SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation

Nature Genetics

Volumn 49, Issue 2, 2017, Pages 289-295

  Wang, Xiaofeng ^a,b,c   Lee, Ryan S ^a,b,c   Alver, Burak H ^c   Haswell, Jeffrey R ^a,b,c   Wang, Su ^c   Mieczkowski, Jakub ^d   Drier, Yotam ^d,e   Gillespie, Shawn M ^d,e   Archer, Tenley C ^c   Wu, Jennifer N ^a,b,c   Tzvetkov, Evgeni P ^a,b,c   Troisi, Emma C ^a,b,c   Pomeroy, Scott L ^c   Biegel, Jaclyn A ^c   Tolstorukov, Michael Y ^f   Bernstein, Bradley E ^d   Park, Peter J ^d,e,g   Roberts, Charles W M ^c,h,i  

^a DANA FARBER CANCER INSTITUTE   (United States)

^b BOSTON CHILDREN S HOSPITAL   (United States)

^c HARVARD MEDICAL SCHOOL   (United States)

^d MASSACHUSETTS GENERAL HOSPITAL   (United States)

^e BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^f CHILDREN S HOSPITAL LOS ANGELES   (United States)

^g HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^h BRIGHAM AND WOMEN S HOSPITAL   (United States)

ⁱ ST JUDE CHILDREN S RESEARCH HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

SPRY1 PROTEIN; SWI/SNF RELATED MATRIX ASSOCIATED ACTIN DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY B MEMBER 1; TRANSCRIPTION FACTOR SOX2; TUMOR MARKER; UNCLASSIFIED DRUG; BANF1 PROTEIN, HUMAN; DNA BINDING PROTEIN; NUCLEAR PROTEIN; SMARCB1 PROTEIN, HUMAN;

ARTICLE; CANCER INHIBITION; CANCER SURVIVAL; ENHANCER REGION; HUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN FUNCTION; PROTEIN TARGETING; RHABDOID TUMOR; CHROMATIN; CHROMATIN ASSEMBLY AND DISASSEMBLY; GENETIC EPIGENESIS; GENETICS; MUTATION; TUMOR CELL LINE;

CELL LINE, TUMOR; CHROMATIN; CHROMATIN ASSEMBLY AND DISASSEMBLY; DNA-BINDING PROTEINS; ENHANCER ELEMENTS, GENETIC; EPIGENESIS, GENETIC; HUMANS; MUTATION; NUCLEAR PROTEINS; RHABDOID TUMOR; SMARCB1 PROTEIN;

EID: 85003875989     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.3746     Document Type: Article

References (78)

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41. Wu, J.I., Lessard, J., Crabtree, G.R. Understanding the words of chromatin regulation. Cell 136, 200-206 (2009).
42. Biegel, J.A. , et al. Germ-line and acquired mutations of INI1 in atypical teratoid and rhabdoid tumors. Cancer Res. 59, 74-79 (1999).
43. Versteege, I. , et al. Truncating mutations of hSNF5/INI1 in aggressive paediatric cancer. Nature 394, 203-206 (1998).
44. Eaton, K.W., Tooke, L.S., Wainwright, L.M., Judkins, A.R., Biegel, J.A. Spectrum of SMARCB1/INI1 mutations in familial and sporadic rhabdoid tumors. Pediatr. Blood Cancer 56, 7-15 (2011).
45. Lee, R.S. , et al. A remarkably simple genome underlies highly malignant pediatric rhabdoid cancers. J. Clin. Invest. 122, 2983-2988 (2012).
46. Hasselblatt, M. , et al. High-resolution genomic analysis suggests the absence of recurrent genomic alterations other than SMARCB1 aberrations in atypical teratoid/rhabdoid tumors. Genes Chromosom. Cancer 52, 185-190 (2013).
47. Lawrence, M.S. , et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 499, 214-218 (2013).
48. Zhou, V.W., Goren, A., Bernstein, B.E. Charting histone modifications and the functional organization of mammalian genomes. Nat. Rev. Genet. 12, 7-18 (2011).
49. Zhu, J. , et al. Genome-wide chromatin state transitions associated with developmental and environmental cues. Cell 152, 642-654 (2013).
50. Roadmap Epigenomics Consortium. , et al. Integrative analysis of 111 reference human epigenomes. Nature 518, 317-330 (2015).
51. Chun, H.-J.E. , et al. Genome-wide profiles of extra-cranial malignant rhabdoid tumors reveal heterogeneity and dysregulated developmental pathways. Cancer Cell 29, 394-406 (2016).
52. Johann, P.D. , et al. Atypical teratoid/rhabdoid tumors are comprised of three epigenetic subgroups with distinct enhancer landscapes. Cancer Cell 29, 379-393 (2016).
53. Wang, S. , et al. Target analysis by integration of transcriptome and ChIP-seq data with BETA. Nat. Protoc. 8, 2502-2515 (2013).
54. Stappenbeck, T.S., Miyoshi, H. The role of stromal stem cells in tissue regeneration and wound repair. Science 324, 1666-1669 (2009).
55. Whyte, W.A. , et al. Master transcription factors and Mediator establish super-enhancers at key cell identity genes. Cell 153, 307-319 (2013).
56. Hnisz, D. , et al. Super-enhancers in the control of cell identity and disease. Cell 155, 934-947 (2013).
57. Bergsland, M. , et al. Sequentially acting Sox transcription factors in neural lineage development. Genes Dev. 25, 2453-2464 (2011).
58. Yu, H. , et al. Frizzled 1 and frizzled 2 genes function in palate, ventricular septum and neural tube closure: general implications for tissue fusion processes. Development 137, 3707-3717 (2010).
59. Abrahams, A., Parker, M.I., Prince, S. The T-box transcription factor Tbx2: its role in development and possible implication in cancer. IUBMB Life 62, 92-102 (2010).
60. Wang, X. , et al. Oncogenesis caused by loss of the SNF5 tumor suppressor is dependent on activity of BRG1, the ATPase of the SWI/SNF chromatin remodeling complex. Cancer Res. 69, 8094-8101 (2009).
61. Isakoff, M.S. , et al. Inactivation of the Snf5 tumor suppressor stimulates cell cycle progression and cooperates with p53 loss in oncogenic transformation. Proc. Natl. Acad. Sci. USA 102, 17745-17750 (2005).
62. Tolstorukov, M.Y. , et al. Swi/Snf chromatin remodeling/tumor suppressor complex establishes nucleosome occupancy at target promoters. Proc. Natl. Acad. Sci. USA 110, 10165-10170 (2013).
63. Yu, Y. , et al. Olig2 targets chromatin remodelers to enhancers to initiate oligodendrocyte differentiation. Cell 152, 248-261 (2013).
64. Bossen, C. , et al. The chromatin remodeler Brg1 activates enhancer repertoires to establish B cell identity and modulate cell growth. Nat. Immunol. 16, 775-784 (2015).
65. Alexander, J.M. , et al. Brg1 modulates enhancer activation in mesoderm lineage commitment. Development 142, 1418-1430 (2015).
66. Doan, D.N. , et al. Loss of the INI1 tumor suppressor does not impair the expression of multiple BRG1-dependent genes or the assembly of SWI/SNF enzymes. Oncogene 23, 3462-3473 (2004).
67. Lovén, J. , et al. Selective inhibition of tumor oncogenes by disruption of super-enhancers. Cell 153, 320-334 (2013).
68. Kaur, H. , et al. The chromatin-modifying protein HMGA2 promotes atypical teratoid/rhabdoid cell tumorigenicity. J. Neuropathol. Exp. Neurol. 74, 177-185 (2015).
69. Wang, X. , et al. TCR-dependent transformation of mature memory phenotype T cells in mice. J. Clin. Invest. 121, 3834-3845 (2011).
70. Helming, K.C. , et al. ARID1B is a specific vulnerability in ARID1A-mutant cancers. Nat. Med. 20, 251-254 (2014).
71. Staahl, B.T. , et al. Kinetic analysis of npBAF to nBAF switching reveals exchange of SS18 with CREST and integration with neural developmental pathways. J. Neurosci. 33, 10348-10361 (2013).
72. 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).
73. Kharchenko, P.V., Tolstorukov, M.Y., Park, P.J. Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat. Biotechnol. 26, 1351-1359 (2008).
74. de Hoon, M.J.L., Imoto, S., Nolan, J., Miyano, S. Open source clustering software. Bioinformatics 20, 1453-1454 (2004).
75. Saldanha, A.J. Java Treeview-extensible visualization of microarray data. Bioinformatics 20, 3246-3248 (2004).
76. Kim, D. , et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36 (2013).
77. Trapnell, C. , et al. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat. Biotechnol. 31, 46-53 (2013).
78. Subramanian, A. , et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 102, 15545-15550 (2005).