The landscape of antisense gene expression in human cancers

Genome Research

Volumn 25, Issue 7, 2015, Pages 1068-1079

  Balbin, O Alejandro ^a,b   Malik, Rohit ^a,b   Dhanasekaran, Saravana M ^a,b   Prensner, John R ^a,b   Cao, Xuhong ^a,b   Wu, Yi Mi ^a,b   Robinson, Dan ^a,b   Wang, Rui ^a,b   Chen, Guoan ^c   Beer, David G ^c   Nesvizhskii, Alexey I ^a,b   Chinnaiyan, Arul M ^a,b,c  

^a UNIVERSITY OF MICHIGAN HEALTH SYSTEM   (United States)

^b UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^c UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTISENSE OLIGONUCLEOTIDE; COMPLEMENTARY RNA; TRANSCRIPTOME;

ARTICLE; CELL PROLIFERATION; GENE EXPRESSION; GENETIC TRANSCRIPTION; HUMAN; NEOPLASM; ONCOGENE; PRIORITY JOURNAL; RNA SEQUENCE; TISSUES; ANTIBODY SPECIFICITY; BIOLOGY; CLUSTER ANALYSIS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE LOCUS; GENETICS; PROCEDURES;

CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENETIC LOCI; HUMANS; NEOPLASMS; ORGAN SPECIFICITY; RNA, ANTISENSE; TRANSCRIPTOME;

EID: 84937040951     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.180596.114     Document Type: Article

References (50)

1. Anders S, Huber W. 2010. Differential expression analysis for sequence count data. Genome Biol 11: R106.
2. Beltran M, Puig I, Peña C, García JM, Álvarez AB, Peña R, Bonilla F, de Herreros AG. 2008. A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial-mesenchymal transition. Genes Dev 22: 756-769.
3. Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, et al. 2005. The transcriptional landscape of the mammalian genome. Science 309: 1559-1563.
4. Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, Patel S, Long J, Stern D, Tammana H, Helt G, et al. 2005. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308: 1149-1154.
5. Congrains A, Kamide K, Ohishi M, Rakugi H. 2013. ANRIL: molecular mechanisms and implications in human health. Int J Mol Sci 14: 1278-1292.
6. Dallosso AR, Hancock AL, Malik S, Salpekar A, King-Underwood L, Pritchard-Jones K, Peters J, Moorwood K, Ward A, Malik KT, et al. 2007. Alternately spliced WT1 antisense transcripts interact with WT1 sense RNA and show epigenetic and splicing defects in cancer. RNA 13: 2287-2299.
7. Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, et al. 2012. Landscape of transcription in human cells. Nature 489: 101-108.
8. Faghihi MA, Wahlestedt C. 2009. Regulatory roles of natural antisense transcripts. Nat Rev Mol Cell Biol 10: 637-643.
9. Faghihi MA, Modarresi F, Khalil AM, Wood DE, Sahagan BG, Morgan TE, Finch CE, St Laurent GIII, Kenny PJ, Wahlestedt C. 2008. Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of β-secretase. Nat Med 14: 723-730.
10. Faghihi MA, Zhang M, Huang J, Modarresi F, Van der Brug MP, Nalls MA, Cookson MR, St-Laurent GIII, Wahlestedt C. 2010. Evidence for natural antisense transcript-mediated inhibition of microRNA function. Genome Biol 11: R56.
11. Flicek P, Ahmed I, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, et al. 2013. Ensembl 2013. Nucleic Acids Res 41: D48-D55.
12. Geng YJ, Xie SL, Li Q, Ma J, Wang GY. 2011. Large intervening non-coding RNA HOTAIR is associated with hepatocellular carcinoma progression. J Int Med Res 39: 2119-2128.
13. Guil S, Esteller M. 2012. Cis-acting noncoding RNAs: friends and foes. Nat Struct Mol Biol 19: 1068-1075.
14. Han Y, Liu Y, Gui Y, Cai Z. 2013. Long intergenic non-coding RNA TUG1 is overexpressed in urothelial carcinoma of the bladder. J Surg Oncol 107: 555-559.
15. He Y, Vogelstein B, Velculescu VE, Papadopoulos N, Kinzler KW. 2008. The antisense transcriptomes of human cells. Science 322: 1855-1857.
16. Huarte M, Guttman M, Feldser D, Garber M, Koziol MJ, Kenzelmann-Broz D, Khalil AM, Zuk O, Amit I, Rabani M, et al. 2010. A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 142: 409-419.
17. Kapranov P, Cawley SE, Drenkow J, Bekiranov S, Strausberg RL, Fodor SP, Gingeras TR. 2002. Large-scale transcriptional activity in chromosomes 21 and 22. Science 296: 916-919.
18. Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackermuller J, Hofacker IL, et al. 2007. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316: 1484-1488.
19. Karolchik D, Barber GP, Casper J, Clawson H, Cline MS, Diekhans M, Dreszer TR, Fujita PA, Guruvadoo L, Haeussler M, et al. 2014. The UCSC Genome Browser database: 2014 update. Nucleic Acids Res 42: D764-D770.
20. Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M, Nishida H, Yap CC, Suzuki M, Kawai J, et al. 2005. Antisense transcription in the mammalian transcriptome. Science 309: 1564-1566.
21. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. 2013a. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14: R36.
22. Kim K, Jutooru I, Chadalapaka G, Johnson G, Frank J, Burghardt R, Kim S, Safe S. 2013b. HOTAIR is a negative prognostic factor and exhibits pro-oncogenic activity in pancreatic cancer. Oncogene 32: 1616-1625.
23. Kogo R, Shimamura T, Mimori K, Kawahara K, Imoto S, Sudo T, Tanaka F, Shibata K, Suzuki A, Komune S, et al. 2011. Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin modification and is associated with poor prognosis in colorectal cancers. Cancer Res 71: 6320-6326.
24. Li S, Liberman LM, Mukherjee N, Benfey PN, Ohler U. 2013. Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data. Genome Res 23: 1730-1739.
25. Liu B, Chen J, Shen B. 2011. Genome-wide analysis of the transcription factor binding preference of human bi-directional promoters and functional annotation of related gene pairs. BMC Syst Biol 5 Suppl 1: S2.
26. Luo JH, Ren B, Keryanov S, Tseng GC, Rao UN, Monga SP, Strom S, Demetris AJ, Nalesnik M, Yu YP, et al. 2006. Transcriptomic and genomic analysis of human hepatocellular carcinomas and hepatoblastomas. Hepatology 44: 1012-1024.
27. Mahmoudi S, Henriksson S, Corcoran M, Méndez-Vidal C, Wiman KG, Farnebo M. 2009. Wrap53, a natural p53 antisense transcript required for p53 induction upon DNA damage. Mol Cell 33: 462-471.
28. Michael DR, Phillips AO, Krupa A, Martin J, Redman JE, Altaher A, Neville RD, Webber J, Kim MY, Bowen T. 2011. The human hyaluronan synthase 2 (HAS2) gene and its natural antisense RNA exhibit coordinated expression in the renal proximal tubular epithelial cell. J Biol Chem 286: 19523-19532.
29. Millar JK, Wilson-Annan JC, Anderson S, Christie S, Taylor MS, Semple CA, Devon RS, St Clair DM, Muir WJ, Blackwood DH, et al. 2000. Disruption of two novel genes by a translocation co-segregating with schizophrenia. Hum Mol Genet 9: 1415-1423.
30. Modarresi F, Faghihi MA, Lopez-Toledano MA, Fatemi RP, Magistri M, Brothers SP, van der Brug MP, Wahlestedt C. 2012. Inhibition of natural antisense transcripts in vivo results in gene-specific transcriptional upregulation. Nat Biotechnol 30: 453-459.
31. Morrissy AS, Griffith M, Marra MA. 2011. Extensive relationship between antisense transcription and alternative splicing in the human genome. Genome Res 21: 1203-1212.
32. Niinuma T, Suzuki H, Nojima M, Nosho K, Yamamoto H, Takamaru H, Yamamoto E, Maruyama R, Nobuoka T, Miyazaki Y, et al. 2012. Upregulation of miR-196a and HOTAIR drive malignant character in gastrointestinal stromal tumors. Cancer Res 72: 1126-1136.
33. Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato N, Saito R, Suzuki H, et al. 2002. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420: 563-573.
34. Parkhomchuk D, Borodina T, Amstislavskiy V, Banaru M, Hallen L, Krobitsch S, Lehrach H, Soldatov A. 2009. Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res 37: e123.
35. Pelechano V, Steinmetz LM. 2013. Gene regulation by antisense transcription. Nat Rev Genet 14: 880-893.
36. Prensner JR, Iyer MK, Balbin OA, Dhanasekaran SM, Cao Q, Brenner JC, Laxman B, Asangani IA, Grasso CS, Kominsky HD, et al. 2011. Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression. Nat Biotechnol 29: 742-749.
37. Scheele C, Petrovic N, Faghihi MA, Lassmann T, Fredriksson K, Rooyackers O, Wahlestedt C, Good L, Timmons JA. 2007. The human PINK1 locus is regulated in vivo by a non-coding natural antisense RNA during modulation of mitochondrial function. BMC Genomics 8: 74.
38. Schmidt LH, Spieker T, Koschmieder S, Schaffers S, Humberg J, Jungen D, Bulk E, Hascher A, Wittmer D, Marra A, et al. 2011. The long noncoding MALAT-1 RNA indicates a poor prognosis in non-small cell lung cancer and induces migration and tumor growth. J Thorac Oncol 6: 1984-1992.
39. Sessa L, Breiling A, Lavorgna G, Silvestri L, Casari G, Orlando V. 2007. Noncoding RNA synthesis and loss of Polycomb group repression accompanies the colinear activation of the human HOXA cluster. RNA 13: 223-239.
40. Silva JM, Boczek NJ, Berres MW, Ma X, Smith DI. 2011. LSINCT5 is over expressed in breast and ovarian cancer and affects cellular proliferation. RNA Biol 8: 496-505.
41. Su WY, Li JT, Cui Y, Hong J, Du W, Wang YC, Lin YW, Xiong H, Wang JL, Kong X, et al. 2012. Bidirectional regulation between WDR83 and its natural antisense transcript DHPS in gastric cancer. Cell Res 22: 1374-1389.
42. Takayama K, Horie-Inoue K, Katayama S, Suzuki T, Tsutsumi S, Ikeda K, Urano T, Fujimura T, Takagi K, Takahashi S, et al. 2013. Androgen-responsive long noncoding RNA CTBP1-AS promotes prostate cancer. EMBO J 32: 1665-1680.
43. Trinklein ND, Aldred SF, Hartman SJ, Schroeder DI, Otillar RP, Myers RM. 2004. An abundance of bidirectional promoters in the human genome. Genome Res 14: 62-66.
44. Wahlestedt C. 2013. Targeting long non-coding RNA to therapeutically upregulate gene expression. Nat Rev Drug Discov 12: 433-446.
45. Wei W, Pelechano V, Jarvelin AI, Steinmetz LM. 2011. Functional consequences of bidirectional promoters. Trends Genet 27: 267-276.
46. Xu Z, Wei W, Gagneur J, Perocchi F, Clauder-Munster S, Camblong J, Guffanti E, Stutz F, Huber W, Steinmetz LM. 2009. Bidirectional promoters generate pervasive transcription in yeast. Nature 457: 1033-1037.
47. Yamaguchi T, Hosono Y, Yanagisawa K, Takahashi T. 2013. NKX2-1/TTF-1: an enigmatic oncogene that functions as a double-edged sword for cancer cell survival and progression. Cancer Cell 23: 718-723.
48. Yassour M, Pfiffner J, Levin JZ, Adiconis X, Gnirke A, Nusbaum C, Thompson DA, Friedman N, Regev A. 2010. Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species. Genome Biol 11: R87.
49. Yu W, Gius D, Onyango P, Muldoon-Jacobs K, Karp J, Feinberg AP, Cui H. 2008. Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature 451: 202-206.
50. Zhang X, Lian Z, Padden C, Gerstein MB, Rozowsky J, Snyder M, Gingeras TR, Kapranov P, Weissman SM, Newburger PE. 2009. A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster. Blood 113: 2526-2534.