Mühlhäusser
S, Grand RS, Stadler MB, Deindl S, Thomä NH. 2026. The human BAF chromatin remodeler
processes nucleosomes bound by pioneer transcription factors OCT4–SOX2. Molecular
Cell. 86(4), 625–639.e8.
mla: Weiss, Joscha, et al. “The Human BAF Chromatin Remodeler Processes Nucleosomes
Bound by Pioneer Transcription Factors OCT4–SOX2.” Molecular Cell, vol.
86, no. 4, Elsevier, 2026, p. 625–639.e8, doi:10.1016/j.molcel.2026.01.021.
short: J. Weiss, L. Vecchia, D. Domjan, S. Cavadini, A. Sabantsev, G. Kempf, G.R.
Pathare, K. Brackmann, A.K. Michael, L. Kater, E. Hietter-Pfeiffer, M. Haddawi,
U.P. Kuber, S. Mühlhäusser, R.S. Grand, M.B. Stadler, S. Deindl, N.H. Thomä, Molecular
Cell 86 (2026) 625–639.e8.
date_created: 2026-03-30T11:58:48Z
date_published: 2026-02-19T00:00:00Z
date_updated: 2026-03-30T12:09:08Z
day: '19'
ddc:
- '570'
department:
- _id: AlMi
doi: 10.1016/j.molcel.2026.01.021
external_id:
pmid:
- '41679301'
file:
- access_level: open_access
checksum: e16a7315b64a706184b177ea1621523c
content_type: application/pdf
creator: dernst
date_created: 2026-03-30T12:04:38Z
date_updated: 2026-03-30T12:04:38Z
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file_size: 9786677
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month: '02'
oa: 1
oa_version: Published Version
page: 625-639.e8
pmid: 1
publication: Molecular Cell
publication_identifier:
issn:
- 1097-2765
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: The human BAF chromatin remodeler processes nucleosomes bound by pioneer transcription
factors OCT4–SOX2
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: 86
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20374'
abstract:
- lang: eng
text: Pioneer transcription factors (TFs) engage chromatinized DNA motifs. However,
it is unclear how the resultant TF-nucleosome complexes are decoded by co-factors.
In humans, the TF p53 regulates cell-cycle progression, apoptosis, and the DNA
damage response, with a large fraction of p53-bound sites residing in nucleosome-harboring
inaccessible chromatin. We examined the interaction of chromatin-bound p53 with
co-factors belonging to the ubiquitin proteasome system (UPS). At two distinct
motif locations on the nucleosome (super-helical location [SHL]−5.7 and SHL+5.9),
the E3 ubiquitin ligase E6-E6AP was unable to bind nucleosome-engaged p53. The
deubiquitinase USP7, on the other hand, readily engages nucleosome-bound p53 in
vitro and in cells. A corresponding cryo-electron microscopy (cryo-EM) structure
shows USP7 engaged with p53 and nucleosomes. Our work illustrates how chromatin
imposes a co-factor-selective barrier for p53 interactors, whereby flexibly tethered
interaction domains of co-factors and TFs govern compatibility between co-factors,
TFs, and chromatin.
acknowledgement: We thank M. Schütz for laboratory management, organization, and assistance
with manuscript editing. We are grateful to all Thomä and Schübeler lab members.
We thank Ulrich Hassiepen from Novartis for his support and insightful discussions
on the kinetic analysis. This work was supported by funding from the European Research
Council (ERC), under the European Union’s H2020 research program (NucEM, grant no.
884331); the Swiss National Science Foundation (SNF, grant no. 310030_301206 and
310030_214852); Krebsforschung (KFS, grant no. KFS-5933-08-2023); Novartis Research
Foundation (to N.H.T.); the Novartis Freenovation (grant no. FN23-0000000514 to
C.R.S.); the National Health and Medical Research Council CJ Martin Fellowship (APP1148380);
the EU Horizon 2020 Research and Innovation Program under the Marie Sklodowska-Curie
grant (grant no. 748760); the South Australian immunoGENomics Cancer Institute grant
funding from the Australian Government; and the Sylvia and Charles Viertel Charitable
Foundation Senior Medical Research Fellowship (to L.I.).
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Deyasini
full_name: Chakraborty, Deyasini
last_name: Chakraborty
- first_name: Colby R.
full_name: Sandate, Colby R.
last_name: Sandate
- first_name: Luke
full_name: Isbel, Luke
last_name: Isbel
- first_name: Georg
full_name: Kempf, Georg
last_name: Kempf
- first_name: Joscha
full_name: Weiss, Joscha
last_name: Weiss
- first_name: Simone
full_name: Cavadini, Simone
last_name: Cavadini
- first_name: Lukas
full_name: Kater, Lukas
last_name: Kater
- first_name: Jan
full_name: Seebacher, Jan
last_name: Seebacher
- first_name: Zuzanna
full_name: Kozicka, Zuzanna
last_name: Kozicka
- first_name: Lisa
full_name: Stoos, Lisa
last_name: Stoos
- first_name: Ralph S.
full_name: Grand, Ralph S.
last_name: Grand
- first_name: Dirk
full_name: Schübeler, Dirk
last_name: Schübeler
- first_name: Alicia
full_name: Michael, Alicia
id: 6437c950-2a03-11ee-914d-d6476dd7b75c
last_name: Michael
orcid: 0000-0002-6080-839X
- first_name: Nicolas H.
full_name: Thomä, Nicolas H.
last_name: Thomä
citation:
ama: Chakraborty D, Sandate CR, Isbel L, et al. Nucleosomes specify co-factor access
to p53. Molecular Cell. 2025;85(15):2919-2936.e12. doi:10.1016/j.molcel.2025.06.027
apa: Chakraborty, D., Sandate, C. R., Isbel, L., Kempf, G., Weiss, J., Cavadini,
S., … Thomä, N. H. (2025). Nucleosomes specify co-factor access to p53. Molecular
Cell. Elsevier. https://doi.org/10.1016/j.molcel.2025.06.027
chicago: Chakraborty, Deyasini, Colby R. Sandate, Luke Isbel, Georg Kempf, Joscha
Weiss, Simone Cavadini, Lukas Kater, et al. “Nucleosomes Specify Co-Factor Access
to P53.” Molecular Cell. Elsevier, 2025. https://doi.org/10.1016/j.molcel.2025.06.027.
ieee: D. Chakraborty et al., “Nucleosomes specify co-factor access to p53,”
Molecular Cell, vol. 85, no. 15. Elsevier, p. 2919–2936.e12, 2025.
ista: Chakraborty D, Sandate CR, Isbel L, Kempf G, Weiss J, Cavadini S, Kater L,
Seebacher J, Kozicka Z, Stoos L, Grand RS, Schübeler D, Michael AK, Thomä NH.
2025. Nucleosomes specify co-factor access to p53. Molecular Cell. 85(15), 2919–2936.e12.
mla: Chakraborty, Deyasini, et al. “Nucleosomes Specify Co-Factor Access to P53.”
Molecular Cell, vol. 85, no. 15, Elsevier, 2025, p. 2919–2936.e12, doi:10.1016/j.molcel.2025.06.027.
short: D. Chakraborty, C.R. Sandate, L. Isbel, G. Kempf, J. Weiss, S. Cavadini,
L. Kater, J. Seebacher, Z. Kozicka, L. Stoos, R.S. Grand, D. Schübeler, A.K. Michael,
N.H. Thomä, Molecular Cell 85 (2025) 2919–2936.e12.
date_created: 2025-09-23T08:56:13Z
date_published: 2025-08-07T00:00:00Z
date_updated: 2025-09-24T08:21:55Z
day: '07'
ddc:
- '570'
department:
- _id: AlMi
doi: 10.1016/j.molcel.2025.06.027
file:
- access_level: open_access
checksum: e60390ca629b350af3221d4718ca6534
content_type: application/pdf
creator: dernst
date_created: 2025-09-24T07:54:03Z
date_updated: 2025-09-24T07:54:03Z
file_id: '20386'
file_name: 2025_MolecularCell_Chakraborty.pdf
file_size: 41813494
relation: main_file
success: 1
file_date_updated: 2025-09-24T07:54:03Z
has_accepted_license: '1'
intvolume: ' 85'
issue: '15'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 2919-2936.e12
publication: Molecular Cell
publication_identifier:
issn:
- 1097-2765
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nucleosomes specify co-factor access to p53
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: 85
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '19443'
abstract:
- lang: eng
text: In cryo-electron microscopy, accurate particle localization and classification
are imperative. Recent deep learning solutions, though successful, require extensive
training datasets. The protracted generation time of physics-based models, often
employed to produce these datasets, limits their broad applicability. We introduce
FakET, a method based on neural style transfer, capable of simulating the forward
operator of any cryo transmission electron microscope. It can be used to adapt
a synthetic training dataset according to reference data producing high-quality
simulated micrographs or tilt-series. To assess the quality of our generated data,
we used it to train a state-of-the-art localization and classification architecture
and compared its performance with a counterpart trained on benchmark data. Remarkably,
our technique matches the performance, boosts data generation speed 750x, uses
33x less memory, and scales well to typical transmission electron microscope detector
sizes. It leverages GPU acceleration and parallel processing. The source code
is available at https://github.com/paloha/faket/.
acknowledgement: The IMP and D.H. are generously funded by Boehringer Ingelheim. We
thank Julius Berner from the Mathematical Data Science group @ UniVie, Ilja Gubins
and Marten Chaillet from the SHREC team, and the members of the Haselbach lab for
helpful discussions.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Pavol
full_name: Harar, Pavol
id: e03d953a-6e8c-11ef-99e4-f0717d385cd5
last_name: Harar
orcid: 0000-0001-5206-1794
- first_name: Lukas
full_name: Herrmann, Lukas
last_name: Herrmann
- first_name: Philipp
full_name: Grohs, Philipp
last_name: Grohs
- first_name: David
full_name: Haselbach, David
last_name: Haselbach
citation:
ama: 'Harar P, Herrmann L, Grohs P, Haselbach D. FakET: Simulating cryo-electron
tomograms with neural style transfer. Structure. 2025;33(4):820-827.e4.
doi:10.1016/j.str.2025.01.020'
apa: 'Harar, P., Herrmann, L., Grohs, P., & Haselbach, D. (2025). FakET: Simulating
cryo-electron tomograms with neural style transfer. Structure. Elsevier.
https://doi.org/10.1016/j.str.2025.01.020'
chicago: 'Harar, Pavol, Lukas Herrmann, Philipp Grohs, and David Haselbach. “FakET:
Simulating Cryo-Electron Tomograms with Neural Style Transfer.” Structure.
Elsevier, 2025. https://doi.org/10.1016/j.str.2025.01.020.'
ieee: 'P. Harar, L. Herrmann, P. Grohs, and D. Haselbach, “FakET: Simulating cryo-electron
tomograms with neural style transfer,” Structure, vol. 33, no. 4. Elsevier,
p. 820–827.e4, 2025.'
ista: 'Harar P, Herrmann L, Grohs P, Haselbach D. 2025. FakET: Simulating cryo-electron
tomograms with neural style transfer. Structure. 33(4), 820–827.e4.'
mla: 'Harar, Pavol, et al. “FakET: Simulating Cryo-Electron Tomograms with Neural
Style Transfer.” Structure, vol. 33, no. 4, Elsevier, 2025, p. 820–827.e4,
doi:10.1016/j.str.2025.01.020.'
short: P. Harar, L. Herrmann, P. Grohs, D. Haselbach, Structure 33 (2025) 820–827.e4.
corr_author: '1'
date_created: 2025-03-23T23:01:27Z
date_published: 2025-04-03T00:00:00Z
date_updated: 2025-09-30T11:13:02Z
day: '03'
ddc:
- '570'
department:
- _id: AlMi
doi: 10.1016/j.str.2025.01.020
external_id:
isi:
- '001463196100001'
pmid:
- '39947174'
file:
- access_level: open_access
checksum: f346bc357a66a88cca3d0eb95793fb73
content_type: application/pdf
creator: dernst
date_created: 2025-08-05T12:15:13Z
date_updated: 2025-08-05T12:15:13Z
file_id: '20130'
file_name: 2025_Structure_Harar.pdf
file_size: 4367530
relation: main_file
success: 1
file_date_updated: 2025-08-05T12:15:13Z
has_accepted_license: '1'
intvolume: ' 33'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 820-827.e4
pmid: 1
publication: Structure
publication_identifier:
eissn:
- 1878-4186
issn:
- 0969-2126
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/paloha/faket/
scopus_import: '1'
status: public
title: 'FakET: Simulating cryo-electron tomograms with neural style transfer'
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: 33
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '20924'
abstract:
- lang: eng
text: "Pioneer transcription factors (TFs) possess the ability to read out DNA motifs
embedded within nucleosomes, driving changes in gene expression during cellular
differentiation and reprogramming. Here, we present selected engagement on nucleosome
sequencing (SeEN-seq), a protocol designed to systematically identify potential
TF-binding sites on the nucleosome. We describe steps for nucleosome library assembly,
SeEN-seq assay, and cryoelectron microscopy (cryo-EM) sample preparation. This
protocol facilitates the preparation of homogeneous pioneer TF-nucleosome complexes
for cryo-EM structure determination using single-particle analysis.\r\nFor complete
details on the use and execution of this protocol, please refer to Michael et
al.1"
acknowledgement: We thank R.H. Kim, A. Casper, and R. Gautsch for sequencing at the
NGS facility (RRID:SCR_025746). K.T. is an Honorary Professor at the Department
of Biology, Ludwig-Maximilians-University, Munich, Germany. This study was funded
by European Research Council grant ERC-CoG-818556 TotipotentZygotChrom (K.T.), Max
Planck Society (K.T.), and ERC Starting Grant “ChromaChrono” 101162145 (A.K.M.).
article_number: '104295'
article_processing_charge: Yes
article_type: original
author:
- first_name: Wataru
full_name: Kobayashi, Wataru
last_name: Kobayashi
- first_name: Alicia
full_name: Michael, Alicia
id: 6437c950-2a03-11ee-914d-d6476dd7b75c
last_name: Michael
orcid: 0000-0002-6080-839X
- first_name: Siwat
full_name: Ruangroengkulrith, Siwat
last_name: Ruangroengkulrith
- first_name: Maximilian
full_name: Kümmecke, Maximilian
last_name: Kümmecke
- first_name: Kikuë
full_name: Tachibana, Kikuë
last_name: Tachibana
citation:
ama: Kobayashi W, Michael AK, Ruangroengkulrith S, Kümmecke M, Tachibana K. Protocol
for integrative analysis of transcription factor-nucleosome interactions using
SeEN-seq and cryo-EM structure determination. STAR Protocols. 2025;7. doi:10.1016/j.xpro.2025.104295
apa: Kobayashi, W., Michael, A. K., Ruangroengkulrith, S., Kümmecke, M., & Tachibana,
K. (2025). Protocol for integrative analysis of transcription factor-nucleosome
interactions using SeEN-seq and cryo-EM structure determination. STAR Protocols.
Elsevier. https://doi.org/10.1016/j.xpro.2025.104295
chicago: Kobayashi, Wataru, Alicia K. Michael, Siwat Ruangroengkulrith, Maximilian
Kümmecke, and Kikuë Tachibana. “Protocol for Integrative Analysis of Transcription
Factor-Nucleosome Interactions Using SeEN-Seq and Cryo-EM Structure Determination.”
STAR Protocols. Elsevier, 2025. https://doi.org/10.1016/j.xpro.2025.104295.
ieee: W. Kobayashi, A. K. Michael, S. Ruangroengkulrith, M. Kümmecke, and K. Tachibana,
“Protocol for integrative analysis of transcription factor-nucleosome interactions
using SeEN-seq and cryo-EM structure determination,” STAR Protocols, vol.
7. Elsevier, 2025.
ista: Kobayashi W, Michael AK, Ruangroengkulrith S, Kümmecke M, Tachibana K. 2025.
Protocol for integrative analysis of transcription factor-nucleosome interactions
using SeEN-seq and cryo-EM structure determination. STAR Protocols. 7, 104295.
mla: Kobayashi, Wataru, et al. “Protocol for Integrative Analysis of Transcription
Factor-Nucleosome Interactions Using SeEN-Seq and Cryo-EM Structure Determination.”
STAR Protocols, vol. 7, 104295, Elsevier, 2025, doi:10.1016/j.xpro.2025.104295.
short: W. Kobayashi, A.K. Michael, S. Ruangroengkulrith, M. Kümmecke, K. Tachibana,
STAR Protocols 7 (2025).
corr_author: '1'
date_created: 2026-01-04T23:01:33Z
date_published: 2025-12-26T00:00:00Z
date_updated: 2026-01-05T11:16:11Z
day: '26'
department:
- _id: AlMi
doi: 10.1016/j.xpro.2025.104295
external_id:
pmid:
- '41455105'
has_accepted_license: '1'
intvolume: ' 7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.xpro.2025.104295
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 9136c684-16d5-11f0-9cad-91c0177b365f
grant_number: '101162145'
name: Circadian structural transitions of chromatin
publication: STAR Protocols
publication_identifier:
eissn:
- 2666-1667
publication_status: epub_ahead
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Protocol for integrative analysis of transcription factor-nucleosome interactions
using SeEN-seq and cryo-EM structure determination
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: 7
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20935'
abstract:
- lang: eng
text: In situ cryo-electron tomography (cryo-ET) has emerged as the method of choice
to investigate the structures of biomolecules in their native context. However,
challenges remain for the efficient production and sharing of large-scale cryo-ET
datasets. Here, we combined cryogenic plasma-based focused ion beam (cryo-PFIB)
milling with recent advances in cryo-ET acquisition and processing to generate
a dataset of 1,829 annotated tomograms of the green alga Chlamydomonas reinhardtii,
which we provide as a community resource to drive method development and inspire
biological discovery. To assay data quality, we performed subtomogram averaging
of both soluble and membrane-bound complexes ranging in size from >3 MDa to ∼200
kDa, including 80S ribosomes, Rubisco, nucleosomes, microtubules, clathrin, photosystem
II, and mitochondrial ATP synthase. The majority of these density maps reached
sub-nanometer resolution, demonstrating the potential of this C. reinhardtii dataset
as well as the promise of modern cryo-ET workflows and open data sharing to empower
visual proteomics.
acknowledgement: Calculations were performed at the Max Planck Institute of Biochemistry
and the Raven Supercomputer of the Max Planck Computing and Data Facility (MPCDF)
in Garching, Germany; at the sciCORE (http://scicore.unibas.ch/) scientific computing
center at the University of Basel, Switzerland; and at Thermo Fisher Scientific,
in Eindhoven, the Netherlands. This work was supported by Thermo Fisher Scientific.
All lamella preparations and tilt-series collections used in this work were conducted
at Thermo Fisher R&D facilities in Brno and Eindhoven, utilizing Arctis and Krios
microscopes. This work was also supported by the ERC consolidator grant “cryOcean”
(fulfilled by the Swiss State Secretariat for Education, Research and Innovation,
M822.00045) as well as a Swiss Nanoscience Institute PhD school grant to B.D.E.
and P.V.d.S., an EMBO long-term postdoctoral fellowship (ALTF-383-2022) to G.T.,
an SNSF Postdoctoral Fellowship (project 210561) to F.W., a Boehringer Ingelheim
Fonds fellowship to L.L., and by the Max Planck Society to J.A.G.B. and J.M.P.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Ron
full_name: Kelley, Ron
last_name: Kelley
- first_name: Sagar
full_name: Khavnekar, Sagar
last_name: Khavnekar
- first_name: Ricardo D.
full_name: Righetto, Ricardo D.
last_name: Righetto
- first_name: Jessica
full_name: Heebner, Jessica
last_name: Heebner
- first_name: Martin
full_name: Obr, Martin
id: 4741CA5A-F248-11E8-B48F-1D18A9856A87
last_name: Obr
orcid: 0000-0003-1756-6564
- first_name: Xianjun
full_name: Zhang, Xianjun
last_name: Zhang
- first_name: Saikat
full_name: Chakraborty, Saikat
last_name: Chakraborty
- first_name: Grigory
full_name: Tagiltsev, Grigory
last_name: Tagiltsev
- first_name: Alicia
full_name: Michael, Alicia
id: 6437c950-2a03-11ee-914d-d6476dd7b75c
last_name: Michael
orcid: 0000-0002-6080-839X
- first_name: Sofie
full_name: Van Dorst, Sofie
last_name: Van Dorst
- first_name: Florent
full_name: Waltz, Florent
last_name: Waltz
- first_name: Caitlyn L.
full_name: Mccafferty, Caitlyn L.
last_name: Mccafferty
- first_name: Lorenz
full_name: Lamm, Lorenz
last_name: Lamm
- first_name: Simon
full_name: Zufferey, Simon
last_name: Zufferey
- first_name: Philippe
full_name: Van Der Stappen, Philippe
last_name: Van Der Stappen
- first_name: Hugo
full_name: Van Den Hoek, Hugo
last_name: Van Den Hoek
- first_name: Wojciech
full_name: Wietrzynski, Wojciech
last_name: Wietrzynski
- first_name: Pavol
full_name: Harar, Pavol
id: e03d953a-6e8c-11ef-99e4-f0717d385cd5
last_name: Harar
orcid: 0000-0001-5206-1794
- first_name: William
full_name: Wan, William
last_name: Wan
- first_name: John A.G.
full_name: Briggs, John A.G.
last_name: Briggs
- first_name: Jürgen M.
full_name: Plitzko, Jürgen M.
last_name: Plitzko
- first_name: Benjamin D.
full_name: Engel, Benjamin D.
last_name: Engel
- first_name: Abhay
full_name: Kotecha, Abhay
last_name: Kotecha
citation:
ama: Kelley R, Khavnekar S, Righetto RD, et al. Toward community-driven visual proteomics
with large-scale cryo-electron tomography of Chlamydomonas reinhardtii. Molecular
Cell. doi:10.1016/j.molcel.2025.11.029
apa: Kelley, R., Khavnekar, S., Righetto, R. D., Heebner, J., Obr, M., Zhang, X.,
… Kotecha, A. (n.d.). Toward community-driven visual proteomics with large-scale
cryo-electron tomography of Chlamydomonas reinhardtii. Molecular Cell.
Elsevier. https://doi.org/10.1016/j.molcel.2025.11.029
chicago: Kelley, Ron, Sagar Khavnekar, Ricardo D. Righetto, Jessica Heebner, Martin
Obr, Xianjun Zhang, Saikat Chakraborty, et al. “Toward Community-Driven Visual
Proteomics with Large-Scale Cryo-Electron Tomography of Chlamydomonas Reinhardtii.”
Molecular Cell. Elsevier, n.d. https://doi.org/10.1016/j.molcel.2025.11.029.
ieee: R. Kelley et al., “Toward community-driven visual proteomics with large-scale
cryo-electron tomography of Chlamydomonas reinhardtii,” Molecular Cell.
Elsevier.
ista: Kelley R, Khavnekar S, Righetto RD, Heebner J, Obr M, Zhang X, Chakraborty
S, Tagiltsev G, Michael AK, Van Dorst S, Waltz F, Mccafferty CL, Lamm L, Zufferey
S, Van Der Stappen P, Van Den Hoek H, Wietrzynski W, Harar P, Wan W, Briggs JAG,
Plitzko JM, Engel BD, Kotecha A. Toward community-driven visual proteomics with
large-scale cryo-electron tomography of Chlamydomonas reinhardtii. Molecular Cell.
mla: Kelley, Ron, et al. “Toward Community-Driven Visual Proteomics with Large-Scale
Cryo-Electron Tomography of Chlamydomonas Reinhardtii.” Molecular Cell,
Elsevier, doi:10.1016/j.molcel.2025.11.029.
short: R. Kelley, S. Khavnekar, R.D. Righetto, J. Heebner, M. Obr, X. Zhang, S.
Chakraborty, G. Tagiltsev, A.K. Michael, S. Van Dorst, F. Waltz, C.L. Mccafferty,
L. Lamm, S. Zufferey, P. Van Der Stappen, H. Van Den Hoek, W. Wietrzynski, P.
Harar, W. Wan, J.A.G. Briggs, J.M. Plitzko, B.D. Engel, A. Kotecha, Molecular
Cell (n.d.).
date_created: 2026-01-04T23:01:36Z
date_published: 2025-12-19T00:00:00Z
date_updated: 2026-01-05T08:32:47Z
day: '19'
ddc:
- '570'
department:
- _id: AlMi
doi: 10.1016/j.molcel.2025.11.029
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.molcel.2025.11.029
month: '12'
oa: 1
oa_version: Published Version
publication: Molecular Cell
publication_identifier:
eissn:
- 1097-4164
issn:
- 1097-2765
publication_status: inpress
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Toward community-driven visual proteomics with large-scale cryo-electron tomography
of Chlamydomonas reinhardtii
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
year: '2025'
...