Publications

2019

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

https://www.ncbi.nlm.nih.gov/pubmed/31029541

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

https://www.ncbi.nlm.nih.gov/pubmed/31363749

2018

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.

https://www.ncbi.nlm.nih.gov/pubmed/30154222

https://genome.cshlp.org/content/28/10/1494.long

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

https://www.ncbi.nlm.nih.gov/pubmed/29809150

https://elifesciences.org/articles/37084

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

https://www.ncbi.nlm.nih.gov/pubmed/29605845

2017

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

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

https://www.ncbi.nlm.nih.gov/pubmed/28304275

https://elifesciences.org/content/6/e21064

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

https://www.ncbi.nlm.nih.gov/pubmed/28287392

https://elifesciences.org/content/6/e22631

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

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

https://www.ncbi.nlm.nih.gov/pubmed/27855777

https://elifesciences.org/content/5/e20235

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

https://www.ncbi.nlm.nih.gov/pubmed/27705745

https://elifesciences.org/content/5/e18591

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

https://www.ncbi.nlm.nih.gov/pubmed/27084945

2015

Dimitrova, E., Turberfield, A.H., Klose, R.J. (2015) Histone demethylases in chromatin biology and beyond. EMBO Rep. 16 (12), 1620-39

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4687429/

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

http://www.ncbi.nlm.nih.gov/pubmed/26420232

http://www.nature.com/nrm/journal/v16/n11/full/nrm4067.html

2014

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

http://www.ncbi.nlm.nih.gov/pubmed/24856970

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

http://www.ncbi.nlm.nih.gov/pubmed/24857660

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

http://www.ncbi.nlm.nih.gov/pubmed/24560929

2013

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

http://www.ncbi.nlm.nih.gov/pubmed/23990804

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

http://www.biochemsoctrans.org/bst/041/0727/bst0410727.htm

http://www.ncbi.nlm.nih.gov/pubmed/23697932

Long, H. K., Sims, D., Heger, A., Blackledge, N. P., Kutter, C., Wright, M. L., Gr├╝tzner, 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

http://www.ncbi.nlm.nih.gov/pubmed/23467541

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43512

2012

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

http://elife.elifesciences.org/content/1/e00205

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE41267

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

http://pubs.acs.org/doi/abs/10.1021/jm300677j

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

http://nar.oxfordjournals.org/content/40/4/e32.long

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

http://mcb.asm.org/content/32/2/479.long

2011

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

http://www.nature.com/embor/journal/v12/n5/full/embor201143a.html

2010

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

Landeira, D., Sauer, S., Poot, R., Dvorkina, M., Mazzarella, L., Jorgensen, H. F., Pereira, C. F., Leleu, M., Piccolo, F. M., Spivakov, M., Brookes, E., Pombo, A., Fisher, C., Skarnes, W. C., Snoek, T., Bezstarosti, K., Demmers, J., Klose, R. J., Casanova, M., Tavares, L., Brockdorff, N., Merkenschlager, M. and Fisher, A. G. (2010) Jarid2 is a PRC2 component in embryonic stem cells required for multi-lineage differentiation and recruitment of PRC1 and RNA Polymerase II to developmental regulators. Nat Cell Biol. 12, 618-624

http://www.nature.com/ncb/journal/v12/n6/full/ncb2065.html

Blackledge, N. P., Zhou, J. C., Tolstorukov, M. Y., Farcas, A. M., Park, P. J. and Klose, R. J. (2010) CpG islands recruit a histone H3 lysine 36 demethylase. Mol Cell. 38, 179-190

http://www.sciencedirect.com/science/article/pii/S1097276510002868

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21202

Blackledge, N. P. and Klose, R. J. (2010) Histone lysine methylation: an epigenetic modification?Epigenomics. 2, 151-161

Loenarz, C., Ge, W., Coleman, M. L., Rose, N. R., Cooper, C. D., Klose, R. J., Ratcliffe, P. J. and Schofield, C. J. (2010) PHF8, a gene associated with cleft lip/palate and mental retardation, encodes for an Nepsilon-dimethyl lysine demethylase. Hum Mol Genet. 19, 217-222

http://hmg.oxfordjournals.org/content/19/2/217.long

2009

Tao, J., Hu, K., Chang, Q., Wu, H., Sherman, N. E., Martinowich, K., Klose, R. J., Schanen, C., Jaenisch, R., Wang, W. and Sun, Y. E. (2009) Phosphorylation of MeCP2 at Serine 80 regulates its chromatin association and neurological function.Proc Natl Acad Sci U S A. 106, 4882-4887

http://www.pnas.org/content/106/12/4882.long

Ng, S. S., Yue, W. W., Oppermann, U. and Klose, R. J. (2009) Dynamic protein methylation in chromatin biology. Cell Mol Life Sci. 66, 407-422

http://link.springer.com/article/10.1007%2Fs00018-008-8303-z

2008

Ho, K. L., McNae, I. W., Schmiedeberg, L., Klose, R. J., Bird, A. P. and Walkinshaw, M. D. (2008) MeCP2 binding to DNA depends upon hydration at methyl-CpG. Mol Cell. 29, 525-531

http://www.sciencedirect.com/science/article/pii/S1097276508000968

Before Oxford

2007

Klose, R. J. and Zhang, Y. (2007) Histone H3 Arg2 methylation provides alternative directions for COMPASS. Nat Struct Mol Biol. 14, 1058-1060

http://www.nature.com/nsmb/journal/v14/n11/full/nsmb1107-1058.html

Klose, R. J., Gardner, K. E., Liang, G., Erdjument-Bromage, H., Tempst, P. and Zhang, Y. (2007) Demethylation of histone H3K36 and H3K9 by Rph1: a vestige of an H3K9 methylation system in Saccharomyces cerevisiae? Mol Cell Biol. 27, 3951-3961

http://mcb.asm.org/content/27/11/3951.long

Yamane, K., Tateishi, K., Klose, R. J., Fang, J., Fabrizio, L. A., Erdjument-Bromage, H., Taylor-Papadimitriou, J., Tempst, P. and Zhang, Y. (2007) PLU-1 is an H3K4 demethylase involved in transcriptional repression and breast cancer cell proliferation. Mol Cell. 25, 801-812

http://www.sciencedirect.com/science/article/pii/S1097276507001463

Lee, N., Zhang, J., Klose, R. J., Erdjument-Bromage, H., Tempst, P., Jones, R. S. and Zhang, Y. (2007) The trithorax-group protein Lid is a histone H3 trimethyl-Lys4 demethylase. Nat Struct Mol Biol. 14, 341-343

http://www.nature.com/nsmb/journal/v14/n4/full/nsmb1216.html

Klose, R. J. and Zhang, Y. (2007) Regulation of histone methylation by demethylimination and demethylation. Nat Rev Mol Cell Biol. 8, 307-318

http://www.nature.com/nrm/journal/v8/n4/full/nrm2143.html

Klose, R. J., Yan, Q., Tothova, Z., Yamane, K., Erdjument-Bromage, H., Tempst, P., Gilliland, D. G., Zhang, Y. and Kaelin, W. G., Jr. (2007) The retinoblastoma binding protein RBP2 is an H3K4 demethylase. Cell. 128, 889-900

http://www.sciencedirect.com/science/article/pii/S0092867407001948

Liang, G., Klose, R. J., Gardner, K. E. and Zhang, Y. (2007) Yeast Jhd2p is a histone H3 Lys4 trimethyl demethylase. Nat Struct Mol Biol. 14, 243-245

http://www.nature.com/nsmb/journal/v14/n3/full/nsmb1204.html

2006

Klose, R. J., Kallin, E. M. and Zhang, Y. (2006) JmjC-domain-containing proteins and histone demethylation. Nat Rev Genet. 7, 715-727

http://www.nature.com/nrg/journal/v7/n9/full/nrg1945.html

Klose, R. J., Yamane, K., Bae, Y., Zhang, D., Erdjument-Bromage, H., Tempst, P., Wong, J. and Zhang, Y. (2006) The transcriptional repressor JHDM3A demethylates trimethyl histone H3 lysine 9 and lysine 36. Nature. 442, 312-316

http://www.nature.com/nature/journal/v442/n7100/full/nature04853.html

Klose, R. J. and Bird, A. P. (2006) Genomic DNA methylation: the mark and its mediators. Trends Biochem Sci. 31, 89-97

http://www.sciencedirect.com/science/article/pii/S096800040500352X

2005

Klose, R. J., Sarraf, S. A., Schmiedeberg, L., McDermott, S. M., Stancheva, I. and Bird, A. P. (2005) DNA binding selectivity of MeCP2 due to a requirement for A/T sequences adjacent to methyl-CpG. Mol Cell. 19, 667-678

http://www.sciencedirect.com/science/article/pii/S1097276505015091

2004

Klose, R. J. and Bird, A. P. (2004) MeCP2 behaves as an elongated monomer that does not stably associate with the Sin3a chromatin remodeling complex. J Biol Chem. 279, 46490-46496

http://www.jbc.org/content/279/45/46490.long

2000

Li, X., Barrett, J., Pang, A., Klose, R. J., Krell, P. J. and Arif, B. M. (2000) Characterization of an overexpressed spindle protein during a baculovirus infection. Virology. 268, 56-67

http://www.sciencedirect.com/science/article/pii/S0042682299901381