Extensive relationship between antisense transcription and alternative splicing in the human genome

Genome Research

Volumn 21, Issue 8, 2011, Pages 1203-1212

  Morrissy, A Sorana ^a   Griffith, Malachi ^a   Marra, Marco A ^a  

^a BRITISH COLUMBIA CANCER AGENCY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ANTISENSE OLIGONUCLEOTIDE; MESSENGER RNA; RNA POLYMERASE II;

ALTERNATIVE RNA SPLICING; ANTISENSE TRANSCRIPTION; ARTICLE; EXON; GENE EXPRESSION; GENE MAPPING; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; HUMAN GENOME; LYMPHOBLASTOID CELL LINE; NUCLEOSOME; PRIORITY JOURNAL; PROMOTER REGION; TRANSCRIPTION REGULATION;

ALTERNATIVE SPLICING; CELL LINE, TUMOR; DNA, ANTISENSE; EXONS; GENOME, HUMAN; HUMANS; TRANSCRIPTION, GENETIC;

METAZOA;

EID: 79960521632     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.113431.110     Document Type: Article

References (59)

1. Allo M, Buggiano V, Fededa JP, Petrillo E, Schor I, de la Mata M, Agirre E, Plass M, Eyras E, Elela SA, et al. 2009. Control of alternative splicing through siRNA-mediated transcriptional gene silencing. Nat Struct Mol Biol 16: 717-724.
2. Annilo T, Kepp K, Laan M. 2009. Natural antisense transcript of natriuretic peptide precursor A (NPPA): structural organization and modulation of NPPA expression. BMC Mol Biol 10: 81. doi: 10.1186/1471-2199-10-81.
3. Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Marshall KA, et al. 2009. NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Res 37: D885-D890.
4. Beltran M, Puig I, Pena C, Garcia JM, Alvarez AB, Pena 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. (Pubitemid 351439107)
5. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, et al. 2008. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456: 53-59.
6. Best DJ, Roberts DE. 1975. Algorithm AS 89: The upper tail probabilities of Spearman's Rho. J R Stat Soc Ser C Appl Stat 24: 377-379.
7. Bowers J, Mitchell J, Beer E, Buzby PR, Causey M, Efcavitch JW, Jarosz M, Krzymanska-Olejnik E, Kung L, Lipson D, et al. 2009. Virtual terminator nucleotides for next-generation DNA sequencing. Nat Methods 6: 593-595.
8. 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.
9. Chen J, Sun M, Kent W, Huang X, Xie H, Wang W, Zhou G, Shi R, Rowley J. 2004. Over 20% of human transcripts might form sense-antisense pairs. Nucleic Acids Res 32: 4812-4820. (Pubitemid 39429685)
10. Chen J, Sun M, Hurst LD, Carmichael GG, Rowley JD. 2005. Genome-wide analysis of coordinate expression and evolution of human cis-encoded sense-antisense transcripts. Trends Genet 21: 326-329. (Pubitemid 40726388)
11. Dahary D, Elroy-Stein O, Sorek R. 2005. Naturally occurring antisense: Transcriptional leakage or real overlap? Genome Res 15: 364-368. (Pubitemid 40467777)
12. de la Mata M, Alonso CR, Kadener S, Fededa JP, Blaustein M, Pelisch F, Cramer P, Bentley D, Kornblihtt AR. 2003. A Slow RNA polymerase II affects alternative splicing in vivo. Mol Cell 12: 525-532. (Pubitemid 37238937)
13. ENCODE Project Consortium. 2004. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 306: 636-640.
14. Engstrom PG, Suzuki H, Ninomiya N, Akalin A, Sessa L, Lavorgna G, Brozzi A, Luzi L, Tan SL, Yang L, et al. 2006. Complex loci in human and mouse genomes. PLoS Genet 2: e47. doi: 10.1371/journal.pgen.0020047.
15. Faulkner GJ, Kimura Y, Daub CO, Wani S, Plessy C, Irvine KM, Schroder K, Cloonan N, Steptoe AL, Lassmann T, et al. 2009. The regulated retrotransposon transcriptome of mammalian cells. Nat Genet 41: 563-571.
16. Galburt EA, Grill SW, Wiedmann A, Lubkowska L, Choy J, Nogales E, Kashlev M, Bustamante C. 2007. Backtracking determines the force sensitivity of RNAP II in a factor-dependent manner. Nature 446: 820-823. (Pubitemid 46582033)
17. Garcia-Blanco M, Baraniak A, Lasda E. 2004. Alternative splicing in disease and therapy. Nat Biotechnol 22: 535-546. (Pubitemid 38585905)
18. Griffith M, Tang MJ, Griffith OL, Morin RD, Chan SY, Asano JK, Zeng T, Flibotte S, Ally A, Baross A, et al. 2008. ALEXA: a microarray design platform for alternative expression analysis. Nat Methods 5: 118. doi: 10.1038/nmeth0208-118. (Pubitemid 351181731)
19. Hastings M, Milcarek C, Martincic K, Peterson M, Munroe S. 1997. Expression of the thyroid hormone receptor gene, erbAα, in B lymphocytes: Alternative mRNA processing is independent of differentiation but correlates with antisense RNA levels. Nucleic Acids Res 25: 4296-4300. (Pubitemid 27485208)
20. Huang RS, Duan S, Bleibel WK, Kistner EO, Zhang W, Clark TA, Chen TX, Schweitzer AC, Blume JE, Cox NJ, et al. 2007. A genome-wide approach to identify genetic variants that contribute to etoposide-induced cytotoxicity. Proc Natl Acad Sci 104: 9758-9763. (Pubitemid 47175340)
21. Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, et al. 2002. The Ensembl genome database project. Nucleic Acids Res 30: 38-41. (Pubitemid 34679498)
22. Kapranov P, Drenkow J, Cheng J, Long J, Helt G, Dike S, Gingeras TR. 2005. Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. Genome Res 15: 987-997. (Pubitemid 40994219)
23. Kiyosawa H, Mise N, Iwase S, Hayashizaki Y, Abe K. 2005. Disclosing hidden transcripts: Mouse natural sense-antisense transcripts tend to be poly(A) negative and nuclear localized. Genome Res 15: 463-474. (Pubitemid 41057810)
24. Krystal GW, Armstrong BC, Battey JF. 1990. N-myc mRNA forms an RNA-RNA duplex with endogenous antisense transcripts. Mol Cell Biol 10: 4180-4191.
25. Kuersten S, Goodwin EB. 2003. The power of the 3′ UTR: translational control and development. Nat Rev Genet 4: 626-637. (Pubitemid 36917504)
26. Kulaeva OI, Gaykalova DA, Pestov NA, Golovastov VV, Vassylyev DG, Artsimovitch I, Studitsky VM. 2009. Mechanism of chromatin remodeling and recovery during passage of RNA polymerase II. Nat Struct Mol Biol 16: 1272-1278.
27. Lavorgna G, Dahary D, Lehner B, Sorek R, Sanderson CM, Casari G. 2004. In search of antisense. Trends Biochem Sci 29: 88-94. (Pubitemid 38186579)
28. Levin JZ, Yassour M, Adiconis X, Nusbaum C, Thompson DA, Friedman N, Gnirke A, Regev A. 2010. Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat Methods 7: 709-715.
29. Licatalosi DD, Darnell RB. 2010. RNA processing and its regulation: global insights into biological networks. Nat Rev Genet 11: 75-87.
30. Listerman I, Sapra AK, Neugebauer KM. 2006. Cotranscriptional coupling of splicing factor recruitment and precursor messenger RNA splicing in mammalian cells. Nat Struct Mol Biol 13: 815-822. (Pubitemid 44338776)
31. Liu G, Loraine A, Shigeta R, Cline M, Cheng J, Valmeekam V, Sun S, Kulp D, Siani-Rose M. 2003. NetAffx: Affymetrix probesets and annotations. Nucleic Acids Res 31: 82-86.
32. Louro R, Nakaya H, Amaral P, Festa F, Sogayar M, da Silva A, Verjovski-Almeida S, Reis E. 2007. Androgen responsive intronic non-coding RNAs. BMC Biol 5: 4. doi: 10.1186/1741-7007-5-4.
33. Mattick J. 2004. RNA regulation: a new genetics? Nat Rev Genet 5: 316-323. (Pubitemid 38435628)
34. Mihalich A, Reina M, Mangioni S, Ponti E, Alberti L, Vigano P, Vignali M, Di Blasio AM. 2003. Different basic fibroblast growth factor and fibroblast growth factor-antisense expression in eutopic endometrial stromal cells derived from women with and without endometriosis. J Clin Endocrinol Metab 88: 2853-2859. (Pubitemid 36724467)
35. Morrissy AS, Morin RD, Delaney A, Zeng T, McDonald H, Jones S, Zhao Y, Hirst M, Marra MA. 2009. Next-generation tag sequencing for cancer gene expression profiling. Genome Res 19: 1825-1835.
36. Nahkuri S, Taft RJ, Mattick JS. 2009. Nucleosomes are preferentially positioned at exons in somatic and sperm cells. Cell Cycle 8: 3420-3424.
37. 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. doi: 10.1093/nar/gkp596.
38. R Development Core Team. 2008. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna. http://www.R-project.org.
39. Reis E, Nakaya H, Louro R, Canavez F, Flatschart A, Almeida G, Egidio C, Paquola A, Machado A, Festa F, et al. 2004. Antisense intronic non-coding RNA levels correlate to the degree of tumor differentiation in prostate cancer. Oncogene 23: 6684-6692. (Pubitemid 39265533)
40. RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group) and the FANTOM Consortium, 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.
41. Romanish MT, Nakamura H, Lai CB, Wang Y, Mager DL. 2009. A novel protein isoform of the multicopy human NAIP gene derives from intragenic Alu SINE promoters. PLoS ONE 4: e5761. doi: 10.1371/journal.pone.0005761.
42. Rosenbloom KR, Dreszer TR, Pheasant M, Barber GP, Meyer LR, Pohl A, Raney BJ, Wang T, Hinrichs AS, Zweig AS, et al. 2010. ENCODE whole-genome data in the UCSC Genome Browser. Nucleic Acids Res 38: D620-D625.
43. SantaLucia J Jr. 1998. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci 95: 1460-1465.
44. Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, Wang Z, Wei G, Zhao K. 2008. Dynamic regulation of nucleosome positioning in the human genome. Cell 132: 887-898. (Pubitemid 351312809)
45. Schwartz S, Meshorer E, Ast G. 2009. Chromatin organization marks exon-intron structure. Nat Struct Mol Biol 16: 990-995.
46. Shearwin KE, Callen BP, Egan JB. 2005. Transcriptional interference - a crash course. Trends Genet 21: 339-345. (Pubitemid 40726391)
47. Spielman RS, Bastone LA, Burdick JT, Morley M, Ewens WJ, Cheung VG. 2007. Common genetic variants account for differences in gene expression among ethnic groups. Nat Genet 39: 226-231. (Pubitemid 46184354)
48. Spies N, Nielsen CB, Padgett RA, Burge CB. 2009. Biased chromatin signatures around polyadenylation sites and exons. Mol Cell 36: 245-254.
49. Storey JD, Madeoy J, Strout JL, Wurfel M, Ronald J, Akey JM. 2007. Gene-expression variation within and among human populations. Am J Hum Genet 80: 502-509.
50. Tilgner H, Nikolaou C, Althammer S, Sammeth M, Beato M, Valcarcel J, Guigo R. 2009. Nucleosome positioning as a determinant of exon recognition. Nat Struct Mol Biol 16: 996-1001.
51. Tufarelli C, Sloane Stanley JA, Garrick D, Sharpe JA, Ayyub H, Wood WG, Higgs DR. 2003. Transcription of antisense RNA leading to gene silencing and methylation as a novel cause of human genetic disease. Nat Genet 34: 157-165. (Pubitemid 36666926)
52. Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, Zeng K, Malek JA, Costa G, McKernan K, et al. 2008. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res 18: 1051-1063. (Pubitemid 351931156)
53. Vanhee-Brossollet C, Vaquero C. 1998. Do natural antisense transcripts make sense in eukaryotes? Gene 211: 1-9. (Pubitemid 28200918)
54. Wang Z, Burge CB. 2008. Splicing regulation: From a parts list of regulatory elements to an integrated splicing code. RNA 14: 802-813. (Pubitemid 351574901)
55. Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB. 2008. Alternative isoform regulation in human tissue transcriptomes. Nature 456: 470-476. (Pubitemid 352759009)
56. Wright SP. 1992. Adjusted P-values for simultaneous inference. Biometrics 48: 1005-1013. (Pubitemid 23066474)
57. Yan M-D, Hong C-C, Lai G-M, Cheng A-L, Lin Y-W, Chuang S-E. 2005. Identification and characterization of a novel gene Saf transcribed from the opposite strand of Fas. Hum Mol Genet 14: 1465-1474. (Pubitemid 40823456)
58. Zhang Y, Liu XS, Liu QR, Wei L. 2006. Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species. Nucleic Acids Res 34: 3465-3475.
59. Zhang W, Duan S, Kistner EO, Bleibel WK, Huang RS, Clark TA, Chen TX, Schweitzer AC, Blume JE, Cox NJ, et al. 2008. Evaluation of genetic variation contributing to differences in gene expression between populations. Am J Hum Genet 82: 631-640.