MBD3 Localizes at Promoters, Gene Bodies and Enhancers of Active Genes

PLoS Genetics

Volumn 9, Issue 12, 2013, Pages

  Shimbo, Takashi ^a   Du, Ying ^a   Grimm, Sara A ^a   Dhasarathy, Archana ^a   Mav, Deepak ^b   Shah, Ruchir R ^b   Shi, Huidong ^c   Wade, Paul A ^a  

^a NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

^b SRA International Inc   (United States)

^c MEDICAL COLLEGE OF GEORGIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA ADENINE METHYLTRANSFERASE; NURD PROTEIN COMPLEX; PEPTIDES AND PROTEINS; PROTEIN MBD3; UNCLASSIFIED DRUG;

ARTICLE; BREAST CANCER; CANCER CELL CULTURE; CHROMATIN IMMUNOPRECIPITATION; CHROMATIN STRUCTURE; CONTROLLED STUDY; CPG ISLAND; ENHANCER REGION; ENZYME ANALYSIS; GENETIC TRANSCRIPTION; GENOME ANALYSIS; HISTONE METHYLATION; HUMAN; HUMAN CELL; NUCLEOSOME; PROMOTER REGION; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN LOCALIZATION;

BASE SEQUENCE; CHROMATIN; DNA-BINDING PROTEINS; ENHANCER ELEMENTS, GENETIC; GENE EXPRESSION REGULATION, NEOPLASTIC; GENOMICS; HISTONE DEACETYLASES; HISTONES; HUMANS; MCF-7 CELLS; NUCLEOSOMES; PROMOTER REGIONS, GENETIC; TRANSCRIPTION INITIATION SITE;

EID: 84892700803     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1004028     Document Type: Article

References (54)

1. Tyler JK, Kadonaga JT, (1999) The "dark side" of chromatin remodeling: repressive effects on transcription. Cell 99: 443-446.
2. Yoshida T, Hazan I, Zhang J, Ng SY, Naito T, et al. (2008) The role of the chromatin remodeler Mi-2beta in hematopoietic stem cell self-renewal and multilineage differentiation. Genes Dev 22: 1174-1189.
3. Williams CJ, Naito T, Arco PG, Seavitt JR, Cashman SM, et al. (2004) The chromatin remodeler Mi-2beta is required for CD4 expression and T cell development. Immunity 20: 719-733.
4. Zhang J, Jackson AF, Naito T, Dose M, Seavitt J, et al. (2012) Harnessing of the nucleosome-remodeling-deacetylase complex controls lymphocyte development and prevents leukemogenesis. Nat Immunol 13: 86-94.
5. Reynolds N, Latos P, Hynes-Allen A, Loos R, Leaford D, et al. (2012) NuRD suppresses pluripotency gene expression to promote transcriptional heterogeneity and lineage commitment. Cell Stem Cell 10: 583-594.
6. Bowen NJ, Fujita N, Kajita M, Wade PA, (2004) Mi-2/NuRD: multiple complexes for many purposes. Biochim Biophys Acta 1677: 52-57.
7. Le Guezennec X, Vermeulen M, Brinkman AB, Hoeijmakers WA, Cohen A, et al. (2006) MBD2/NuRD and MBD3/NuRD, two distinct complexes with different biochemical and functional properties. Mol Cell Biol 26: 843-851.
8. Hendrich B, Bird A, (1998) Identification and characterization of a family of mammalian methyl-CpG binding proteins. Mol Cell Biol 18: 6538-6547.
9. Yildirim O, Li R, Hung JH, Chen PB, Dong X, et al. (2011) Mbd3/NURD complex regulates expression of 5-hydroxymethylcytosine marked genes in embryonic stem cells. Cell 147: 1498-1510.
10. Whyte WA, Bilodeau S, Orlando DA, Hoke HA, Frampton GM, et al. (2012) Enhancer decommissioning by LSD1 during embryonic stem cell differentiation. Nature 482: 221-225.
11. Reynolds N, Salmon-Divon M, Dvinge H, Hynes-Allen A, Balasooriya G, et al. (2011) NuRD-mediated deacetylation of H3K27 facilitates recruitment of Polycomb Repressive Complex 2 to direct gene repression. Embo J 31: 593-605.
12. Hu G, Wade PA, (2012) NuRD and pluripotency: a complex balancing act. Cell Stem Cell 10: 497-503.
13. Ram O, Goren A, Amit I, Shoresh N, Yosef N, et al. (2011) Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells. Cell 147: 1628-1639.
14. van Steensel B, Henikoff S, (2000) Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18: 424-428.
15. Neve RM, Chin K, Fridlyand J, Yeh J, Baehner FL, et al. (2006) A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes. Cancer Cell 10: 515-527.
16. Weber M, Davies JJ, Wittig D, Oakeley EJ, Haase M, et al. (2005) Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 37: 853-862.
17. Fujita N, Jaye DL, Kajita M, Geigerman C, Moreno CS, et al. (2003) MTA3, a Mi-2/NuRD complex subunit, regulates an invasive growth pathway in breast cancer. Cell 113: 207-219.
18. Fujita N, Wade PA, (2004) Use of bifunctional cross-linking reagents in mapping genomic distribution of chromatin remodeling complexes. Methods 33: 81-85.
19. Zang C, Schones DE, Zeng C, Cui K, Zhao K, et al. (2009) A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics 25: 1952-1958.
20. ENCODE_Project_Consortium (2011) A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol 9: e1001046.
21. Hashimoto H, Liu Y, Upadhyay AK, Chang Y, Howerton SB, et al. (2012) Recognition and potential mechanisms for replication and erasure of cytosine hydroxymethylation. Nucleic Acids Res 40: 4841-4849.
22. Spruijt CG, Gnerlich F, Smits AH, Pfaffeneder T, Jansen PW, et al. (2013) Dynamic Readers for 5-(Hydroxy)Methylcytosine and Its Oxidized Derivatives. Cell 152: 1146-1159.
23. Carter D, Chakalova L, Osborne CS, Dai YF, Fraser P, (2002) Long-range chromatin regulatory interactions in vivo. Nat Genet 32: 623-626.
24. Zhang J, Poh HM, Peh SQ, Sia YY, Li G, et al. (2012) ChIA-PET analysis of transcriptional chromatin interactions. Methods 58: 289-299.
25. Dekker J, Rippe K, Dekker M, Kleckner N, (2002) Capturing chromosome conformation. Science 295: 1306-1311.
26. Butler JS, Koutelou E, Schibler AC, Dent SY, (2012) Histone-modifying enzymes: regulators of developmental decisions and drivers of human disease. Epigenomics 4: 163-177.
27. Shu XS, Li L, Tao Q, (2012) Chromatin regulators with tumor suppressor properties and their alterations in human cancers. Epigenomics 4: 537-549.
28. Nishioka K, Chuikov S, Sarma K, Erdjument-Bromage H, Allis CD, et al. (2002) Set9, a novel histone H3 methyltransferase that facilitates transcription by precluding histone tail modifications required for heterochromatin formation. Genes Dev 16: 479-489.
29. Zegerman P, Canas B, Pappin D, Kouzarides T, (2002) Histone H3 lysine 4 methylation disrupts binding of nucleosome remodeling and deacetylase (NuRD) repressor complex. J Biol Chem 277: 11621-11624.
30. Gunther K, Rust M, Leers J, Boettger T, Scharfe M, et al. (2013) Differential roles for MBD2 and MBD3 at methylated CpG islands, active promoters and binding to exon sequences. Nucleic Acids Res 41: 3010-3021.
31. Baubec T, Ivanek R, Lienert F, Schubeler D, (2013) Methylation-Dependent and-Independent Genomic Targeting Principles of the MBD Protein Family. Cell 153: 480-492.
32. Jackson V, Shires A, Chalkley R, Granner DK, (1975) Studies on highly metabolically active acetylation and phosphorylation of histones. J Biol Chem 250: 4856-4863.
33. Wang Z, Zang C, Cui K, Schones DE, Barski A, et al. (2009) Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes. Cell 138: 1019-1031.
34. Musselman CA, Ramirez J, Sims JK, Mansfield RE, Oliver SS, et al. (2012) Bivalent recognition of nucleosomes by the tandem PHD fingers of the CHD4 ATPase is required for CHD4-mediated repression. Proc Natl Acad Sci U S A 109: 787-792.
35. Musselman CA, Mansfield RE, Garske AL, Davrazou F, Kwan AH, et al. (2009) Binding of the CHD4 PHD2 finger to histone H3 is modulated by covalent modifications. Biochem J 423: 179-187.
36. Hendrich B, Bird A, (1998) Identification and characterization of a family of mammalian methyl-CpG binding proteins. Molecular and cellular biology 18: 6538-6547.
37. Wade PA, (2001) Methyl CpG binding proteins: coupling chromatin architecture to gene regulation. Oncogene 20: 3166-3173.
38. Zhao S, Choi M, Overton JD, Bellone S, Roque DM, et al. (2013) Landscape of somatic single-nucleotide and copy-number mutations in uterine serous carcinoma. Proceedings of the National Academy of Sciences 110: 2916-2921.
39. Le Gallo M, O'Hara AJ, Rudd ML, Urick ME, Hansen NF, et al. (2012) Exome sequencing of serous endometrial tumors identifies recurrent somatic mutations in chromatin-remodeling and ubiquitin ligase complex genes. Nature genetics 44: 1310-1315.
40. Lai AY, Fatemi M, Dhasarathy A, Malone C, Sobol SE, et al. (2010) DNA methylation prevents CTCF-mediated silencing of the oncogene BCL6 in B cell lymphomas. J Exp Med 207: 1939-1950.
41. Onder TT, Kara N, Cherry A, Sinha AU, Zhu N, et al. (2012) Chromatin-modifying enzymes as modulators of reprogramming. Nature 483: 598-602.
42. Greil F, Moorman C, van Steensel B, (2006) DamID: mapping of in vivo protein-genome interactions using tethered DNA adenine methyltransferase. Methods Enzymol 410: 342-359.
43. Wand M, (1997) Data-based choice of histogram bin width. The American Statistician 51: 59-64.
44. Bieda M, Xu X, Singer MA, Green R, Farnham PJ, (2006) Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome. Genome research 16: 595-605.
45. Hastie T, Tibshirani R (1990) Generalized additive models. New York: Chapman & Hall/CRC.
46. Scacheri PC, Crawford GE, Davis S, (2006) Statistics for ChIP-chip and DNase hypersensitivity experiments on NimbleGen arrays. Methods in enzymology 411: 270.
47. Charafe-Jauffret E, Ginestier C, Monville F, Finetti P, Adelaide J, et al. (2006) Gene expression profiling of breast cell lines identifies potential new basal markers. Oncogene 25: 2273-2284.
48. Weber M, Hellmann I, Stadler MB, Ramos L, Pääbo S, et al. (2007) Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nature genetics 39: 457-466.
49. Whyte WA, Orlando DA, Hnisz D, Abraham BJ, Lin CY, et al. (2013) Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell 153: 307-319.
50. Li Z, Gadue P, Chen K, Jiao Y, Tuteja G, et al. (2012) Foxa2 and H2A. Z mediate nucleosome depletion during embryonic stem cell differentiation. Cell 151: 1608-1616.
51. Langmead B, Trapnell C, Pop M, Salzberg SL, (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25.
52. Quinlan AR, Hall IM, (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842.
53. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, et al. (2002) The human genome browser at UCSC. Genome Res 12: 996-1006.
54. Khaitan D, Sankpal UT, Weksler B, Meister EA, Romero IA, et al. (2009) Role of KCNMA1 gene in breast cancer invasion and metastasis to brain. BMC Cancer 9: 258.