Systematic analysis of alternative promoters correlated with alternative splicing in human genes

Genomics

Volumn 93, Issue 5, 2009, Pages 420-425

  Ma, Xiaojuan ^a,b   Li Ling, Jesse ^c,d   Huang, Qianli ^b   Chen, Xi ^a   Hou, Lin ^a   Ma, Fei ^b  

^a LIAONING NORMAL UNIVERSITY   (China)

^b NANJING NORMAL UNIVERSITY   (China)

^c CHINA MEDICAL UNIVERSITY   (China)

^d NORTHEASTERN UNIVERSITY   (China)

Author keywords

Alternative promoter; Alternative splicing; CpG islands; Human genome; Regulatory elements

Indexed keywords

ALTERNATIVE RNA SPLICING; ARTICLE; BINDING SITE; CPG ISLAND; DNA BASE COMPOSITION; GENE EXPRESSION; HUMAN; PRIORITY JOURNAL; PROMOTER REGION; REGULATORY SEQUENCE; STATISTICAL ANALYSIS; TATA BOX; TRANSCRIPTION FACTOR BINDING SITE; TRANSCRIPTION INITIATION SITE;

ALTERNATIVE SPLICING; BASE COMPOSITION; BASE SEQUENCE; BINDING SITES; HUMANS; PROMOTER REGIONS, GENETIC; REPETITIVE SEQUENCES, NUCLEIC ACID; SEQUENCE ANALYSIS, DNA; TRANSCRIPTION FACTORS; TRANSCRIPTION INITIATION SITE; TRANSCRIPTION, GENETIC;

EID: 64149128626     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2009.01.008     Document Type: Article

References (48)

1. Stamm S., et al. Function of alternative splicing. Gene 344 (2005) 1-20
2. Maniatis T., and Tasic B. Alternative pre-mRNA splicing and proteome expansion in metazoans. Nature 418 (2002) 236-243
3. Kan Z., States D., and Gish W. Selecting for functional alternative splices in ESTs. Genome Res. 12 (2002) 1837-1845
4. Modrek B., and Lee C. A genomic view of alternative splicing. Nat. Genet. 30 (2002) 13-19
5. Modrek B., and Lee C.J. Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss. Nat. Genet. 34 (2003) 177-180
6. Lander E.S., et al. Initial sequencing and analysis of the human genome. Nature 409 (2001) 860-921
7. Caceres J.F., and Kornblihtt A.R. Alternative splicing: multiple control mechanisms and involvement in human disease. Trends Genet. 18 (2002) 186-193
8. Dredge B.K., Polydorides A.D., and Darnell R.B. The splice of life: alternative splicing and neurological disease. Nat. Rev. Neurosci. 2 (2001) 43-50
9. Garcia-Blanco M.A., Baraniak A.P., and Lasda E.L. Alternative splicing in disease and therapy. Nat. Biotechnol. 22 (2004) 535-546
10. Kimura K., et al. Diversification of transcriptional modulation: large-scale of human genes identification and characterization of putative alternative promoters. Genome Res. 16 (2006) 55-65
11. Maniatis T., and Reed R. An extensive network of coupling among gene expression machines. Nature 416 (2002) 499-506
12. Das R., et al. Functional coupling of RNAP II transcription to spliceosome assembly. Genes Dev. 20 (2006) 1100-1109
13. Dye M.J., Gromak N., and Proudfoot N. Exon tethering in transcription by RNA polymerase II. Mol. Cell 21 (2006) 849-859
14. Listerman I., Sapra A.K., and Neugebauer K.M. Cotranscriptional coupling of splicing factor recruitment and precursor messenger RNA splicing in mammalian cells. Nat. Struct. Mol. Biol. 13 (2006) 815-822
15. Meshorer E., et al. Combinatorial complexity of 5′ alternative acetylcholinesterase transcripts and protein products. J. Biol. Chem. 279 (2004) 29740-29751
16. Viegas L.R., Vicent G.P., Baranao J.L., Beato M., and Pecci A. Steroid hormones induce bcl-X gene expression through direct activation of distal promoter P4. J. Biol. Chem. 279 (2004) 9831-9839
17. Cramer P., Pesce C.G., Baralle F.E., and Kornblihtt A.R. Functional association between promoter structure and transcript alternative splicing. Proc. Natl. Acad. Sci. 94 (1997) 11456-11460
18. Kornblihtt A.R. Promoter usage and alternative splicing. Curr Opin Cell Biol. 17 (2005) 262-268
19. Parra M.K., Tan J.S., Mohandas N., and Conboy J.G. Intrasplicing coordinates alternative first exons with alternative splicing in the protein 4.1R gene. EMBO J. 27 (2008) 122-131
20. Abnizova I., Boekhorst R., Walter K., and Gilks W.R. Some statistical properties of regulatory DNA sequences, and their use in predicting regulatory regions in the Drosophila genome: the fluffy-tail test. BMC Bioinformatics 6 (2005) 109
21. Xuan Z., Zhao F., Wang J., Chen G., and Zhang M.Q. Genome-wide promoter extraction and analysis in human, mouse, and rat. Genome Biol. 6 (2005) R72
22. Kadener S., et al. Antagonistic effects of T-Ag and VP16 reveal a role for RNA pol II elongation on alternative splicing. EMBO J. 20 (2001) 5759-5768
23. Bird A.P. CpG-rich islands and the function of DNA methylation. Nature 321 (1986) 209-213
24. Smale S.T., and Kadonaga J.T. The RNA polymerase II core Promoter. Annu. Rev. Biochem. 72 (2003) 449-479
25. Yamashita R., Suzuki Y., Sugano S., and Nakai K. Genome-wide analysis reveals strong correlation between CpG islands with nearby transcription start sites of genes and their tissue specificity. Gene 350 (2005) 129-136
26. Gardiner-Garden M., and Frommer M. CpG islands in vertebrate genomes. J. Mol. Biol. 196 (1987) 261-282
27. Szafranski K., Lehmann R., Parra G., Guigo R., and Glöckner G. Gene organization features in A/T-rich organisms. J. Mol. Evol. 60 (2005) 90-98
28. Aerts S., Thijs G., Dabrowski M., Moreau Y., and De Moor B. Comprehensive analysis of the base composition around the transcription start site in Metazoa. BMC Genomics 5 (2004) 34
29. Vinogradov A.E. DNA helix: the importance of being GC-rich. Nucleic Acids Res. 31 (2003) 1838-1844
30. Bajic V.B., et al. Mice and men: their promoter properties. PLoS Genet. 2 (2006) e45
31. International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 409 (2001) 860-921
32. Simons C., Pheasant M., Makunin I.V., and Mattick J.S. Transposon-free regions in mammalian genomes. Genome Res. 16 (2006) 164-172
33. Batzer M.A., and Deininger P.L. Alu repeats and human genomic diversity. Nat. Rev. Genet. 3 (2002) 370-379
34. Chen J.M., Stenson P.D., Cooper D.N., and Ferec C.A. Systematic analysis of LINE-1 endonuclease-dependent retrotranspositional events causing human genetic disease. Hum. Genet. 117 (2005) 411-427
35. Hedges D.J., and Batzer M.A. From the margins of the genome: mobile elements shape primate evolution. Bioessays 27 (2005) 785-794
36. Marino-Ramirez L., and Jordan I.K. Transposable element derived DnaseI-hyper sensitive sites in the human genome. Biol. Direct. 1 (2006) 20
37. Kashi Y., and King D.G. Simple sequence repeats as advantageous mutators in evolution. Trends Genet. 22 (2006) 253-259
38. Zheng C.L., Fu X.D., and Gribskov M. Characteristics and regulatory elements defining constitutive splicing and different modes of alternative splicing in human and mouse. RNA 11 (2005) 1777-1787
39. Tirosh I., and Barkai N. Two strategies for gene regulation by promoter nucleosomes. Genome Res. 18 (2008) 1084-1091
40. Eichler E.E., and Sankoff D. Structural dynamics of eukaryotic chromosome evolution. Science 301 (2003) 793-797
41. Versteeg R., et al. The human transcriptome map reveals extremes in gene density, intron length, GC-content, and repeat pattern for domains of highly and weakly expressed genes. Genome Res. 13 (2003) 1998-2004
42. Batada N.N., and Hurst L.D. Evolution of chromosome organization driven by selection for reduced gene expression noise. Nat. Genet. 39 (2007) 945-949
43. Morris D.P., and Greenleaf A.L. The splicing factor, Prp40, binds the phosphorylated carboxyl-terminal domain of RNA polymerase II. J. Biol. Chem. 275 (2000) 39935-39943
44. Rosonina E., et al. Role for PSF in mediating transcriptional activator-dependent stimulation of pre-mRNA processing in vivo. Mol. Cell Biol. 25 (2005) 6734-6746
45. Suzuki Y., Yamashita R., Sugano S., and Nakai K. DBTSS, DataBase of Transcriptional Start Sites: progress report 2004. Nucleic Acids Res. 32 (2004) 78-81
46. Aerts S., et al. TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis. Nucleic Acids Res. 33 (2005) 393-396
47. Wingender E. TRANSFAC, TRANSPATH and CYTOMER as starting points for an ontology of regulatory networks. In Silico Biol. 4 (2004) 55-61
48. Jurka J. Repbase update: a database and an electronic journal of repetitive elements. Trends Genet. 16 (2000) 418-420