pseudoMap: An innovative and comprehensive resource for identification of siRNA-mediated mechanisms in human transcribed pseudogenes

Database

Volumn 2013, Issue , 2013, Pages

  Chan, Wen Ling ^a   Yang, Wen Kuang ^b,c   Huang, Hsien Da ^a   Chang, Jan Gowth ^b,d  

^a NATIONAL CHIAO TUNG UNIVERSITY   (Taiwan)

^b CHINA MEDICAL UNIVERSITY HOSPITAL   (Taiwan)

^c CHINA MEDICAL UNIVERSITY   (Taiwan)

^d CHINA MEDICAL UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; SMALL INTERFERING RNA;

ANIMAL; ARTICLE; COMPUTER INTERFACE; DNA SEQUENCE; GENE EXPRESSION REGULATION; GENETIC DATABASE; GENETIC TRANSCRIPTION; GENETICS; HUMAN; INTERNET; METABOLISM; MOUSE; PSEUDOGENE;

ANIMALS; DATABASES, GENETIC; GENE EXPRESSION REGULATION; HUMANS; INTERNET; MICE; MICRORNAS; PSEUDOGENES; RNA, SMALL INTERFERING; SEQUENCE ANALYSIS, DNA; TRANSCRIPTION, GENETIC; USER-COMPUTER INTERFACE;

MLCS; MLOWN;

EID: 84879346069     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bat001     Document Type: Article

References (56)

1. Mighell,A.J., Smith,N.R., Robinson,P.A. et al. (2000) Vertebrate pseudogenes. FEBS Lett., 468, 109-114.
2. Torrents,D., Suyama,M., Zdobnov,E. et al. (2003) A genome-wide survey of human pseudogenes. Genome Res., 13, 2559-2567.
3. Balasubramanian,S., Zheng,D., Liu,Y.J. et al. (2009) Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes. Genome Biol., 10, R2.
4. Harrison,P. and Yu,Z. (2007) Frame disruptions in human mRNA transcripts, and their relationship with splicing and protein structures. BMC Genomics, 8, 371.
5. Harrison,P.M., Zheng,D., Zhang,Z. et al. (2005) Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability. Nucleic Acids Res., 33, 2374-2383.
6. Imanishi,T., Itoh,T., Suzuki,Y. et al. (2004) Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol., 2, e162.
7. Khachane,A.N. and Harrison,P.M. (2009) Assessing the genomic evidence for conserved transcribed pseudogenes under selection. BMC Genomics, 10, 435.
8. Vinckenbosch,N., Dupanloup,I. and Kaessmann,H. (2006) Evolutionary fate of retroposed gene copies in the human genome. Proc. Natl Acad. Sci. USA, 103, 3220-3225.
9. Zheng,D., Zhang,Z., Harrison,P.M. et al. (2005) Integrated pseudogene annotation for human chromosome 22: evidence for transcription. J. Mol. Biol., 349, 27-45.
10. Zheng,D., Frankish,A., Baertsch,R. et al. (2007) Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Res., 17, 839-851.
11. McCarrey,J.R. and Riggs,A.D. (1986) Determinator-inhibitor pairs as a mechanism for threshold setting in development: a possible function for pseudogenes. Proc. Natl Acad. Sci. USA, 83, 679-683.
12. Zou,C., Lehti-Shiu,M.D., Thibaud-Nissen,F. et al. (2009) Evolutionary and expression signatures of pseudogenes in Arabidopsis and rice. Plant Physiol., 151, 3-15.
13. Korneev,S. and O'Shea,M. (2002) Evolution of nitric oxide synthase regulatory genes by DNA inversion. Mol. Biol. Evol., 19, 1228-1233.
14. Korneev,S.A., Park,J.H. and O'Shea,M. (1999) Neuronal expression of neural nitric oxide synthase (nNOS) protein is suppressed by an antisense RNA transcribed from an NOS pseudogene. J. Neurosci., 19, 7711-7720.
15. Hirotsune,S., Yoshida,N., Chen,A. et al. (2003) An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene. Nature, 423, 91-96.
16. Gray,T.A., Wilson,A., Fortin,P.J. et al. (2006) The putatively functional Mkrn1-p1 pseudogene is neither expressed nor imprinted, nor does it regulate its source gene in trans. Proc. Natl Acad. Sci. USA, 103, 12039-12044.
17. Poliseno,L., Salmena,L., Zhang,J. et al. (2010) A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature, 465, 1033-1038.
18. Han,Y.J., Ma,S.F., Yourek,G. et al. (2011) A transcribed pseudogene of MYLK promotes cell proliferation. FASEB J., 25, 2305-2312.
19. Kim,D.H. and Rossi,J.J. (2007) Strategies for silencing human disease using RNA interference. Nat. Rev. Genet., 8, 173-184.
20. Czech,B., Malone,C.D., Zhou,R. et al. (2008) An endogenous small interfering RNA pathway in Drosophila. Nature, 453, 798-802.
21. Ghildiyal,M., Seitz,H., Horwich,M.D. et al. (2008) Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cells. Science, 320, 1077-1081.
22. Kawamura,Y., Saito,K., Kin,T. et al. (2008) Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells. Nature, 453, 793-797.
23. Okamura,K., Chung,W.J., Ruby,J.G. et al. (2008) The Drosophila hairpin RNA pathway generates endogenous short interfering RNAs. Nature, 453, 803-806.
24. Tam,O.H., Aravin,A.A., Stein,P. et al. (2008) Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature, 453, 534-538.
25. Watanabe,T., Totoki,Y., Toyoda,A. et al. (2008) Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature, 453, 539-543.
26. Flicek,P., Amode,M.R., Barrell,D. et al. (2012) Ensembl 2012. Nucleic Acids Res., 40, D84-D90.
27. Mituyama,T., Yamada,K., Hattori,E. et al. (2009) The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs. Nucleic Acids Res., 37, D89-D92.
28. Carninci,P., Kasukawa,T., Katayama,S. et al. (2005) The transcriptional landscape of the mammalian genome. Science, 309, 1559-1563.
29. Kozomara,A. and Griffiths-Jones,S. (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res, 39, D152-D157.
30. Griffiths-Jones,S., Saini,H.K., van Dongen,S. et al. (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res., 36, D154-D158.
31. He,S., Liu,C., Skogerbo,G. et al. (2008) NONCODE v2.0: decoding the non-coding. Nucleic Acids Res., 36, D170-D172.
32. Griffiths-Jones,S., Moxon,S., Marshall,M. et al. (2005) Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res., 33, D121-D124.
33. Pang,K.C., Stephen,S., Dinger,M.E. et al. (2007) RNAdb 2.0-an expanded database of mammalian non-coding RNAs. Nucleic Acids Res., 35, D178-D182.
34. Lestrade,L. and Weber,M.J. (2006) snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs. Nucleic Acids Res., 34, D158-D162.
35. Morin,R.D., O'Connor,M.D., Griffith,M. et al. (2008) Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res., 18, 610-621.
36. Seila,A.C., Calabrese,J.M., Levine,S.S. et al. (2008) Divergent transcription from active promoters. Science, 322, 1849-1851.
37. Yeo,G.W., Xu,X., Liang,T.Y. et al. (2007) Alternative splicing events identified in human embryonic stem cells and neural progenitors. PLoS Comput. Biol., 3, 1951-1967.
38. Hou,J., Lin,L., Zhou,W. et al. (2011) Identification of miRNomes in human liver and hepatocellular carcinoma reveals miR-199a/b-3p as therapeutic target for hepatocellular carcinoma. Cancer Cell, 19, 232-243.
39. Kent,W.J., Sugnet,C.W., Furey,T.S. et al. (2002) The human genome browser at UCSC. Genome Res., 12, 996-1006.
40. Zuker,M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406-3415.
41. Hsu,S.D., Chu,C.H., Tsou,A.P. et al. (2008) miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes. Nucleic Acids Res., 36, D165-D169.
42. Friedman,R.C., Farh,K.K., Burge,C.B. et al. (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res., 19, 92-105.
43. Grimson,A., Farh,K.K., Johnston,W.K. et al. (2007) MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol. Cell, 27, 91-105.
44. Lewis,B.P., Burge,C.B. and Bartel,D.P. (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell, 120, 15-20.
45. John,B., Enright,A.J., Aravin,A. et al. (2004) Human MicroRNA targets. PLoS Biol., 2, e363.
46. Kruger,J. and Rehmsmeier,M. (2006) RNAhybrid: microRNA target prediction easy, fast and flexible. Nucleic Acids Res., 34, W451-W454.
47. Barrett,T. and Edgar,R. (2006) Gene expression omnibus: microarray data storage, submission, retrieval, and analysis. Methods Enzymol., 411, 352-369.
48. Su,A.I., Wiltshire,T., Batalov,S. et al. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl Acad. Sci. USA, 101, 6062-6067.
49. Roth,R.B., Hevezi,P., Lee,J. et al. (2006) Gene expression analyses reveal molecular relationships among 20 regions of the human CNS. Neurogenetics, 7, 67-80.
50. Yu,K., Ganesan,K., Tan,L.K. et al. (2008) A precisely regulated gene expression cassette potently modulates metastasis and survival in multiple solid cancers. PLoS Genet., 4, e1000129.
51. Altschul,S.F., Gish,W., Miller,W. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
52. Stelzer,G., Dalah,I., Stein,T.I. et al. (2011) In-silico human genomics with GeneCards. Hum. Genomics, 5, 709-717.
53. Karro,J.E., Yan,Y., Zheng,D. et al. (2007) Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation. Nucleic Acids Res., 35, D55-D60.
54. Khelifi,A., Duret,L. and Mouchiroud,D. (2005) HOPPSIGEN: a database of human and mouse processed pseudogenes. Nucleic Acids Res., 33, D59-D66.
55. Ortutay,C. and Vihinen,M. (2008) PseudoGeneQuest-service for identification of different pseudogene types in the human genome. BMC Bioinformatics, 9, 299.
56. Bischof,J.M., Chiang,A.P., Scheetz,T.E. et al. (2006) Genome-wide identification of pseudogenes capable of disease-causing gene conversion. Hum. Mutat., 27, 545-552.