Erratum: Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus (Cell Research (2014) 24 (513-531) DOI: 10.1038/cr.2014.35);Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus

Cell Research

Volumn 24, Issue 5, 2014, Pages 513-531

  Xiang, Jian Feng ^a   Yin, Qing Fei ^a   Chen, Tian ^a   Zhang, Yang ^a   Zhang, Xiao Ou ^b   Wu, Zheng ^a   Zhang, Shaofeng ^a   Wang, Hai Bin ^c   Ge, Junhui ^c   Lu, Xuhua ^c   Yang, Li ^b   Chen, Ling Ling ^b  

^a INSTITUTE OF BIOCHEMISTRY AND CELL BIOLOGY   (China)

^b Shanghai Jiao Tong University Affiliated Sixth People s Hospital   (China)

^c SECOND MILITARY MEDICAL UNIVERSITY   (China)

Author keywords

CCAT1 L lncRNA; chromatin looping; CTCF; MYC; super enhancer

Indexed keywords

CCAT1 LONG NONCODING RNA, HUMAN; CCCTC-BINDING FACTOR; CHROMATIN; LONG UNTRANSLATED RNA; MYC PROTEIN; REPRESSOR PROTEIN;

CHEMISTRY; CHROMATIN; COLON; COLORECTAL TUMOR; ENHANCER REGION; GENE EXPRESSION REGULATION; GENE LOCUS; GENE SILENCING; GENETICS; HUMAN; METABOLISM; ONCOGENE MYC; PATHOLOGY; PROMOTER REGION; RECTUM; TUMOR CELL LINE;

CELL LINE, TUMOR; CHROMATIN; COLON; COLORECTAL NEOPLASMS; ENHANCER ELEMENTS, GENETIC; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE KNOCKDOWN TECHNIQUES; GENES, MYC; GENETIC LOCI; HUMANS; PROMOTER REGIONS, GENETIC; PROTO-ONCOGENE PROTEINS C-MYC; RECTUM; REPRESSOR PROTEINS; RNA, LONG NONCODING;

EID: 84899939074     PISSN: 10010602     EISSN: 17487838     Source Type: Journal    
DOI: 10.1038/cr.2014.117     Document Type: Erratum

References (61)

1. Rinn JL, Chang HY. Genome regulation by long noncoding RNAs. Annu Rev Biochem 2012; 81:145-166.
2. Ulitsky I, Bartel DP. lincRNAs: genomics, evolution, and mechanisms. Cell 2013;154:26-46.
3. Gutschner T, Diederichs S. The hallmarks of cancer: a long non-coding RNA point of view. RNA Biol 2012; 9:703-719.
4. Gupta RA, Shah N, Wang KC, et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 2010; 464:1071-1076.
5. Huarte M, Guttman M, Feldser D, et al. A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 2010; 142:409-419.
6. Yoon JH, Abdelmohsen K, Srikantan S, et al. LincRNA-p21 suppresses target mRNA translation. Mol Cell 2012; 47:648-655.
7. Gutschner T, Hammerle M, Eissmann M, et al. The noncoding RNA MALAT1 is a critical regulator of the metastasis pheno-type of lung cancer cells. Cancer Res 2013; 73:1180-1189.
8. Tripathi V, Shen Z, Chakraborty A, et al. Long noncoding RNA MALAT1 controls cell cycle progression by regulating the expression of oncogenic transcription factor B-MYB. PLoS Genet 2013; 9:e1003368.
9. Bulger M, Groudine M. Functional and mechanistic diversity of distal transcription enhancers. Cell 2011; 144:327-339.
10. Orom UA, Shiekhattar R. Long noncoding RNAs usher in a new era in the biology of enhancers. Cell 2013; 154:1190-1193.
11. Kim TK, Hemberg M, Gray JM, et al. Widespread transcription at neuronal activity-regulated enhancers. Nature 2010; 465:182-187.
12. Lai F, Orom UA, Cesaroni M, et al. Activating RNAs associate with Mediator to enhance chromatin architecture and transcription. Nature 2013; 494:497-501.
13. Lam MT, Cho H, Lesch HP, et al. Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription. Nature 2013; 498:511-515.
14. Li W, Notani D, Ma Q, et al. Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation. Nature 2013; 498:516-520.
15. Mousavi K, Zare H, Dell'orso S, et al. eRNAs promote transcription by establishing chromatin accessibility at defined genomic loci. Mol Cell 2013; 51:606-617.
16. Orom UA, Derrien T, Beringer M, et al. Long noncoding RNAs with enhancer-like function in human cells. Cell 2010; 143:46-58.
17. Loven J, Hoke HA, Lin C Y, et al. Selective inhibition of tumor oncogenes by disruption of super-enhancers. Cell 2013; 153:320-334.
18. Whyte WA, Orlando DA, Hnisz D, et al. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell 2013; 153:307-319.
19. Ahmadiyeh N, Pomerantz MM, Grisanzio C, et al. 8q24 prostate, breast, and colon cancer risk loci show tissue-specific long-range interaction with MYC. Proc Natl Acad Sci USA 2010; 107:9742-9746.
20. Hnisz D, Abraham BJ, Lee TI, et al. Super-enhancers in the control of cell identity and disease. Cell 2013; 155:934-947.
21. Levens D. How the c-myc promoter works and why it sometimes does not. J Natl Cancer Inst Monogr 2008; 39:41-43.
22. Pomerantz MM, Ahmadiyeh N, Jia L, et al. The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer. Nat Genet 2009; 41:882-884.
23. Tuupanen S, Turunen M, Lehtonen R, et al. The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling. Nat Genet 2009; 41:885-890.
24. Sur IK, Hallikas O, Vaharautio A, et al. Mice lacking a Myc enhancer that includes human SNP rs6983267 are resistant to intestinal tumors. Science 2012; 338:1360-1363.
25. Chung S, Nakagawa H, Uemura M, et al. Association of a novel long non-coding RNA in 8q24 with prostate cancer susceptibility. Cancer Sci 2011; 102:245-252.
26. Yang L, Lin C, Jin C, et al. lncRNA-dependent mechanisms of androgen-receptor-regulated gene activation programs. Nature 2013; 500:598-602.
27. Nissan A, Stojadinovic A, Mitrani-Rosenbaum S, et al. Colon cancer associated transcript-1: a novel RNA expressed in malignant and pre-malignant human tissues. Int J Cancer J 2012; 130:1598-1606.
28. Alaiyan B, Ilyayev N, Stojadinovic A, et al. Differential expression of colon cancer associated transcript1 (CCAT1) along the colonic adenoma-carcinoma sequence. BMC Cancer 2013; 13:196.
29. Ling H, Spizzo R, Atlasi Y, et al. CCAT2, a novel noncoding RNA mapping to 8q24, underlies metastatic progression and chromosomal instability in colon cancer. Genome Res 2013; 23:1446-1461.
30. Augui S, Nora EP, Heard E. Regulation of X-chromosome inactivation by the X-inactivation centre. Nat Rev Genet 2011; 12:429-442.
31. Kam Y, Rubinstein A, Naik S, et al. Detection of a long non-coding RNA (CCAT1) in living cells and human adenocar-cinoma of colon tissues using FIT-PNA molecular beacons. Cancer Letters 2013 Feb 14. doi: 10.1016/j.canlet.2013.02. 014
32. Yin QF, Yang L, Zhang Y, et al. Long noncoding RNAs with snoRNA ends. Mol Cell 2012; 48:219-230.
33. Zhang Y, Zhang XO, Chen T, et al. Circular intronic long non-coding RNAs. Mol Cell 2013; 51:792-806.
34. Gaj T, Gersbach CA, Barbas CF 3rd. ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol 2013; 31:397-405.
35. Gutschner T, Baas M, Diederichs S. Noncoding RNA gene silencing through genomic integration of RNA destabilizing elements using zinc fnger nucleases. Genome Res 2011; 21:1944-1954.
36. Maston GA, Evans SK, Green MR. Transcriptional regulatory elements in the human genome. Annu Rev Genom Hum Genet 2006; 7:29-59.
37. Corzo C, Petzold M, Mayol X, et al. RxFISH karyotype and MYC amplifcation in the HT-29 colon adenocarcinoma cell line. Genes Chromosomes Cancer 2003; 36:425-426.
38. Kawai K, Viars C, Arden K, et al. Comprehensive karyotyping of the HT-29 colon adenocarcinoma cell line. Genes Chromosomes Cancer 2002; 34:1-8.
39. Consortium EP, Bernstein BE, Birney E, et al. An integrated encyclopedia of DNA elements in the human genome. Nature 2012; 489:57-74.
40. Ong CT, Corces VG. Enhancer function: new insights into the regulation of tissue-specifc gene expression. Nat Rev Genet 2011; 12:283-293.
41. Stadhouders R, Kolovos P, Brouwer R, et al. Multiplexed chromosome conformation capture sequencing for rapid genome-scale high-resolution detection of long-range chromatin interactions. Nat Protoc 2013; 8:509-524.
42. He TC, Sparks AB, Rago C, et al. Identifcation of c-MYC as a target of the APC pathway. Science 1998; 281:1509-1512.
43. Handoko L, Xu H, Li G, et al. CTCF-mediated functional chromatin interactome in pluripotent cells. Nat Genet 2011; 43:630-638.
44. Phillips-Cremins JE, Sauria ME, Sanyal A, et al. Architectural protein subclasses shape 3D organization of genomes during lineage commitment. Cell 2013; 153:1281-1295.
45. Sanyal A, Lajoie BR, Jain G, Dekker J. The long-range interaction landscape of gene promoters. Nature 2012; 489:109-113.
46. Burdach J, O'Connell MR, Mackay JP, Crossley M. Two-timing zinc fnger transcription factors liaising with RNA. Trends Biochem Sci 2012; 37:199-205.
47. Cassiday LA, Maher LJ 3rd. Having it both ways: transcription factors that bind DNA and RNA. Nucleic Acids Res 2002; 30:4118-4126.
48. De Santa F, Barozzi I, Mietton F, et al. A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS Biol 2010; 8:e1000384.
49. Hah N, Murakami S, Nagari A, Danko CG, Kraus WL. Enhancer transcripts mark active estrogen receptor binding sites. Genome Res 2013; 23:1210-1223.
50. Phillips JE, Corces VG. CTCF: master weaver of the genome. Cell 2009; 137:1194-1211.
51. Herold M, Bartkuhn M, Renkawitz R. CTCF: insights into insulator function during development. Development 2012; 139:1045-1057.
52. Sun S, Del Rosario BC, Szanto A, et al. Jpx RNA activates Xist by evicting CTCF. Cell 2013; 153:1537-1551.
53. Taft RJ, Hawkins PG, Mattick JS, Morris KV. The relationship between transcription initiation RNAs and CCCTC-binding factor (CTCF) localization. Epigenet Chromatin 2011; 4:13.
54. Yao H, Brick K, Evrard Y, et al. Mediation of CTCF transcrip-tional insulation by DEAD-box RNA-binding protein p68 and steroid receptor RNA activator SRA. Genes Dev 2010; 24: 2543-2555.
55. Zhang B, Arun G, Mao YS, et al. The lncRNA Malat1 is dispensable for mouse development but its transcription plays a cis-regulatory role in the adult. Cell Rep 2012; 2:111-123.
56. Yang L, Duff MO, Graveley BR, Carmichael GG, Chen LL. Genomewide characterization of non-polyadenylated RNAs. Genome Biol 2011;12:R16.
57. Klattenhoff CA, Scheuermann JC, Surface LE, et al. Braveheart, a long noncoding RNA required for cardiovascular lineage commitment. Cell 2013; 152:570-583.
58. Tsai MC, Manor O, Wan Y, et al. Long noncoding RNA as modular scaffold of histone modifcation complexes. Science 2010; 329:689-693.
59. Hagege H, Klous P, Braem C, et al. Quantitative analysis of chromosome conformation capture assays (3C-qPCR). Nat Protoc 2007; 2:1722-1733.
60. Dostie J, Dekker J. Mapping networks of physical interactions between genomic elements using 5C technology. Nat Protoc 2007; 2:988-1002.
61. Cermak T, Doyle EL, Christian M, et al. Effcient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucl Acids Res 2011; 39:e82.