FBXL10 protects Polycomb-bound genes from hypermethylation

Nature Genetics

Volumn 47, Issue 5, 2015, Pages 479-485

  Boulard, Mathieu ^a   Edwards, John R ^b   Bestor, Timothy H ^a  

^a Columbia University ^*  (United States)

^b WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BMI1 PROTEIN; CHROMOSOME PROTEIN; POLYCOMB REPRESSIVE COMPLEX 2; PROTEIN FBXL10; UNCLASSIFIED DRUG; F BOX PROTEIN; HISTONE DEMETHYLASE; KDM2B PROTEIN, MOUSE; POLYCOMB GROUP PROTEIN; RNF2 PROTEIN, MOUSE; UBIQUITIN PROTEIN LIGASE;

ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL MODEL; ARTICLE; CONTROLLED STUDY; DNA METHYLATION; EMBRYO; EMBRYO DEATH; EMBRYO DEVELOPMENT; FEMALE; GENE INACTIVATION; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN FUNCTION; ANIMAL; C57BL MOUSE; CELL CULTURE; CPG ISLAND; EMBRYONIC STEM CELL; GENE ONTOLOGY; GENETIC EPIGENESIS; GENETIC TRANSCRIPTION; MALE; METABOLISM; PHYSIOLOGY; TRANSGENIC MOUSE;

ANIMALS; CELLS, CULTURED; CPG ISLANDS; DNA METHYLATION; EMBRYONIC STEM CELLS; EPIGENESIS, GENETIC; F-BOX PROTEINS; GENE ONTOLOGY; JUMONJI DOMAIN-CONTAINING HISTONE DEMETHYLASES; MALE; MICE, INBRED C57BL; MICE, TRANSGENIC; POLYCOMB REPRESSIVE COMPLEX 1; POLYCOMB-GROUP PROTEINS; PROMOTER REGIONS, GENETIC; TRANSCRIPTION, GENETIC; UBIQUITIN-PROTEIN LIGASES;

EID: 84929131103     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.3272     Document Type: Article

References (40)

1. Goll, M.G. & Bestor, T.H. Eukaryotic cytosine methyltransferases. Annu. Rev. Biochem. 74, 481-514 (2005
2. Boyer, L.A. et al. Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 441, 349-353 (2006
3. Beuchle, D., Struhl, G. & Müller, J. Polycomb group proteins and heritable silencing of Drosophila Hox genes. Development 128, 993-1004 (2001
4. Tanay, A., O'Donnell, A.H., Damelin, M. & Bestor, T.H. Hyperconserved CpG domains underlie Polycomb-binding sites. Proc. Natl. Acad. Sci. USA 104, 5521-5526 (2007
5. Ziller, M.J. et al. Charting a dynamic DNA methylation landscape of the human genome. Nature 500, 477-481 (2013
6. He, J. et al. Kdm2b maintains murine embryonic stem cell status by recruiting PRC1 complex to CpG islands of developmental genes. Nat. Cell Biol. 15, 373-384 (2013
7. Pasqualucci, L. et al. Analysis of the coding genome of diffuse large B-cell lymphoma. Nat. Genet. 43, 830-837 (2011
8. Suzuki, T., Minehata, K.-I., Akagi, K., Jenkins, N.A. & Copeland, N.G. Tumor suppressor gene identification using retroviral insertional mutagenesis in Blm-deficient mice. EMBO J. 25, 3422-3431 (2006
9. Farcas, A.M. et al. KDM2B links the Polycomb Repressive Complex 1 (PRC1) to recognition of CpG islands. eLife 1, e00205 (2012
10. He, J., Kallin, E.M., Tsukada, Y.-I. & Zhang, Y. The H3K36 demethylase Jhdm1b/Kdm2b regulates cell proliferation and senescence through p15Ink4b. Nat. Struct. Mol. Biol. 15, 1169-1175 (2008
11. Gearhart, M.D., Corcoran, C.M., Wamstad, J.A. & Bardwell, V.J. Polycomb group and SCF ubiquitin ligases are found in a novel BCOR complex that is recruited to BCL6 targets. Mol. Cell. Biol. 26, 6880-6889 (2006
12. Wu, X., Johansen, J.V. & Helin, K. Fbxl10/Kdm2b recruits Polycomb repressive complex 1 to CpG islands and regulates H2A ubiquitylation. Mol. Cell 49, 1134-1146 (2013
13. Turner, S.A. & Bracken, A.P.A. 'Complex Eissue: deciphering the role of variant PRC1 in ESCs. Cell Stem Cell 12, 145-146 (2013
14. Fukuda, T., Tokunaga, A., Sakamoto, R. & Yoshida, N. Fbxl10/Kdm2b deficiency accelerates neural progenitor cell death and leads to exencephaly. Mol. Cell. Neurosci. 46, 614-624 (2011
15. Blackledge, N.P. et al. Variant PRC1 complex-dependent H2A ubiquitylation drives PRC2 recruitment and Polycomb domain formation. Cell 157, 1445-1459 (2014
16. Testoni, S. et al. KDM2B is implicated in bovine lethal multi-organic developmental dysplasia. PLoS ONE 7, e45634 (2012
17. Gu, H. et al. Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. Nat. Protoc. 6, 468-481 (2011
18. Boyle, P. et al. Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling. Genome Biol. 13, R92 (2012
19. Frescas, D., Guardavaccaro, D., Bassermann, F., Koyama-Nasu, R. & Pagano, M. JHDM1B/FBXL10 is a nucleolar protein that represses transcription of ribosomal RNA genes. Nature 450, 309-313 (2007
20. Duffiè, R. et al. The Gpr1/Zdbf2 locus provides new paradigms for transient and dynamic genomic imprinting in mammals. Genes Dev. 28, 463-478 (2014
21. Leeb, M. & Wutz, A. Ring1B is crucial for the regulation of developmental control genes and PRC1 proteins but not X inactivation in embryonic cells. J. Cell Biol. 178, 219-229 (2007
22. Morin-Kensicki, E.M., Faust, C., LaMantia, C. & Magnuson, T. Cell and tissue requirements for the geneeed during mouse gastrulation and organogenesis. Genesis 31, 142-146 (2002
23. Tavares, L. et al. RYBP-PRC1 complexes mediate H2A ubiquitylation at Polycomb target sites independently of PRC2 and H3K27me3. Cell 148, 664-678 (2012
24. Leitch, H.G. et al. Naive pluripotency is associated with global DNA hypomethylation. Nat. Struct. Mol. Biol. 20, 311-316 (2013
25. Carlone, D.L. et al. Reduced genomic cytosine methylation and defective cellular differentiation in embryonic stem cells lacking CpG binding protein. Mol. Cell. Biol. 25, 4881-4891 (2005
26. Pemberton, H. et al. Genome-wide co-localization of Polycomb orthologs and their effects on gene expression in human fibroblas00ts. Genome Biol. 15, R23 (2014
27. Kalb, R. et al. Histone H2A monoubiquitination promotes histone H3 methylation in Polycomb repression. Nat. Struct. Mol. Biol. 21, 569-571 (2014
28. Lorincz, M.C., Schübeler, D., Hutchinson, S.R., Dickerson, D.R. & Groudine, M. DNA methylation density influences the stability of an epigenetic imprint and Dnmt3a/b-independent De novo methylation. Mol. Cell. Biol. 22, 7572-7580 (2002
29. Biniszkiewicz, D. et al. Dnmt1 overexpression causes genomic hypermethylation, loss of imprinting, and embryonic lethality. Mol. Cell. Biol. 22, 2124-2135 (2002
30. Xi, Y. & Li, W. BSMAP: whole genome bisulfite sequence MAPping program. BMC Bioinformatics 10, 232 (2009
31. Brookes, E. et al. Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ESCs. Cell Stem Cell 10, 157-170 (2012
32. Marson, A. et al. Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 134, 521-533 (2008
33. Lienert, F. et al. Genomic prevalence of heterochromatic H3K9me2 and transcription do not discriminate pluripotent from terminally differentiated cells. PLoS Genet. 7, e1002090 (2011
34. Peng, J.C. et al. Jarid2/Jumonji coordinates control of PRC2 enzymatic activity and target gene occupancy in pluripotent cells. Cell 139, 1290-1302 (2009
35. Seila, A.C. et al. Divergent transcription from active promoters. Science 322, 1849-1851 (2008
36. Schmitz, S.U. et al. Jarid1b targets genes regulating development and is involved in neural differentiation. EMBO J. 30, 4586-4600 (2011
37. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009
38. Trapnell, C., Pachter, L. & Salzberg, S.L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 25, 1110-1111 (2009
39. Robinson, M.D., McCarthy, D.J. & Smyth, G.K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140 (2010
40. Kumaki, Y., Oda, M. & Okano, M. QUMA: quantification tool for methylation analysis. Nucleic Acids Res. 36, W170-W175 (2008