Distribution and intensity of constraint in mammalian genomic sequence

Genome Research

Volumn 15, Issue 7, 2005, Pages 901-913

  Cooper, Gregory M ^a   Stone, Eric A ^a,b   Asimenos, George ^c   Green, Eric D ^d   Batzoglou, Serafim ^c   Sidow, Arend ^a,b  

^a STANFORD UNIVERSITY   (United States)

^b STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c Stanford University   (United States)

^d NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SUBSTITUTION; ARTICLE; CORRELATION ANALYSIS; DNA SEQUENCE; EVOLUTION; GENE CLUSTER; GENE LOCUS; GENOME; GENOME ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; STATISTICAL SIGNIFICANCE;

ANIMALS; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; CYSTIC FIBROSIS TRANSMEMBRANE CONDUCTANCE REGULATOR; EVOLUTION, MOLECULAR; GENE COMPONENTS; GENE EXPRESSION PROFILING; GENOME; HUMANS; INTERSPERSED REPETITIVE SEQUENCES; MAMMALS; MOLECULAR SEQUENCE DATA; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID;

MAMMALIA;

EID: 22244452677     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.3577405     Document Type: Article

References (63)

1. Aparicio, S., Chapman, J., Stupka, E., Putnam, N., Chia, J.M., Dehal, P., Christoffels, A., Rash, S., Hoon, S., Smit, A., et al. 2002. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297: 1301-1310.
2. Arnone, M.I. and Davidson, E.H. 1997. The hardwiring of development: Organization and function of genomic regulatory systems. Development 124: 1851-1864.
3. Bejerano, G., Pheasant, M., Makunin, I., Stephen, S., Kent, W.J., Mattick, J.S., and Haussler, D. 2004. Ultraconserved elements in the human genome. Science 304: 1321-1325.
4. Berman, B.P., Nibu, Y., Pfeiffer, B.D., Tomancak, P., Celniker, S.E., Levine, M., Rubin, G.M., and Eisen, M.B. 2002. Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc. Natl. Acad. Sci. 99: 757-762.
5. Blakesley, R.W., Hansen, N.F., Mullikin, J.C., Thomas, P.J., McDowell, J.C., Maskeri, B., Young, A.C., Benjamin, B., Brooks, S.Y., Coleman, B.I., et al. 2004. An intermediate grade of finished genomic sequence suitable for comparative analyses. Genome Res. 14: 2235-2244.
6. Boffelli, D., McAuliffe, J., Ovcharenko, D., Lewis, K.D., Ovcharenko, I., Pachter, L., and Rubin, E.M. 2003. Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science 299: 1391-1394.
7. Botstein, D. and Risch, N. 2003. Discovering genotypes underlying human phenotypes: Past successes for mendelian disease, future approaches for complex disease. Nat. Genet. 33: 228-237.
8. Britten, R.J. 1997. Mobile elements inserted in the distant past have taken on important functions. Gene 205: 177-182.
9. Brudno, M., Do, C.B., Cooper, G.M., Kim, M.F., Davydov, E., Green, E.D., Sidow, A., and Batzoglou, S. 2003a. LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA. Genome Res. 13: 721-731.
10. Brudno, M., Malde, S., Poliakov, A., Do, C.B., Couronne, O., Dubchak, I., and Batzoglou, S. 2003b. Glocal alignment: Finding rearrangements during alignment. Bioinformatics 19: i54-i62.
11. Brudno, M., Poliakov, A., Salamov, A., Cooper, G.M., Sidow, A., Rubin, E.M., Solovyev, V., Batzoglou, S., and Dubchak, I. 2004. Automated whole-genome multiple alignment of rat, mouse, and human. Genome Res. 14: 685-692.
12. Brugger, S.M., Merrill, A.E., Torres-Vazquez, J., Wu, N., Ting, M.C., Cho, J.Y., Dobias, S.L., Yi, S.E., Lyons, K., Bell, J.R., et al. 2004. A phylogenetically conserved cis-regulatory module in the Msx2 promoter is sufficient for BMP-dependent transcription in murine and Drosophila embryos. Development 131: 5153-5165.
13. Chang-Yeh, A., Mold, D.E., and Huang, R.C. 1991. Identification of a novel murine IAP-promoted placenta-expressed gene. Nucleic Acids Res. 19: 3667-3672.
14. Collins, F.S., Green, E.D., Guttmacher, A.E., and Guyer, M.S. 2003. A vision for the future of genomics research. Nature 422: 835-847.
15. Cooper, G.M. and Sidow, A. 2003. Genomic regulatory regions: Insights from comparative sequence analysis. Curr. Opin. Genet. Dev. 13: 604-610.
16. Cooper, G.M., Brudno, M., Green, E.D., Batzoglou, S., and Sidow, A. 2003. Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes. Genome Res. 13: 813-820.
17. Cooper, G.M., Brudno, M., Stone, E.A., Dubchak, I., Batzoglou, S., and Sidow, A. 2004a. Characterization of evolutionary rates and constraints in three Mammalian genomes. Genome Res. 14: 539-548.
18. Cooper, G.M., Singaravelu, S.A., and Sidow, A. 2004b. ABC: Software for interactive browsing of genomic multiple sequence alignment data. BMC Bioinform. 5: 192.
19. Dermitzakis, E.T., Reymond, A., Lyle, R., Scamuffa, N., Ucla, C., Deutsch, S., Stevenson, B.J., Flegel, V., Bucher, P., Jongeneel, C.V., et al. 2002. Numerous potentially functional but non-genic conserved sequences on human chromosome 21. Nature 420: 578-582.
20. Dermitzakis, E.T., Reymond, A., Scamuffa, N., Ucla, C., Kirkness, E., Rossier, C., and Antonarakis, S.E. 2003. Evolutionary discrimination of mammalian conserved non-genic sequences (CNGs). Science 302: 1033-1035.
21. Dubchak, I., Brudno, M., Loots, G.G., Pachter, L., Mayor, C., Rubin, E.M., and Frazer, K.A. 2000. Active conservation of noncoding sequences revealed by three-way species comparisons. Genome Res. 10: 1304-1306.
22. Ellegren, H., Smith, N.G., and Webster, M.T. 2003. Mutation rate variation in the mammalian genome. Curr. Opin. Genet. Dev. 13: 562-568.
23. The ENCODE Project Consortium. 2004. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 306: 636-640.
24. Eyre-Walker, A. and Keightley, P.D. 1999. High genomic deleterious mutation rates in hominids. Nature 397: 344-347.
25. Friedman, N., Ninio, M., Pe'er, I., and Pupko, T. 2002. A structural EM algorithm for phylogenetic inference. J. Comput. Biol. 9: 331-353.
26. Ghanem, N., Jarinova, O., Amores, A., Long, Q., Hatch, G., Park, B.K., Rubenstein, J.L., and Ekker, M. 2003. Regulatory roles of conserved intergenic domains in vertebrate Dlx bigene clusters. Genome Res. 13: 533-543.
27. Göttgens, B., Barton, L.M., Chapman, M.A., Sinclair, A.M., Knudsen, B., Grafham, D., Gilbert, J.G., Rogers, J., Bentley, D.R., and Green, A.R. 2002. Transcriptional regulation of the stem cell leukemia gene (SCL)-comparative analysis of five vertebrate SCL loci. Genome Res. 12: 749-759.
28. Gumucio, D.L., Heilstedt-Williamson, H., Gray, T.A., Tarle, S.A., Shelton, D.A., Tagle, D.A., Slightom, J.L., Goodman, M., and Collins, F.S. 1992. Phylogenetic footprinting reveals a nuclear protein which binds to silencer sequences in the human γ and ε globin genes. Mol. Cell. Biol. 12: 4919-4929.
29. Hardison, R.C. 2000. Conserved noncoding sequences are reliable guides to regulatory elements. Trends Genet. 16: 369-372.
30. Hardison, R.C., Roskin, K.M., Yang, S., Diekhans, M., Kent, W.J., Weber, R., Elnitski, L., Li, J., O'Connor, M., Kolbe, D., et al. 2003. Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Res. 13: 13-26.
31. Hart, M.C., Korshunova, Y.O., and Cooper, J.A. 1997. Vertebrates have conserved capping protein α isoforms with specific expression patterns. Cell. Motil. Cytoskeleton 38: 120-132.
32. Hasegawa, M., Kishino, H., and Yano, T. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22: 160-174.
33. Hillier, L.W., Miller, W., Birney, E., Warren, W., Hardison, R.C., Ponting, C.P., Bork, P., Burt, D.W., Groenen, M.A., Delany, M.E., et al. 2004. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432: 695-716.
34. Hwang, D.G. and Green, P. 2004. Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution. Proc. Natl. Acad. Sci. 101: 13994-14001.
35. Jordan, I.K., Rogozin, I.B., Glazko, G.V., and Koonin, E.V. 2003. Origin of a substantial fraction of human regulatory sequences from transposable elements. Trends Genet. 19: 68-72.
36. Keightley, P.D., Lercher, M.J., and Eyre-Walker, A. 2005. Evidence for widespread degradation of gene control regions in hominid genomes. PLoS Biol. 3: e42.
37. Khambata-Ford, S., Liu, Y., Gleason, C., Dickson, M., Altman, R.B., Batzoglou, S., and Myers, R.M. 2003. Identification of promoter regions in the human genome by using a retroviral plasmid library-based functional reporter gene assay. Genome Res. 13: 1765-1774.
38. Kimura, M. 1983. The neutral theory of molecular evolution. Cambridge University Press, Cambridge, New York.
39. Li, W.-H. 1997. Molecular evolution. Sinauer Associates, Sunderland, MA.
40. Madsen, O., Scally, M., Douady, C.J., Kao, D.J., DeBry, R.W., Adkins, R., Amrine, H.M., Stanhope, M.J., de Jong, W.W., and Springer, M.S. 2001. Parallel adaptive radiations in two major clades of placental mammals. Nature 409: 610-614.
41. Margulies, E.H., Blanchette, M., Haussler, D., and Green, E.D. 2003. Identification and characterization of multi-species conserved sequences. Genome Res. 13: 2507-2518.
42. Markstein, M., Markstein, P., Markstein, V., and Levine, M.S. 2002. Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo. Proc. Natl. Acad. Sci. 99: 763-768.
43. Mayor, C., Brudno, M., Schwartz, J.R., Poliakov, A., Rubin, E.M., Frazer, K.A., Pachter, L.S., and Dubchak, I. 2000. VISTA : Visualizing global DNA sequence alignments of arbitrary length. Bioinformatics 16: 1046-1047.
44. Mouse Genome Sequencing Consortium. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
45. Murphy, W.J., Eizirik, E., Johnson, W.E., Zhang, Y.P., Ryder, O.A., and O'Brien, S.J. 2001. Molecular phylogenetics and the origins of placental mammals. Nature 409: 614-618.
46. 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.
47. Nobrega, M.A., Ovcharenko, I., Afzal, V., and Rubin, E.M. 2003. Scanning human gene deserts for long-range enhancers. Science 302: 413.
48. O'Brien, S.J., Menotti-Raymond, M., Murphy, W.J., Nash, W.G., Wienberg, J., Stanyon, R., Copeland, N.G., Jenkins, N.A., Womack, J.E., and Marshall Graves, J.A. 1999. The promise of comparative genomics in mammals. Science 286: 458-462, 479-481.
49. Peaston, A.E., Evsikov, A.V., Graber, J.H., de Vries, W.N., Holbrook, A.E., Solter, D., and Knowles, B.B. 2004. Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos. Dev. Cell 7: 597-606.
50. Pennacchio, L.A. and Rubin, E.M. 2001. Genomic strategies to identify mammalian regulatory sequences. Nat. Rev. Genet. 2: 100-109.
51. Pennacchio, L.A., Olivier, M., Hubacek, J.A., Cohen, J.C., Cox, D.R., Fruchart, J.C., Krauss, R.M., and Rubin, E.M. 2001. An apolipoprotein influencing triglycerides in humans and mice revealed by comparative sequencing. Science 294: 169-173.
52. Pruitt, K.D. and Maglott, D.R. 2001. RefSeq and LocusLink: NCBI gene-centered resources. Nucleic Acids Res. 29: 137-140.
53. Rat Genome Sequencing Project Consortium. 2004. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428: 493-521.
54. Shah, N., Couronne, O., Pennacchio, L.A., Brudno, M., Batzoglou, S., Bethel, E.W., Rubin, E.M., Hamann, B., and Dubchak, I. 2004. Phylo-VISTA: Interactive visualization of multiple DNA sequence alignments. Bioinformatics 20: 636-643.
55. Siepel, A. and Haussler, D. 2004a. Combining phylogenetic and hidden Markov models in biosequence analysis. J. Comput. Biol. 11: 413-428.
56. _. 2004b. Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. Mol. Biol. Evol. 21: 468-488.
57. Silva, J.C., Shabalina, S.A., Harris, D.G., Spouge, J.L., and Kondrashovi, A.S. 2003. Conserved fragments of transposable elements in intergenic regions: Evidence for widespread recruitment of MIR- and L2-derived sequences within the mouse and human genomes. Genet. Res. 82: 1-18.
58. Sorek, R. and Ast, G. 2003. Intronic sequences flanking alternatively spliced exons are conserved between human and mouse. Genome Res. 13: 1631-1637.
59. Sumiyama, K., Kim, C.B., and Ruddle, F.H. 2001. An efficient cis-element discovery method using multiple sequence comparisons based on evolutionary relationships. Genomics 71: 260-262.
60. Thomas, J.W., Touchman, J.W., Blakesley, R.W., Bouffard, G.G., Beckstrom-Sternberg, S.M., Margulies, E.H., Blanchette, M., Siepel, A.C., Thomas, P.J., McDowell, J.C., et al. 2003. Comparative analyses of multi-species sequences from targeted genomic regions. Nature 424: 788-793.
61. Woolfe, A., Goodson, M., Goode, D.K., Snell, P., McEwen, G.K., Vavouri, T., Smith, S.F., North, P., Callaway, H., Kelly, K., et al. 2004. Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol. 3: e7.
62. Yang, Z. 1997. PAML: A program package for phylogenetic analysis by maximum likelihood. CABIOS 13: 555-556.
63. Yang, S., Smit, A.F., Schwartz, S., Chiaromonte, F., Roskin, K.M., Haussler, D., Miller, W., and Hardison, R.C. 2004. Patterns of insertions and their covariation with substitutions in the rat, mouse, and human genomes. Genome Res. 14: 517-527.