Linking long non-coding RNAs and SWI/SNF complexes to chromatin remodeling in cancer

Molecular Cancer

Volumn 16, Issue 1, 2017, Pages

  Tang, Yanyan ^a,b   Wang, Jinpeng ^a,b   Lian, Yu ^a,b   Fan, Chunmei ^b   Zhang, Ping ^b   Wu, Yingfen ^b   Li, Xiayu ^b   Xiong, Fang ^a   Li, Xiaoling ^a,b   Li, Guiyuan ^a,b   Xiong, Wei ^a,b   Zeng, Zhaoyang ^a,b  

^a CENTRAL SOUTH UNIVERSITY   (China)

^b CENTRAL SOUTH UNIVERSITY   (China)

Author keywords

Carcinogenesis; Chromatin remodeling; Gene expression; Long non coding RNAs (lncRNAs); The SWI SNF complexes

Indexed keywords

LONG UNTRANSLATED RNA; SWI/SNF RELATED MATRIX ASSOCIATED ACTIN DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY B MEMBER 1; MULTIPROTEIN COMPLEX; NONHISTONE PROTEIN; PROTEIN BINDING;

CARCINOGENESIS; CHROMATIN ASSEMBLY AND DISASSEMBLY; CHROMATIN STRUCTURE; GENE EXPRESSION REGULATION; GENE INTERACTION; GENETIC TRANSCRIPTION; HUMAN; HYDROLYSIS; MALIGNANT NEOPLASM; MUTATION; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN RNA BINDING; PROTEIN STRUCTURE; REVIEW; RNA TRANSCRIPTION; ANIMAL; CELL TRANSFORMATION; GENETICS; METABOLISM; NEOPLASM;

ANIMALS; CELL TRANSFORMATION, NEOPLASTIC; CHROMATIN ASSEMBLY AND DISASSEMBLY; CHROMOSOMAL PROTEINS, NON-HISTONE; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; MULTIPROTEIN COMPLEXES; NEOPLASMS; PROTEIN BINDING; RNA, LONG NONCODING;

EID: 85013102429     PISSN: None     EISSN: 14764598     Source Type: Journal    
DOI: 10.1186/s12943-017-0612-0     Document Type: Review

References (59)

1. Farrants AK. Chromatin remodelling and actin organisation. FEBS Lett. 2008;582:2041-50.
2. Clapier CR, Cairns BR. The biology of chromatin remodeling complexes. Annu Rev Biochem. 2009;78:273-304.
3. Kasten MM, Clapier CR, Cairns BR. SnapShot: chromatin remodeling: SWI/SNF. Cell. 2011;144:e310-1.
4. Reisman D, Glaros S, Thompson EA. The SWI/SNF complex and cancer. Oncogene. 2009;28:1653-68.
5. Hohmann AF, Vakoc CR. A rationale to target the SWI/SNF complex for cancer therapy. Trends Genet. 2014;30:356-63.
6. Gong Z, Zhang S, Zhang W, Huang H, Li Q, Deng H, et al. Long non-coding RNAs in cancer. Sci China Life Sci. 2012;55:1120-4.
7. Lian Y, Li XY, Tang YY, Yang LT, Li XL, Xiong W, et al. Long Non-coding RNAs Function as Competing Endogenous RNAs to Regulate Cancer Progression. Prog Biochem Biophys. 2016;43:219-25.
8. Gong Z, Zhang S, Zeng Z, Wu H, Yang Q, Xiong F, et al. LOC401317, a p53-regulated long non-coding RNA, inhibits cell proliferation and induces apoptosis in the nasopharyngeal carcinoma cell line HNE2. Plos One. 2014;9:e110674.
9. Wang Y, Mo Y, Gong Z, Yang X, Yang M, Zhang S, et al. Circular RNAs in human cancer. A Mol Cancer. 2017;16:25.
10. Yu J, Liu Y, Guo C, Zhang S, Gong Z, Tang Y, et al. Upregulated long non-coding RNA LINC00152 expression is associated with progression and poor prognosis of tongue squamous cell carcinoma. J Cancer. 2017;8:523-30.
11. Yang L, Tang Y, He Y, Wang Y, Lian Y, Xiong F, et al. High Expression of LINC01420 indicates an unfavorable prognosis and modulates cell migration and invasion in nasopharyngeal carcinoma. J Cancer. 2017;8:97-103.
12. Bo H, Gong Z, Zhang W, Li X, Zeng Y, Liao Q, et al. Upregulated long non-coding RNA AFAP1-AS1 expression is associated with progression and poor prognosis of nasopharyngeal carcinoma. Oncotarget. 2015;6:20404-18.
13. Zeng Z, Bo H, Gong Z, Lian Y, Li X, Li X, et al. AFAP1-AS1, a long noncoding RNA upregulated in lung cancer and promotes invasion and metastasis. Tumour Biol. 2016;37:729-37.
14. Wang Y, Xue D, Li Y, Pan X, Zhang X, Kuang B, et al. The long noncoding RNA MALAT-1 is a novel biomarker in various cancers: a meta-analysis based on the GEO database and literature. J Cancer. 2016;7:991-1001.
15. He B, Li W, Wu Y, Wei F, Gong Z, Bo H, et al. Epstein-Barr virus-encoded miR-BART6-3p inhibits cancer cell metastasis and invasion by targeting long non-coding RNA LOC553103. Cell Death Dis. 2016;7:e2353.
16. Gong Z, Yang Q, Zeng Z, Zhang W, Li X, Zu X, et al. An integrative transcriptomic analysis reveals p53 regulated miRNA, mRNA, and lncRNA networks in nasopharyngeal carcinoma. Tumour Biol. 2016;37:3683-95.
17. Carlson M, Osmond BC, Botstein D. Mutants of yeast defective in sucrose utilization. Genetics. 1981;98:25-40.
18. Neigeborn L, Carlson M. Genes affecting the regulation of SUC2 gene expression by glucose repression in Saccharomyces cerevisiae. Genetics. 1984;108:845-58.
19. Peterson CL, Dingwall A, Scott MP. Five SWI/SNF gene products are components of a large multisubunit complex required for transcriptional enhancement. Proc Natl Acad Sci U S A. 1994;91:2905-8.
20. Muchardt C, Yaniv M. ATP-dependent chromatin remodelling: SWI/SNF and Co. are on the job. J Mol Biol. 1999;293:187-98.
21. Smith-Roe SL, Nakamura J, Holley D, Chastain 2nd PD, Rosson GB, Simpson DA, et al. SWI/SNF complexes are required for full activation of the DNA-damage response. Oncotarget. 2015;6:732-45.
22. Wang X, Haswell JR, Roberts CW. Molecular pathways: SWI/SNF (BAF) complexes are frequently mutated in cancer--mechanisms and potential therapeutic insights. Clin Cancer Res. 2014;20:21-7.
23. Phelan ML, Sif S, Narlikar GJ, Kingston RE. Reconstitution of a core chromatin remodeling complex from SWI/SNF subunits. Mol Cell. 1999;3:247-53.
24. Xu K, Xiong W, Zhou M, Wang H, Yang J, Li X, et al. Integrating ChIP-sequencing and digital gene expression profiling to identify BRD7 downstream genes and construct their regulating network. Mol Cell Biochem. 2016;411:57-71.
25. Peterson CL, Workman JL. Promoter targeting and chromatin remodeling by the SWI/SNF complex. Curr Opin Genet Dev. 2000;10:187-92.
26. Wilson CJ, Chao DM, Imbalzano AN, Schnitzler GR, Kingston RE, Young RA. RNA polymerase II holoenzyme contains SWI/SNF regulators involved in chromatin remodeling. Cell. 1996;84:235-44.
27. Owen-Hughes T, Utley RT, Cote J, Peterson CL, Workman JL. Persistent site-specific remodeling of a nucleosome array by transient action of the SWI/SNF complex. Science. 1996;273:513-6.
28. Gangaraju VK, Bartholomew B. Mechanisms of ATP dependent chromatin remodeling. Mutat Res. 2007;618:3-17.
29. Zhang B, Chambers KJ, Faller DV, Wang S. Reprogramming of the SWI/SNF complex for co-activation or co-repression in prohibitin-mediated estrogen receptor regulation. Oncogene. 2007;26:7153-7.
30. Jiang C, Pugh BF. Nucleosome positioning and gene regulation: advances through genomics. Nat Rev Genet. 2009;10:161-72.
31. Hargreaves DC, Crabtree GR. ATP-dependent chromatin remodeling: genetics, genomics and mechanisms. Cell Res. 2011;21:396-420.
32. Han P, Chang CP. Long non-coding RNA and chromatin remodeling. RNA Biol. 2015;12:1094-8.
33. Prensner JR, Iyer MK, Sahu A, Asangani IA, Cao Q, Patel L, et al. The long noncoding RNA SChLAP1 promotes aggressive prostate cancer and antagonizes the SWI/SNF complex. Nat Genet. 2013;45:1392-8.
34. Lee RS, Roberts CWM. Linking the SWI/SNF complex to prostate cancer. Nat Genet. 2013;45:1268-9.
35. Wang X, Gong Y, Jin B, Wu C, Yang J, Wang L, et al. Long non-coding RNA urothelial carcinoma associated 1 induces cell replication by inhibiting BRG1 in 5637 cells. Oncol Rep. 2014;32:1281-90.
36. Gao C, Zhang J, Wang Q, Ren C. Overexpression of lncRNA NEAT1 mitigates multidrug resistance by inhibiting ABCG2 in leukemia. Oncol Lett. 2016;12:1051-7.
37. Song Y, Li X, Zeng Z, Li Q, Gong Z, Liao Q, et al. Epstein-Barr virus encoded miR-BART11 promotes inflammation-induced carcinogenesis by targeting FOXP1. Oncotarget. 2016;7:36783-99.
38. Sun C, Li S, Zhang F, Xi Y, Wang L, Bi Y, et al. Long non-coding RNA NEAT1 promotes non-small cell lung cancer progression through regulation of miR-377-3p-E2F3 pathway. Oncotarget. 2016;7:51784-814.
39. Ke H, Zhao L, Feng X, Xu H, Zou L, Yang Q, et al. NEAT1 is Required for Survival of Breast Cancer Cells Through FUS and miR-548. Gene Regul Syst Biol. 2016;10:11-7.
40. Fu JW, Kong Y, Sun X. Long noncoding RNA NEAT1 is an unfavorable prognostic factor and regulates migration and invasion in gastric cancer. J Cancer Res Clin Oncol. 2016;142:1571-9.
41. Kawaguchi T, Tanigawa A, Naganuma T, Ohkawa Y, Souquere S, Pierron G, et al. SWI/SNF chromatin-remodeling complexes function in noncoding RNA-dependent assembly of nuclear bodies. Proc Natl Acad Sci U S A. 2015;112:4304-9.
42. Adriaens C, Standaert L, Barra J, Latil M, Verfaillie A, Kalev P, et al. p53 induces formation of NEAT1 lncRNA-containing paraspeckles that modulate replication stress response and chemosensitivity. Nat Med. 2016;22:861-8.
43. Cajigas I, Leib DE, Cochrane J, Luo H, Swyter KR, Chen S, et al. Evf2 lncRNA/BRG1/DLX1 interactions reveal RNA-dependent inhibition of chromatin remodeling. Development. 2015;142:2641-52.
44. Tantai J, Hu D, Yang Y, Geng J. Combined identification of long non-coding RNA XIST and HIF1A-AS1 in serum as an effective screening for non-small cell lung cancer. Int J Clin Exp Pathol. 2015;8:7887-95.
45. Wang S, Zhang X, Yuan Y, Tan M, Zhang L, Xue X, et al. BRG1 expression is increased in thoracic aortic aneurysms and regulates proliferation and apoptosis of vascular smooth muscle cells through the long non-coding RNA HIF1A-AS1 in vitro. Eur J Cardiothorac Surg. 2015;47:439-46.
46. Wang Y, He L, Du Y, Zhu P, Huang G, Luo J, et al. The long noncoding RNA lncTCF7 promotes self-renewal of human liver cancer stem cells through activation of Wnt signaling. Cell Stem Cell. 2015;16:413-25.
47. Liang F, Li Q, Li X, Li Z, Gong Z, Deng H, et al. TSC22D2 interacts with PKM2 and inhibits cell growth in colorectal cancer. A Int J Oncol. 2016;49:1046-56.
48. Hu G, Gong AY, Wang Y, Ma S, Chen X, Chen J, et al. LincRNA-Cox2 promotes late inflammatory gene transcription in macrophages through modulating SWI/SNF-mediated chromatin remodeling. J Immunol. 2016;196:2799-808.
49. Wang L, Zhao Z, Meyer MB, Saha S, Yu M, Guo A, et al. CARM1 methylates chromatin remodeling factor BAF155 to enhance tumor progression and metastasis. Cancer Cell. 2014;25:21-36.
50. Cheng SW, Davies KP, Yung E, Beltran RJ, Yu J, Kalpana GV. c-MYC interacts with INI1/hSNF5 and requires the SWI/SNF complex for transactivation function. Nat Genet. 1999;22:102-5.
51. Nagl Jr NG, Zweitzig DR, Thimmapaya B, Beck Jr GR, Moran E. The c-myc gene is a direct target of mammalian SWI/SNF-related complexes during differentiation-associated cell cycle arrest. Cancer Res. 2006;66:1289-93.
52. Shi J, Whyte WA, Zepeda-Mendoza CJ, Milazzo JP, Shen C, Roe JS, et al. Role of SWI/SNF in acute leukemia maintenance and enhancer-mediated Myc regulation. Genes Dev. 2013;27:2648-62.
53. Thomas LR, Wang Q, Grieb BC, Phan J, Foshage AM, Sun Q, et al. Interaction with WDR5 promotes target gene recognition and tumorigenesis by MYC. Mol Cell. 2015;58:440-52.
54. Romero OA, Torres-Diz M, Pros E, Savola S, Gomez A, Moran S, et al. MAX inactivation in small cell lung cancer disrupts MYC-SWI/SNF programs and is synthetic lethal with BRG1. Cancer Discov. 2014;4:292-303.
55. Li Q, Chen P, Zeng Z, Liang F, Song Y, Xiong F, et al. Yeast two-hybrid screening identified WDR77 as a novel interacting partner of TSC22D2. Tumour Biol. 2016;37:12503-12.
56. Fischer B, Sandmann T, Horn T, Billmann M, Chaudhary V, Huber W, et al. A map of directional genetic interactions in a metazoan cell. Elife. 2015;4:e05464.
57. Medina PP, Romero OA, Kohno T, Montuenga LM, Pio R, Yokota J, et al. Frequent BRG1/SMARCA4-inactivating mutations in human lung cancer cell lines. Hum Mutat. 2008;29:617-22.
58. Young NP, Jacks T. Tissue-specific p19Arf regulation dictates the response to oncogenic K-ras. Proc Natl Acad Sci U S A. 2010;107:10184-9.
59. von Figura G, Fukuda A, Roy N, Liku ME, Morris Iv JP, Kim GE, et al. The chromatin regulator Brg1 suppresses formation of intraductal papillary mucinous neoplasm and pancreatic ductal adenocarcinoma. Nat Cell Biol. 2014;16:255-67.