Publications
2021
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
PRC1 drives Polycomb-mediated gene repression by controlling transcription initiation and burst frequency
Dobrinić, P., Szczurek, A.T. & Klose, R.J. PRC1 drives Polycomb-mediated gene repression by controlling transcription initiation and burst frequency. Nat Struct Mol Biol 28, 811–824 (2021). https://doi.org/10.1038/s41594-021-00661-y
Live-cell single particle tracking of PRC1 reveals a highly dynamic system with low target site occupancy
Huseyin, M.K., Klose, R.J. Live-cell single particle tracking of PRC1 reveals a highly dynamic system with low target site occupancy. Nat Commun 12, 887 (2021).
https://doi.org/10.1038/s41467-021-21130-6
2020
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
bioRxiv 2020.11.13.381251; doi: https://doi.org/10.1101/2020.11.13.381251
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
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
2018
Polycomb repressive complex 1 shapes the nucleosome landscape but not accessibility at target genes.
King H.W., Fursova N.A., Blackledge N.P., Klose R.J. (2018) Polycomb repressive complex 1 shapes the nucleosome landscape but not accessibility at target genes. Genome Res. 28(10):1494-1507.
Histone H2A monoubiquitylation and p38-MAPKs regulate immediate-early gene-like reactivation of latent retrovirus HTLV-1
Kulkarni A, Taylor GP, Klose RJ, Schofield CJ, Bangham CR. Histone H2A monoubiquitylation and p38-MAPKs regulate immediate-early gene-like reactivation of latent retrovirus HTLV-1. JCI Insight. 2018 Oct 18;3(20):e123196. doi: 10.1172/jci.insight.123196. PMID: 30333309; PMCID: PMC6237452.
PMID: 30333309
PMCID: PMC6237452
FBXL19 recruits CDK-Mediator to CpG islands of developmental genes priming them for activation during lineage commitment
Dimitrova E., Kondo T., Feldmann A., Nakayama M., Koseki Y., Konietzny R., Kessler B.M., Koseki H., Klose R.J. (2018) FBXL19 recruits CDK-Mediator to CpG islands of developmental genes priming them for activation during lineage commitment. elife. 7,e37084
Biochemical Identification of Nonmethylated DNA by BioCAP-Seq
Long H.K., Rose N.R., Blackledge N.P., Klose R.J. (2018) Biochemical Identification of Nonmethylated DNA by BioCAP-Seq. Methods Mol Biol. 1766:15-29
2017
The SET1 Complex Selects Actively Transcribed Target Genes via Multivalent Interaction with CpG Island Chromatin
Brown D.A., Di Cerbo V., Feldmann A., Ahn J., Ito S., Blackledge N.P., Nakayama M., McClellan M., Dimitrova E., Turberfield A.H., Long H.K., King H.W., Kriaucionis S., Schermelleh L., Kutateladze T.G., Koseki H., Klose R.J. (2017) The SET1 Complex Selects Actively Transcribed Target Genes via Multivalent Interaction with CpG Island Chromatin. Cell Rep. 20(10):2313-2327
https://www.ncbi.nlm.nih.gov/pubmed/28877467
http://www.sciencedirect.com/science/article/pii/S2211124717311373?via%3Dihub
PCGF6-PRC1 suppresses premature differentiation of mouse embryonic stem cells by regulating germ cell-related genes
Endoh, M., Endo, T.A., Shinga, J., Hayashi, K., Farcas, A., Ma, K.W., Ito, S., Sharif, J., Endoh, T., Onaga, N., Nakayama, M., Ishikura, T., Masui, O., Kessler, B.M., Suda, T., Ohara, O., Okuda, A., Klose, R., Koseki, H. (2017) PCGF6-PRC1 suppresses premature differentiation of mouse embryonic stem cells by regulating germ cell-related genes. elife. 6,e21064
The pioneer factor OCT4 requires the chromatin remodeller BRG1 to support gene regulatory element function in mouse embryonic stem cells
King, H.W., Klose, R.J. (2017) The pioneer factor OCT4 requires the chromatin remodeller BRG1 to support gene regulatory element function in mouse embryonic stem cells. elife. 6,e22631
MLL-AF4 Spreading Identifies Binding Sites that Are Distinct from Super-Enhancers and that Govern Sensitivity to DOT1L Inhibition in Leukemia
Kerry, J., Godfrey, L., Repapi, E., Tapia, M., Blackledge, N.P., Ma, H., Ballabio, E., O’Byrne, S., Ponthan, F., Heidenreich, O., Roy, A., Roberts, I., Konopleva, M., Klose, R.J., Geng, H., Milne, T.A. (2017) MLL-AF4 Spreading Identifies Binding Sites that Are Distinct from Super-Enhancers and that Govern Sensitivity to DOT1L Inhibition in Leukemia. Cell Rep. 18(2),482-495
https://www.ncbi.nlm.nih.gov/pubmed/28076791
http://www.sciencedirect.com/science/article/pii/S2211124716317612
2016
Successful transmission and transcriptional deployment of a human chromosome via mouse male meiosis
Ernst, C., Pike, J., Aitken, S.J., Long, H.K., Eling, N., Stojic, L., Ward, M.C., Connor, F., Rayner, T.F., Lukk, M., Klose, R.J., Kutter, C., Odom, D.T. (2016) Successful transmission and transcriptional deployment of a human chromosome via mouse male meiosis. elife. 5,e20235