Publications
2023
Polycomb sustains promoters in a deep OFF-state by limiting PIC formation to counteract transcription
Aleksander T. Szczurek, Emilia Dimitrova, Jessica R. Kelley, Robert J. Klose
bioRxiv 2023.06.13.544762; doi: https://doi.org/10.1101/2023.06.13.544762
Recycling of modified H2A-H2B provides short-term memory of chromatin states
Flury V, Reverón-Gómez N, Alcaraz N, Stewart-Morgan KR, Wenger A, Klose RJ, Groth A. Cell. 2023 Mar 2;186(5):1050-1065.e19. Epub 2023 Feb 6.
PMID: 36750094; PMCID: PMC9994263.
doi: 10.1016/j.cell.2023.01.007.
A CpG island-encoded mechanism protects genes from premature transcription termination
Hughes AL, Szczurek AT, Kelley JR, Lastuvkova A, Turberfield AH, Dimitrova E, Blackledge NP, Klose RJ.
Nat Commun. 2023 Feb 9;14(1):726.
doi: 10.1038/s41467-023-36236-2. PMID: 36759609; PMCID: PMC9911701.
Changes in PRC1 activity during interphase modulate lineage transition in pluripotent cells
Asenjo HG, Alcazar-Fabra M, Espinosa-Martínez M, Lopez-Onieva L, Gallardo A, Dimitrova E, Feldmann A, Pachano T, Martorell-Marugán J, Carmona-Sáez P, Sanchez-Pozo A, Rada-Iglesias Á, Klose RJ, Landeira D. Nat Commun. 2023 Jan 12;14(1):180. PMID: 36635295; PMCID: PMC9837203.
doi: 10.1038/s41467-023-35859-9.
2022
PCGF1-PRC1 links chromatin repression with DNA replication during hematopoietic cell lineage commitment
Takano J, Ito S, Dong Y, Sharif J, Nakajima-Takagi Y, Umeyama T, Han YW, Isono K, Kondo T, Iizuka Y, Miyai T, Koseki Y, Ikegaya M, Sakihara M, Nakayama M, Ohara O, Hasegawa Y, Hashimoto K, Arner E, Klose RJ, Iwama A, Koseki H, Ikawa T. Nat Commun. 2022 Nov 28;13(1):7159.
PMID: 36443290; PMCID: PMC9705430.
doi: 10.1038/s41467-022-34856-8.
Distinct roles for CKM-Mediator in controlling Polycomb-dependent chromosomal interactions and priming genes for induction
Dimitrova E, Feldmann A, van der Weide RH, Flach KD, Lastuvkova A, de Wit E, Klose RJ. Nat Struct Mol Biol. 2022 Oct;29(10):1000-1010.
doi: 10.1038/s41594-022-00840-5.
Epub 2022 Oct 11. PMID: 36220895; PMCID: PMC9568430.
2021
The molecular principles of gene regulation by Polycomb repressive complexes
Blackledge NP, Klose RJ.
Nat Rev Mol Cell Biol. 2021 Dec;22(12):815-833.
doi: 10.1038/s41580-021-00398-y.
Epub 2021 Aug 16. PMID: 34400841; PMCID: PMC7612013.
PRC1 drives Polycomb-mediated gene repression by controlling transcription initiation and burst frequency
Dobrinić, P., Szczurek, A.T. & Klose, R.J
Nat Struct Mol Biol 28, 811–824 (2021).
https://doi.org/10.1038/s41594-021-00661-y
Getting under the skin of Polycomb-dependent gene regulation
Neil P. Blackledge and Robert J. Klose
doi:10.1101/gad.348257.121Genes & Dev. 2021. 35: 301-303
Variant PCGF1-PRC1 links PRC2 recruitment with differentiation-associated transcriptional inactivation at target genes
Sugishita H, Kondo T, Ito S, Nakayama M, Yakushiji-Kaminatsui N, Kawakami E, Koseki Y, Ohinata Y, Sharif J, Harachi M, Blackledge NP, Klose RJ, Koseki H. Nat Commun. 2021 Sep 9;12(1):5341.
doi: 10.1038/s41467-021-24894-z.
PMID: 34504070; PMCID: PMC8429492.
BAP1 constrains pervasive H2AK119ub1 to control the transcriptional potential of the genome
Nadezda A. Fursova, Anne H. Turberfield, Neil P. Blackledge, Emma L. Findlater, Anna Lastuvkova, Miles K. Huseyin, Paula Dobrinić, Robert J. Klose
Genes Dev. 2021 May 1;35(9-10):749-770. Epub 2021 Apr 22.
doi: 10.1101/gad.347005.120.
PMID: 33888563; PMCID: PMC8091973.
Live-cell single particle tracking of PRC1 reveals a highly dynamic system with low target site occupancy
Huseyin, M.K., Klose, R
Nat Commun 12, 887 (2021).
https://doi.org/10.1038/s41467-021-21130-6
2020
Distinct contributions of DNA methylation and histone acetylation to the genomic occupancy of transcription factors
Cusack M, King HW, Spingardi P, Kessler BM, Klose RJ, Kriaucionis S. Distinct contributions of DNA methylation and histone acetylation to the genomic occupancy of transcription factors. Genome Res. 2020 Oct;30(10):1393-1406. doi: 10.1101/gr.257576.119. Epub 2020 Sep 22. PMID: 32963030; PMCID: PMC7605266.
PMID: 32963030
PMCID: PMC7605266
PRC1 drives Polycomb-mediated gene repression by controlling transcription initiation and burst frequency
Paula Dobrinić, Aleksander T. Szczurek, Robert J. Klose
bioRxiv 2020.10.09.333294; doi: https://doi.org/10.1101/2020.10.09.333294
Understanding the interplay between CpG island-associated gene promoters and H3K4 methylation
Hughes AL, Kelley JR, Klose RJ. Understanding the interplay between CpG island-associated gene promoters and H3K4 methylation. Biochim Biophys Acta Gene Regul Mech. 2020 Aug;1863(8):194567. doi: 10.1016/j.bbagrm.2020.194567. Epub 2020 Apr 29. PMID: 32360393; PMCID: PMC7294231.
PMID: 32360393
PMCID: PMC7294231
Identifying proteins bound to native mitotic ESC chromosomes reveals chromatin repressors are important for compaction
Djeghloul D, Patel B, Kramer H, Dimond A, Whilding C, Brown K, Kohler AC, Feytout A, Veland N, Elliott J, Bharat TAM, Tarafder AK, Löwe J, Ng BL, Guo Y, Guy J, Huseyin MK, Klose RJ, Merkenschlager M, Fisher AG. Identifying proteins bound to native mitotic ESC chromosomes reveals chromatin repressors are important for compaction. Nat Commun. 2020 Aug 17;11(1):4118. doi: 10.1038/s41467-020-17823-z. PMID: 32807789; PMCID: PMC7431861.
PMID: 32807789
PMCID: PMC7431861
Analysis of Genome Architecture during SCNT Reveals a Role of Cohesin in Impeding Minor ZGA
Zhang K, Wu DY, Zheng H, Wang Y, Sun QR, Liu X, Wang LY, Xiong WJ, Wang Q, Rhodes JDP, Xu K, Li L, Lin Z, Yu G, Xia W, Huang B, Du Z, Yao Y, Nasmyth KA, Klose RJ, Miao YL, Xie W. Analysis of Genome Architecture during SCNT Reveals a Role of Cohesin in Impeding Minor ZGA. Mol Cell. 2020 Jul 16;79(2):234-250.e9. doi: 10.1016/j.molcel.2020.06.001. Epub 2020 Jun 23. PMID: 32579944.
PMID: 32579944
Live-cell single particle tracking of PRC1 reveals a highly dynamic system with low target site occupancy
Miles K. Huseyin, Robert J. Klose
bioRxiv 2020.04.25.061358; doi: https://doi.org/10.1101/2020.04.25.061358
CDK-Mediator and FBXL19 prime developmental genes for activation by promoting atypical regulatory interactions
Feldmann A, Dimitrova E, Kenney A, Lastuvkova A, Klose RJ. CDK-Mediator and FBXL19 prime developmental genes for activation by promoting atypical regulatory interactions. Nucleic Acids Res. 2020 Apr 6;48(6):2942-2955. doi: 10.1093/nar/gkaa064. PMID: 31996894; PMCID: PMC7102981.
PMID: 31996894
PMCID: PMC7102981
DOI: 10.1093/nar/gkaa064
Understanding the interplay between CpG island-associated gene promoters and H3K4 methylation
Hughes AL, Kelley JR, Klose RJ. Understanding the interplay between CpG island-associated gene promoters and H3K4 methylation. Biochim Biophys Acta Gene Regul Mech. 2020 Aug;1863(8):194567. Epub 2020 Apr 29. PMID: 32360393; PMCID: PMC7294231.
doi: 10.1016/j.bbagrm.2020.194567.
ATACing DNA Methylation during Differentiation
Kriaucionis S, Klose RJ. ATACing DNA Methylation during Differentiation. Mol Cell. 2020 Mar 19;77(6):1159-1161. doi: 10.1016/j.molcel.2020.02.026. PMID: 32200796.
PMID: 32200796
PRC1 Catalytic Activity Is Central to Polycomb System Function
Blackledge NP, Fursova NA, Kelley JR, Huseyin MK, Feldmann A, Klose RJ. PRC1 Catalytic Activity Is Central to Polycomb System Function. Mol Cell. 2020 Feb 20;77(4):857-874.e9. doi: 10.1016/j.molcel.2019.12.001. Epub 2019 Dec 27. PMID: 31883950; PMCID: PMC7033600.
PMID: 31883950
PMCID: PMC7033600
Cohesin Disrupts Polycomb-Dependent Chromosome Interactions in Embryonic Stem Cells
Rhodes JDP, Feldmann A, Hernández-Rodríguez B, Díaz N, Brown JM, Fursova NA, Blackledge NP, Prathapan P, Dobrinic P, Huseyin MK, Szczurek A, Kruse K, Nasmyth KA, Buckle VJ, Vaquerizas JM, Klose RJ. Cohesin Disrupts Polycomb-Dependent Chromosome Interactions in Embryonic Stem Cells. Cell Rep. 2020 Jan 21;30(3):820-835.e10. doi: 10.1016/j.celrep.2019.12.057. PMID: 31968256; PMCID: PMC6988126.
PMID: 31968256
PMCID: PMC6988126
2019
KDM2 proteins constrain transcription from CpG island gene promoters independently of their histone demethylase activity
Turberfield AH, Kondo T, Nakayama M, Koseki Y, King HW, Koseki H, Klose RJ.( 2019) KDM2 proteins constrain transcription from CpG island gene promoters independently of their histone demethylase activity.
Nucleic Acids Res. 2019 Sep 26;47(17):9005-9023. doi: 10.1093/nar/gkz607.
PMID:31363749
Synergy between Variant PRC1 Complexes Defines Polycomb-Mediated Gene Repression
Fursova NA, Blackledge NP, Nakayama M, Ito S, Koseki Y, Farcas AM, King HW, Koseki H, Klose RJ. (2019) Synergy between Variant PRC1 Complexes Defines Polycomb-Mediated Gene Repression.
Mol Cell. 2019 Jun 6;74(5):1020-1036.e8. doi: 10.1016/j.molcel.2019.03.024.
PMID:31029541