Bidirectional Promoters as Important Drivers for the Emergence of Species-Specific Transcripts

PLoS ONE

Volumn 8, Issue 2, 2013, Pages

  Gotea, Valer ^a   Petrykowska, Hanna M ^a   Elnitski, Laura ^a  

^a NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

ARTICLE; BIOACCUMULATION; COMPUTER MODEL; EVOLUTIONARY ADAPTATION; FUNCTIONAL GENOMICS; GENETIC CODE; GENETIC CONSERVATION; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; HUMAN; NONHUMAN; NUCLEOTIDE SEQUENCE; PROMOTER REGION; RNA SPLICING; SCORING SYSTEM; SPECIES DIFFERENCE; TRANSCRIPTION INITIATION; TRANSCRIPTOMICS; TRANSPOSON;

ADAPTATION, PHYSIOLOGICAL; ANIMALS; BASE SEQUENCE; CHICKENS; CONSERVED SEQUENCE; DNA TRANSPOSABLE ELEMENTS; EXONS; GENOME, HUMAN; HUMANS; MICE; MOLECULAR SEQUENCE DATA; MUTATION; PROMOTER REGIONS, GENETIC; RNA SPLICE SITES; RNA SPLICING; RNA, MESSENGER; SELECTION, GENETIC; SPECIES SPECIFICITY; TRANSCRIPTION, GENETIC; VERTEBRATES;

EID: 84874523987     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0057323     Document Type: Article

References (54)

1. Conant GC, Wagner A, (2005) The rarity of gene shuffling in conserved genes. Genome Biol 6: R50.
2. Muller HJ, (1918) Genetic Variability, Twin Hybrids and Constant Hybrids, in a Case of Balanced Lethal Factors. Genetics 3: 422-499.
3. Muller HJ, (1935) A viable two-gene deficiency- Phaenotypically resembling the corresponding hypomorphic mutations. Journal of Heredity 26: 469-478.
4. Spofford JB (1969) Heterosis and Evolution of Duplications. American Naturalist 103: 407-&.
5. Nei M, (1969) Gene duplication and nucleotide substitution in evolution. Nature 221: 40-42.
6. Fitch WM, (1966) Evidence suggesting a partial, internal duplication in the ancestral gene for heme-containing globins. J Mol Biol 16: 17-27.
7. Ingram VM, (1961) Gene evolution and the haemoglobins. Nature 189: 704-708.
8. Ohno S (1970) Evolution by gene duplication. Berlin, New York,: Springer-Verlag. xv, 160 p. p.
9. Jacob F, (1977) Evolution and tinkering. Science 196: 1161-1166.
10. Piontkivska H, Yang MQ, Larkin DM, Lewin HA, Reecy J, et al. (2009) Cross-species mapping of bidirectional promoters enables prediction of unannotated 5′ UTRs and identification of species-specific transcripts. BMC Genomics 10: 189.
11. Yang Z, Huang J, (2011) De novo origin of new genes with introns in Plasmodium vivax. FEBS Lett 585: 641-644.
12. Cai J, Zhao R, Jiang H, Wang W, (2008) De novo origination of a new protein-coding gene in Saccharomyces cerevisiae. Genetics 179: 487-496.
13. Carvunis AR, Rolland T, Wapinski I, Calderwood MA, Yildirim MA, et al. (2012) Proto-genes and de novo gene birth. Nature.
14. Levine MT, Jones CD, Kern AD, Lindfors HA, Begun DJ, (2006) Novel genes derived from noncoding DNA in Drosophila melanogaster are frequently X-linked and exhibit testis-biased expression. Proc Natl Acad Sci U S A 103: 9935-9939.
15. Begun DJ, Lindfors HA, Kern AD, Jones CD, (2007) Evidence for de novo evolution of testis-expressed genes in the Drosophila yakuba/Drosophila erecta clade. Genetics 176: 1131-1137.
16. Zhou Q, Zhang G, Zhang Y, Xu S, Zhao R, et al. (2008) On the origin of new genes in Drosophila. Genome Res 18: 1446-1455.
17. Johnson ME, Viggiano L, Bailey JA, Abdul-Rauf M, Goodwin G, et al. (2001) Positive selection of a gene family during the emergence of humans and African apes. Nature 413: 514-519.
18. Toll-Riera M, Bosch N, Bellora N, Castelo R, Armengol L, et al. (2009) Origin of primate orphan genes: a comparative genomics approach. Mol Biol Evol 26: 603-612.
19. Knowles DG, McLysaght A, (2009) Recent de novo origin of human protein-coding genes. Genome Res 19: 1752-1759.
20. Kaessmann H, (2010) Origins, evolution, and phenotypic impact of new genes. Genome Res 20: 1313-1326.
21. Seila AC, Calabrese JM, Levine SS, Yeo GW, Rahl PB, et al. (2008) Divergent transcription from active promoters. Science 322: 1849-1851.
22. Preker P, Nielsen J, Kammler S, Lykke-Andersen S, Christensen MS, et al. (2008) RNA exosome depletion reveals transcription upstream of active human promoters. Science 322: 1851-1854.
23. van Bakel H, Nislow C, Blencowe BJ, Hughes TR, (2010) Most "dark matter" transcripts are associated with known genes. PLoS Biol 8: e1000371.
24. Adachi N, Lieber MR, (2002) Bidirectional gene organization: a common architectural feature of the human genome. Cell 109: 807-809.
25. Howald C, Tanzer A, Chrast J, Kokocinski F, Derrien T, et al. (2012) Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome. Genome Res 22: 1698-1710.
26. 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 5Suppl 1: S2.
27. Trinklein ND, Aldred SF, Hartman SJ, Schroeder DI, Otillar RP, et al. (2004) An abundance of bidirectional promoters in the human genome. Genome Res 14: 62-66.
28. Pohl AA, Sugnet CW, Clark TA, Smith K, Fujita PA, et al. (2009) Affy exon tissues: exon levels in normal tissues in human, mouse and rat. Bioinformatics 25: 2442-2443.
29. Jacox E, Gotea V, Ovcharenko I, Elnitski L, (2010) Tissue-specific and ubiquitous expression patterns from alternative promoters of human genes. PLoS One 5: e12274.
30. Brawand D, Soumillon M, Necsulea A, Julien P, Csardi G, et al. (2011) The evolution of gene expression levels in mammalian organs. Nature 478: 343-348.
31. Shimada MK, Hayakawa Y, Takeda J, Gojobori T, Imanishi T, (2010) A comprehensive survey of human polymorphisms at conserved splice dinucleotides and its evolutionary relationship with alternative splicing. BMC Evol Biol 10: 122.
32. Yeo G, Burge CB, (2004) Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J Comput Biol 11: 377-394.
33. Dogan RI, Getoor L, Wilbur WJ, Mount SM, (2007) SplicePort-an interactive splice-site analysis tool. Nucleic Acids Res 35: W285-291.
34. Makalowski W, Mitchell GA, Labuda D, (1994) Alu sequences in the coding regions of mRNA: a source of protein variability. Trends Genet 10: 188-193.
35. Kostka D, Hubisz MJ, Siepel A, Pollard KS, (2012) The role of GC-biased gene conversion in shaping the fastest evolving regions of the human genome. Mol Biol Evol 29: 1047-1057.
36. Hanawalt PC, Spivak G, (2008) Transcription-coupled DNA repair: two decades of progress and surprises. Nat Rev Mol Cell Biol 9: 958-970.
37. Witherspoon DJ, Watkins WS, Zhang Y, Xing J, Tolpinrud WL, et al. (2009) Alu repeats increase local recombination rates. BMC Genomics 10: 530.
38. Ratnakumar A, Mousset S, Glemin S, Berglund J, Galtier N, et al. (2010) Detecting positive selection within genomes: the problem of biased gene conversion. Philos Trans R Soc Lond B Biol Sci 365: 2571-2580.
39. Pollard KS, Salama SR, King B, Kern AD, Dreszer T, et al. (2006) Forces shaping the fastest evolving regions in the human genome. PLoS Genet 2: e168.
40. Woolfe A, Mullikin JC, Elnitski L, (2010) Genomic features defining exonic variants that modulate splicing. Genome Biol 11: R20.
41. Tan-Wong SM, Zaugg JB, Camblong J, Xu Z, Zhang DW, et al. (2012) Gene loops enhance transcriptional directionality. Science 338: 671-675.
42. Lin JM, Collins PJ, Trinklein ND, Fu Y, Xi H, et al. (2007) Transcription factor binding and modified histones in human bidirectional promoters. Genome Res 17: 818-827.
43. Anno YN, Myslinski E, Ngondo-Mbongo RP, Krol A, Poch O, et al. (2011) Genome-wide evidence for an essential role of the human Staf/ZNF143 transcription factor in bidirectional transcription. Nucleic Acids Res 39: 3116-3127.
44. Xie H, Wang M, Bonaldo Mde F, Smith C, Rajaram V, et al. (2009) High-throughput sequence-based epigenomic analysis of Alu repeats in human cerebellum. Nucleic Acids Res 37: 4331-4340.
45. Rubin CM, VandeVoort CA, Teplitz RL, Schmid CW, (1994) Alu repeated DNAs are differentially methylated in primate germ cells. Nucleic Acids Res 22: 5121-5127.
46. Saxena A, Carninci P, (2011) Long non-coding RNA modifies chromatin: epigenetic silencing by long non-coding RNAs. Bioessays 33: 830-839.
47. Orom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, et al. (2010) Long noncoding RNAs with enhancer-like function in human cells. Cell 143: 46-58.
48. Ponting CP, Oliver PL, Reik W, (2009) Evolution and functions of long noncoding RNAs. Cell 136: 629-641.
49. Kalitsis P, Saffery R, (2009) Inherent promoter bidirectionality facilitates maintenance of sequence integrity and transcription of parasitic DNA in mammalian genomes. BMC Genomics 10: 498.
50. Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, et al. (2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 15: 1034-1050.
51. Goecks J, Nekrutenko A, Taylor J, (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 11: R86.
52. Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, et al. (2005) Galaxy: a platform for interactive large-scale genome analysis. Genome Res 15: 1451-1455.
53. Tang H, Lewontin RC, (1999) Locating regions of differential variability in DNA and protein sequences. Genetics 153: 485-495.
54. Katzman S, Kern AD, Pollard KS, Salama SR, Haussler D, (2010) GC-biased evolution near human accelerated regions. PLoS Genet 6: e1000960.