Publications
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
RYBP stimulates PRC1 to shape chromatin-based communication between Polycomb repressive complexes
Rose, N.R., King, H.W., Blackledge, N.P., Fursova, N.A., Ember, K.J., Fischer, R., Kessler, B.M., Klose, R.J. (2016) RYBP stimulates PRC1 to shape chromatin-based communication between Polycomb repressive complexes. elife. 5,e18591
Protection of CpG islands from DNA methylation is DNA-encoded and evolutionarily conserved
Long, H.K., King, H.W., Patient, R.K., Odom, D.T., Klose, R.J. (2016) Protection of CpG islands from DNA methylation is DNA-encoded and evolutionarily conserved. Nucleic Acids Res. 44(14), 6693-6706
2015
Histone demethylases in chromatin biology and beyond
Dimitrova, E., Turberfield, A.H., Klose, R.J. (2015) Histone demethylases in chromatin biology and beyond. EMBO Rep. 16 (12), 1620-39
Targeting Polycomb systems to regulate gene expression: modifications to a complex story
Blackledge, N.P., Rose, N.R., Klose, R.J. (2015) Targeting Polycomb systems to regulate gene expression: modifications to a complex story. Nat Rev Mol Cell Biol. 16 (11), 643-9
2014
Targeting polycomb to pericentric heterochromatin in embryonic stem cells reveals a role for H2AK119u1 in PRC2 recruitment
Cooper, S., Dienstbier, M., Hassan, R., Schermelleh, L., Sharif, J., Blackledge, N.P., De Marco, V., Elderkin, S., Koseki, H., Klose, R., Heger, A., Brockdorff, N. Targeting Polycomb to Pericentric Heterochromatin in Embryonic Stem Cells Reveals a Role for H2AK119u1 in PRC2 Recruitment. Cell Reports. 7 (5), 1456-1470
http://www.sciencedirect.com/science/article/pii/S221112471400299X
Variant PRC1 complex-dependent H2A ubiquitylation drives PRC2 recruitment and polycomb domain formation
Blackledge, N.P., Farcas, A.M., Kondo, T., King, H.W., McGouran, J.F., Hanssen, L.L., Ito, S., Cooper, S., Kondo, K., Koseki, Y., Ishikura, T., Long, H.K., Sheahan, T.W., Brockdorff, N., Kessler, B.M., Koseki, H., Klose, R.J. (2014) Variant PRC1 Complex-Dependent H2A Ubiquitylation Drives PRC2 Recruitment and Polycomb Domain Formation. Cell. 157 (6), 1445-1459
http://www.sciencedirect.com/science/article/pii/S0092867414005893
Understanding the relationship between DNA methylation and histone lysine methylation
Rose, N. R. and Klose R. J. Understanding the relationship between DNA methylation and histone lysine methylation. Biochimica et Biophysica Acta (BBA) – Gene Regulatory Mechanisms. 1839 (12), 1362-1372
http://www.sciencedirect.com/science/article/pii/S1874939914000285
2013
Chromatin sampling–an emerging perspective on targeting polycomb repressor proteins
Klose, R. J., Cooper, S., Farcas, A. M., Blackledge, N. P., and Brockdorff, N. (2013) Chromatin sampling–an emerging perspective on targeting polycomb repressor proteins. PLoS Genet. 9, e1003717
http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003717
ZF-CxxC domain-containing proteins, CpG islands and the chromatin connection
Long, H. K., Blackledge, N. P. and Klose, R. J. (2013) ZF-CxxC domain-containing proteins, CpG islands and the chromatin connection. Biochem Soc Trans. 41, 727-740
Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates
Long, H. K., Sims, D., Heger, A., Blackledge, N. P., Kutter, C., Wright, M. L., Grützner, F., Odom, D. T., Patient, R., Ponting, C. P. and Klose, R. J. (2013) Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates. elife. 2, e00348
http://elife.elifesciences.org/content/2/e00348
2012
KDM2B links the Polycomb Repressive Complex 1 (PRC1) to recognition of CpG islands
Farcas, A. M., Blackledge, N. P., Sudbery, I., Long, H. K., McGouran, J. F., Rose, N. R., Lee, S., Sims, D., Cerase, A., Sheahan, T. W., Koseki, H., Brockdorff, N., Ponting, C. P., Kessler, B. M. and Klose, R. J. (2012) KDM2B links the Polycomb Repressive Complex 1 (PRC1) to recognition of CpG islands. elife. 1, e00205
Plant Growth Regulator Daminozide Is a Selective Inhibitor of Human KDM2/7 Histone Demethylases
Rose, N. R., Woon, E. C., Tumber, A., Walport, L. J., Chowdhury, R., Li, X. S., King, O. N., Lejeune, C., Ng, S. S., Krojer, T., Chan, M. C., Rydzik, A. M., Hopkinson, R. J., Che, K. H., Daniel, M., Strain-Damerell, C., Gileadi, C., Kochan, G., Leung, I. K., Dunford, J., Yeoh, K. K., Ratcliffe, P. J., Burgess-Brown, N., von Delft, F., Muller, S., Marsden, B., Brennan, P. E., McDonough, M. A., Oppermann, U., Klose, R. J., Schofield, C. J. and Kawamura, A. (2012) Plant growth regulator daminozide is a selective inhibitor of human KDM2/7 histone demethylases. J Med Chem. 55, 6639-6643
Bio-CAP: a versatile and highly sensitive technique to purify and characterise regions of non-methylated DNA
Blackledge, N. P., Long, H. K., Zhou, J. C., Kriaucionis, S., Patient, R. and Klose, R. J. (2012) Bio-CAP: a versatile and highly sensitive technique to purify and characterise regions of non-methylated DNA. Nucleic Acids Res. 40, e32
2011
Recognition of CpG Island Chromatin by KDM2A Requires Direct and Specific Interaction with Linker DNA
Zhou, J. C., Blackledge, N. P., Farcas, A. M. andKlose, R. J. (2012) Recognition of CpG island chromatin by KDM2A requires direct and specific interaction with linker DNA. Mol Cell Biol. 32, 479-489
The oncometabolite 2-hydroxyglutarate inhibits histone lysine demethylases
Chowdhury, R., Yeoh, K. K., Tian, Y. M., Hillringhaus, L., Bagg, E. A., Rose, N. R., Leung, I. K., Li, X. S., Woon, E. C., Yang, M., McDonough, M. A., King, O. N., Clifton, I. J., Klose, R. J., Claridge, T. D., Ratcliffe, P. J., Schofield, C. J. and Kawamura, A. (2011) The oncometabolite 2-hydroxyglutarate inhibits histone lysine demethylases. EMBO Rep. 12, 463-469
2010
Quantitative High-Throughput Screening Identifies 8-Hydroxyquinolines as Cell-Active Histone Demethylase Inhibitors
King, O. N., Li, X. S., Sakurai, M., Kawamura, A., Rose, N. R., Ng, S. S., Quinn, A. M., Rai, G., Mott, B. T., Beswick, P., Klose, R. J., Oppermann, U., Jadhav, A., Heightman, T. D., Maloney, D. J., Schofield, C. J. and Simeonov, A. (2010) Quantitative high-throughput screening identifies 8-hydroxyquinolines as cell-active histone demethylase inhibitors. PLoS One. 5, e15535
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0015535