Distribution and characterization of regulatory elements in the human genome

Genome Research

Volumn 12, Issue 12, 2002, Pages 1827-1836

  Majewski, Jacek ^a   Ott, Jurg ^a  

^a ROCKEFELLER UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DINUCLEOTIDE; NUCLEOTIDE; TRINUCLEOTIDE;

CPG ISLAND; EXON; GENE EXPRESSION; GENETIC TRANSCRIPTION; HUMAN; HUMAN GENOME; INTRON; PRIORITY JOURNAL; REGULATORY SEQUENCE; REVIEW; RNA SPLICING; TRANSCRIPTION REGULATION;

BASE COMPOSITION; CHROMOSOME MAPPING; DATABASES, GENETIC; DNA TRANSPOSABLE ELEMENTS; EXONS; GENOME, HUMAN; HUMANS; INTRONS; MICROSATELLITE REPEATS; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; REGULATORY SEQUENCES, NUCLEIC ACID; SHORT INTERSPERSED NUCLEOTIDE ELEMENTS;

EID: 0036911605     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.606402     Document Type: Review

References (36)

1. Ars, E., Serra, E., Garcia, J., Kruyer, H., Gaona, A., Lazaro, C., and Estivill, X. 2000. Mutations affecting mRNA splicing are the most common molecular defects in patients with neurofibromatosis type 1. Hum. Mol. Genet. 9: 237-247.
2. Bernardi, G. 2000. Isochores and the evolutionary genomics of vertebrates. Gene 241: 3-17.
3. Bernardi, G., Olofsson, B., Filipski, J., Zerial, M., Salinas, J., Cuny, G., Meunier-Rotival, M., and Rodier, F. 1985. The mosaic genome of warm-blooded vertebrates. Science 228: 953-958.
4. Blencowe, B.J. 2000. Exonic splicing enhancers: Mechanism of action, diversity and role in human genetic diseases. Trends Biochem. Sci. 25: 106-110.
5. Brett, D., Hanke, J., Lehmann, G., Haase, S., Delbruck, S., Krueger, S., Reich, J., and Bork, P. 2000. EST comparison indicates 38% of human mRNAs contain possible alternative splice forms. FEBS Lett. 474: 83-86.
6. Brudno, M., Gelfand, M.S., Spengler, S., Zorn, M., Dubchak, I., and Conboy, J.G. 2001. Computational analysis of candidate intron regulatory elements for tissue-specific alternative pre-mRNA splicing. Nucleic Acids Res. 29: 2338-2348.
7. Campanero, M.R., Armstrong, M.I., and Flemington, E.K. 2000. CpG methylation as a mechanism for the regulation of E2F activity. Proc. Natl. Acad. Sci. 97: 6481-6486.
8. Carlo, T., Sierra, R., and Berget, S.M. 2000. A 5′ splice site-proximal enhancer binds SF1 and activates exon bridging of a microexon. Mol. Cell. Biol. 20: 3988-3995.
9. Cartegni, L., Chew, S.L., and Krainer, A.R. 2002. Listening to silence and understanding nonsense: Exonic mutations that affect splicing. Nat. Rev. Genet. 3: 285-298.
10. Cross, S.H. and Bird, A.P. 1995. CpG islands and genes. Curr. Opin. Genet. Dev. 5: 309-314.
11. Davuluri, R.V., Suzuki, Y., Sugano, S., and Zhang, M.Q. 2000. CART classification of human 5′ UTR sequences. Genome Res. 10: 1807-1816.
12. Deutsch, M. and Long, M. 1999. Intron-exon structures of eukaryotic model organisms. Nucleic Acids Res. 27: 3219-3228.
13. Engelbrecht J., Knudsen S., and Brunak S. 1992. G+C-rich tract in 5′ end of human introns. J. Mol. Biol. 227: 108-113.
14. Fairbrother, W.G., Yeh, R.F., Sharp, P.A., and Burge, C.B. 2002. Predictive identification of exonic splicing enhancers in human genes. Science 297: 1007-1013.
15. Hastings, M. L., and Krainer, A. R. 2001. Pre-mRNA splicing in the new millennium. Curr. Opin. Cell. Biol. 13: 302-309.
16. Hastings, M.L., Wilson, C.M., and Munroe, S.H. 2001. A purine-rich intronic element enhances alternative splicing of thyroid hormone receptor mRNA. RNA 7: 859-874.
17. Jensen, K.B., Dredge, B.K., Stefani, G., Zhong, R., Buckanovich, R.J., Okano, H.J., Yang, Y.Y., and Darnell, R.B. 2000. Nova-1 regulates neuron-specific alternative splicing and is essential for neuronal viability. Neuron 25: 359-371.
18. Kent, W.J. and Zahler, A.M. 2000. Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment. Genome Res. 10: 1115-1125.
19. Kent, W.J., Sugnet, C.W., Furey, T.S., Roskin, K.M., Pringle, T.H., Zahler, A.M., and Haussler, A.D. 2002. The Human Genome Browser at UCSC. Genome Res. 12: 996-1006.
20. Klesert, T.R., Otten, A.D., Bird, T.D., and Tapscott, S.J. 1997. Trinucleotide repeat expansion at the myotonic dystrophy locus reduces expression of DMAHP. Nat. Genet. 16: 402-406.
21. Lamb, B.T., Satyamoorthy, K., Li, L., Solter, D., and Howe, C.C. 1991. CpG methylation of an endogenous retroviral enhancer inhibits transcription factor binding and activity. Gene Expr. 1: 185-196
22. Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., et al. 2001. Initial sequencing and analysis of the human genome. Nature 409: 860-921.
23. Lim, L.P. and Burge, C.B. 2001. A computational analysis of sequence features involved in recognition of short introns. Proc. Natl. Acad. Sci. 98: 11193-11198.
24. Makalowski, W. 2000. Genomic scrap yard: How genomes utilize all that junk. Gene 259: 61-67.
25. McCullough, A.J. and Berget, S.M. 1997. G triplets located throughout a class of small vertebrate introns enforce intron borders and regulate splice site selection. Mol. Cell. Biol. 17: 4562-4571.
26. McCullough, A.J. and Schuler, M.A. 1997. Intronic and exonic sequences modulate 5′ splice site selection in plant nuclei. Nucleic Acids Res. 25: 1071-1077.
27. Mironov, A.A., Fickett, J.W., and Gelfand, M.S. 1999. Frequent alternative splicing of human genes. Genome Res. 9: 1288-1293.
28. Nekrutenko, A. and Li, W.H. 2001. Transposable elements are found in a large number of human protein-coding genes. Trends Genet. 17: 619-621.
29. Rowen, L., Young, J., Birditt, B., Kaur, A., Madan, A., Philipps, D.L., Qin, S., Minx, P., Wilson, R.K., Hood, L., et al. 2002. Analysis of the human neurexin genes: Alternative splicing and the generation of protein diversity. Genomics 79: 587-597.
30. Sachidanandam, R., Weissman, D., Schmidt, S.C., Kakol, J.M., Stein, L.D., Marth, G., Sherry, S., Mullikin, J.C., Mortimore, B.J., Willey, D.L., et al. 2001. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409: 928-933.
31. Siegfried, Z., Eden, S., Mendelsohn, M., Feng, X., Tsuberi, B.Z., and Cedar, H. 1999. DNA methylation represses transcription in vivo. Nat. Genet. 22: 203-206.
32. Sirand-Pugnet, P., Durosay, P., Brody, E., and Marie, J. 1995. An intronic (A/U)GGG repeat enhances the splicing of an alternative intron of the chicken β-tropomyosin pre-mRNA. Nucleic Acids Res. 23: 3501-3507.
33. Smit, A.F. 1996. The origin of interspersed repeats in the human genome. Curr. Opin. Genet. Dev. 6: 743-748.
34. Suzuki, Y., Yamashita, R., Nakai, K., and Sugano, S. 2002. DBTSS: Database of human transcriptional start sites and full-length cDNAs. Nucleic Acids Res. 30: 328-331.
35. Takai, D. and Jones, P.A. 2002. Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc. Natl. Acad. Sci. 99: 3740-3745.
36. Zheng, Z.M., Quintero, J., Reid, E.S., Gocke, C., and Baker, C.C. 2000. Optimization of a weak 3′ splice site counteracts the function of a bovine papillomavirus type 1 exonic splicing suppressor in vitro and in vivo. J. Virol. 74: 5902-5910.