The GENCODE pseudogene resource

Genome Biology

Volumn 13, Issue 9, 2012, Pages

  Pei, Baikang ^a   Sisu, Cristina ^a   Frankish, Adam ^b   Howald, Cédric ^c   Habegger, Lukas ^a   Mu, Xinmeng J ^a   Harte, Rachel ^d   Balasubramanian, Suganthi ^a   Tanzer, Andrea ^e   Diekhans, Mark ^d   Reymond, Alexandre ^c   Hubbard, Tim J ^b   Harrow, Jennifer ^b   Gerstein, Mark B ^a,f  

^a YALE UNIVERSITY   (United States)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^c UNIVERSITY OF LAUSANNE   (Switzerland)

^d University of California Santa Cruz   (United States)

^e CENTRE FOR GENOMIC REGULATION CRG   (Spain)

^f Yale University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA POLYMERASE II; TRANSCRIPTION FACTOR;

ARTICLE; BINDING SITE; CHROMATIN; COMPUTER MODEL; FUNCTIONAL GENOMICS; GENE IDENTIFICATION; GENE LOCATION; GENE LOCUS; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC CODE; GENETIC CONSERVATION; GENETIC DATABASE; GENETIC RESOURCE; GENETIC SELECTION; GENETIC VARIABILITY; GENOME ANALYSIS; HUMAN; HUMAN VERSUS ANIMAL COMPARISON; MOLECULAR EVOLUTION; MOUSE; NONHUMAN; PROMOTER REGION; PSEUDOGENE; RAT; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA BINDING; SEQUENCE HOMOLOGY; TISSUE SPECIFICITY; ANIMAL; BIOLOGICAL MODEL; CHEMISTRY; DNA SEQUENCE; GENETIC TRANSCRIPTION; GENETICS; HUMAN GENOME; METABOLISM; MOLECULAR GENETICS; PHYLOGENY; PRIMATE; REGULATORY SEQUENCE; STATISTICAL MODEL;

PRIMATES;

ANIMALS; BINDING SITES; CHROMATIN; GENOME, HUMAN; HUMANS; MODELS, GENETIC; MODELS, STATISTICAL; MOLECULAR SEQUENCE ANNOTATION; PHYLOGENY; PRIMATES; PSEUDOGENES; REGULATORY SEQUENCES, NUCLEIC ACID; RNA POLYMERASE II; SELECTION, GENETIC; SEQUENCE ANALYSIS, DNA; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 84865726286     PISSN: None     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2012-13-9-r51     Document Type: Article

References (64)

1. Mighell AJ, Smith NR, Robinson PA, Markham AF. Vertebrate pseudogenes. FEBS Lett 2000, 468:109-114.
2. Harrison PM, Echols N, Gerstein MB. Digging for dead genes: an analysis of the characteristics of the pseudogene population in the Caenorhabditis elegans genome. Nucleic Acids Res 2001, 29:818-830.
3. Echols N, Harrison PM, Balasubramanian S, Luscombe NM, Bertone P, Zhang Z, B GM. Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes comparing genes and pseudogenes. Nucleic Acids Res 2002, 30:2515-2523.
4. Balakirev E, Ayala F. Pseudogenes: are they "junk" or functional DNA?. Annu Rev Genet 2003, 37:123-151.
5. Zhang ZD, Frankish A, Hunt T, Harrow J, Gerstein MB. Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates. Genome Biol 2010, 11:R26.
6. Harrison PM, Gerstein M. Studying genomes through the aeons: protein families pseudogenes and proteome evolution. J Mol Biol 2002, 318:1155-1174.
7. Vinckenbosch N, Dupanloup I, Kaessmann H. Evolutionary fate of retroposed gene copies Evolutionary fate of retroposed gene copies in the human genome. Proc Natl Acad Sci USA 2006, 103:3220-3225.
8. Ding W, Lin L, Chen B, Dai J. L1 elements processed pseudogenes and retrogenes in mammalian genomes. IUBMB Life 2006, 58:677-685.
9. Karro JE, Yan Y, Zheng D, Zhang Z, Carriero N, Cayting P, Harrison PM, Gerstein M. Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation. Nucleic Acids Res 2007, 35:D55-D60.
10. Ohshima K, Hattori M, Yada T, Gojobori T, Sakaki Y, Okada N. Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates. Genome Biol 2003, 4:R74.
11. Torrents D, Suyama M, Zdobnov E, Bork P. A genome-wide survey of human pseudogenes. Genome Res 2003, 13:2559-2567.
12. Zhang Z, Gerstein M. Large-scale analysis of pseudogenes in the human genome. Curr Opin Genet Dev 2004, 14:328-335.
13. Balasubramanian S, Zheng D, Liu YJ, Fang G, Frankish A, Carriero N, Robilotto R, Cayting P, Gerstein M. Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes. Genome Biol 2009, 10:R2.
14. Harrison PM, Zheng D, Zhang Z, Carriero N, Gerstein M. Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability. Nucleic Acids Res 2005, 33:2374-2383.
15. Svensson T, Arvestad L, Lagergren J. Genome-wide survey for biologically functional pseudogenes. PLoS Comput Biol 2006, 2:e46.
16. Zheng D, Frankish A, Baertsch R, Kapranov P, Reymond A, Woh Choo S, Y L, Denoeud F, Antonarakis SE, Snyder M, Ruan Y, Wei CL, Gingeras TR, Guigó R, Harrow J, Gerstein MB. Pseudogenes in the ENCODE regions: consensus annotation analysis of transcription and evolution. Genome Res 2007, 17:839-851.
17. Firth MC, Wilming LG, Forrest A, Kawaji H, Tan SL, Washlestedt C, Bajic VB, Kai C, Kawai J, Carninci P, Hayashizaki Y, Bailey TL, Huminiecki L. Pseudo-messenger RNA: phantoms of the transcriptome. PLoS Genet 2006, 2:e23.
18. Enrique MM, Nancy M, Miguel AA. Functional evidence of post-transcriptional regulation by pseudogenes. Biochimie 2011, 93:1916-1921.
19. Poliseno L, Salmena L, Zhang J, Carver B, Haveman WJ, Pandolfi PP. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature 2010, 465:1033-1038.
20. Tam OH, Aravin AA, Stein P, Girard A, Murchison EP, Cheloufi S, Hodges E, Anger M, Sachidanandam R, Schultz RM, Hannon GJ. Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature 2008, 453:534-538.
21. Piehler AP, Hellum M, Wenzel JJ, Kaminski E, Haug KB, Kierulf P, Kaminski WE. The human ABC transporter pseudogene family: Evidence for transcription and gene-pseudogene interference. BMC Genomics 2008, 9:165.
22. Han YJ, Ma SF, Yourek G, Park YD, Garcia JG. A transcribed pseudogene of MYLK promotes cell proliferation. FASEB J 2011, 25:2305-2312.
23. Watanabe T, Totoki Y, Toyoda A, Kanedo M, Kuramochi-Miyagawa S, Obata Y, Chiba H, Kohara Y, Kono T, Nakano T, Surani MA, Sakaki Y, Sasaki H. Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature 2008, 453:539-543.
24. Sasidharan R, Gerstein M. Genomics: Protein fossils live on as RNA. Nature 2008, 453:729-731.
25. Guo X, Zhang Z, Gerstein MB, Zheng D. Small RNAs originated from pseudogenes: cis- or trans-acting?. PLoS Comput Biol 2009, 5:e1000449.
26. Hawkins PG, Morris KV. Transcriptional regulation of Oct4 by a long non-coding RNA antisense to Oct4-pseudogene 5. Transcription 2010, 1:165-175.
27. Salmena L, Carracedo A, Pandolfi PP. Tenets of PTEN Tumor Suppression. Cell 2008, 133:403-414.
28. Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, Swarbreck D, Rossier D, Ucla C, Hubbard T, Antonarakis SE, Guigo R. GENCODE: producing a reference annotation for ENCODE. Genome Biol 2006, 7:S4.1-S4.9.
29. Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken B, Barrell D, Zadissa A, Searle S, Barnes I, Bignell A, Boychenko V, Hunt T, Kay M, Mukherjee G, Rajan J, Despacio-Reyes G, Saunders G, Steward C, Harte R, Lin M, Howald C, Tanzer A, Derrien T, Chrast J, Walters N, Balasubramanian S, Pei B, Tress M, et al. GENCODE: The reference human genome annotation for the ENCODE project. Genome Res 2012, doi: 10.1101/gr.135350.111.
30. Cochrane G, Karsch-Mizarchi I, Nakamura Y, . International Nucleotide Sequence Database Collaboration The International Nucleotide Sequence Database Collaboration. Nucleic Acids Res 2011, 39:D15-D18. International Nucleotide Sequence Database Collaboration.
31. Zhu J, Sanborn JZ, Diekhans M, Lowe CB, Pringle TH, Haussler D. Comparative genomics search for losses of long-established genes on the human lineage. PLoS Comput Biol 2007, 3:e247.
32. Duret L, Chureau C, Samain S, Weissenbach J, Avner P. The Xist RNA gene evolved in eutherians by pseudogenization of a protein-coding gene. Science 2006, 312:1653-1655.
33. Kaessmann H, Vinckenbosch N, Long M. RNA-based gene duplication: mechanistic and evolutionary insights. Nat Rev Genet 2010, 10:19-31.
34. PsiDr - The Pseudogene Decoration Resource. , http://www.pseudogenes.org/psidr
35. PsiDr - The Pseudogene Decoration Resource mirror. , http://www.gencodegenes.org/psidr
36. Zhang Z, Carriero N, Zheng D, Karro J, Harrison PM, Gerstein MB. PseudoPipe: an automated pseudogene identification pipeline. Bioinformatics 2006, 22:1437-1439.
37. Baertsch R, Diekans M, Kent WJ, Haussler D, Brosius J. Retrocopy contributions to the evolution of the human genome. BMC Genomics 2008, 9:466.
38. Zhang Z, Carriero N, Gerstein M. Comparative analysis of processed pseudogenes in the mouse and human genomes. Trends Genet 2004, 20:62-67.
39. Clamp M, Fry B, Kamal M, Xie X, Cuff J, Lin MF, Kellis M, Lindblad-Toh K, Lander ES. Distinguishing protein-coding and noncoding genes in the human genome. Proc Natl Acad Sci USA 2007, 104:19428-19433.
40. Zhang Z, Harrison P, Gerstein M. Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome. Genome Res 2002, 12:1466-1482.
41. Liu YJ, Zheng D, Balasubramanian S, Carriero N, Khurana E, Robilotto R, Gerstein MB. Comprehensive analysis of the pseudogenes of glycolytic enzymes in vertebrates: the anomalously high number of GAPDH pseudogenes highlights a recent burst of retrotrans-positional activity. BMC Genomics 2009, 10:480.
42. Zhang Z, Carriero N, Gerstein MB. Comparative analysis of processed pseudogenes in the mouse and human genomes. Trends Genet 2004, 20:62-67.
43. Kim PM, Lam HY, Urban AE, Korbel JO, Affourtit J, Grubert F, Chen X, Weissman S, Snyder M, Gerstein MB. Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history. Genome Res 2008, 18:1865-1874.
44. Howald C, Tanzer A, Chrast J, Kokocinski F, Derrien T, Walters N, Gonzalez JM, Frankish A, Aken BL, Hourlier T, Vogel JH, White S, Searle MJ, Harrow J, Hubbard T, Guigo R, Reymond A. Experimental validation of the GENCODE annotation reveals that RNAseq transcriptome profiling pinpoints a large number of new linc genes but commonly misses rare transcripts. Genome Res 2012, doi: 10.1101/gr.134478.111.
45. Washietl S, Pedersen JS, Korbel JO, Stocsits C, Gruber AR, Hackermüller J, Hertel J, Lindemeyer M, Reiche K, Tanzer A, Ucla C, Wyss C, Antonarakis SE, Denoeud F, Lagarde J, Drenkow J, Kapranov P, Gingeras TR, Guigó R, Snyder M, Gerstein MB, Reymond A, Hofacker IL, Stadler PF. Structured RNAs in the ENCODE selected regions of the human genome. Genome Res 2007, 17:852-864.
46. Denoeud F, Kapranov P, Ucla C, Frankish A, Castelo R, Drenkow J, Lagarde J, Alioto T, Manzano C, Chrast J, Dike S, Wyss C, Henrichsen CN, Holroyd N, Dickson MC, Taylor R, Hance Z, Foissac S, Myers RM, Rogers J, Hubbard T, Harrow J, Guigó R, Gingeras TR, Antonarakis SE, Reymond A. Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Res 2007, 17:746-759.
47. The 1000 Genomes Project Consortium A map of human genome variation from population-scale sequencing. Nature 2010, 467:1061-1073. The 1000 Genomes Project Consortium.
48. Hoffman M, Ernst J, Wilder S, Harris B, Dunham I, Hardison R, Birney E, Kellis M, Stafford Noble W. Unsupervised segmentation of ENCODE chromatin data. Genome Res 2012, GRCP011.
49. Yip KY, Cheng C, Bhardwaj N, Brown JB, Leng J, Kundaje A, Rozowsky J, Birney E, Bickel PJ, Snyder M, Gerstein MB. Genome-wide analysis of the binding sites of more than 100 transcription-related factors defines different types of genomic regions with distinct biological properties. Genome Res 2012, GRPC033.
50. Zheng D, Gerstein MB. The ambiguous boundary between genes and pseudogenes: the dead rise up or do they?. Trends Genet 2007, 23:219-224.
51. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402.
52. Searle SM, Gilbert J, Iyer V, Clamp M. The otter annotation system. Genome Res 2004, 14:963-970.
53. Sonnhammer ELL, Durbin R. A workbench for large scale sequence homology analysis. Comput Appl Biosci 1994, 10:301-307.
54. Harris R. Improved pairwise alignment of genomic DNA. PhD Thesis 2007, Pennsylvania State University.
55. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Hausler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res 2003, 13:103-107.
56. Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res 2002, 12:656-664.
57. Kent WJ, Baertsch R, Hinrichs A, Miller W, Hausler D. Evolution's cauldron: Duplication deletion and rearrangement in the mouse and human genomes. Proc Natl Acad Sci USA 2003, 100:11484-11489.
58. Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, Cline MS, Goldman M, Barber GP, Clawson H, Coelho A, Diekhans M, Dreszer TR, Giardine BM, Harte RA, Hillman-Jackson J, Hsu F, Kirkup V, Kuhn RM, Learned K, Li CH, Meyer LR, Pohl A, Raney BJ, Rosenbloom KR, Smith KE, Haussler D, Kent WJ. The UCSC Genome Browser database: update 2011. Nucleic Acids Res 2010, (39):1-7.
59. Wilming LG, Gilbert JG, Howe K, Trevanion S, Hubbard T, Harrow JL. The vertebrate genome annotation (Vega) database. Nucleic Acids Res 2008, 36:D753-D760.
60. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10:R25.
61. Habegger L, Sboner A, Gianoulis TA, Rozowsky J, Agarwal A, Snyder M, Gerstein MB. RSEQtools: a modular framework to analyze RNA-Seq data using compact anonymized data summaries. Bioinformatics 2011, 27:281-283.
62. Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Stat Soc B 1995, 57:289-300.
63. Heintzman ND, Stuart RK, Fu Y, Ching CW, Hawkins RD, Barrera LO, Van Calcar S, Qu C, Ching KA, Wang W, Weng Z, Green RD, Crawford GE, Ren B. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet 2007, 39:311-318.
64. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K. High-resolution profiling of histone methylations in the human genome. Cell 2007, 129:823-837.