Analysis of multiple genomic sequence alignments: A web resource, online tools, and lessons learned from analysis of mammalian SCL loci

Genome Research

Volumn 14, Issue 2, 2004, Pages 313-318

  Chapman, Michael A ^a   Donaldson, Ian J ^a   Gilbert, James ^b   Grafham, Darren ^b   Rogers, Jane ^b   Green, Anthony R ^a   Göttgens, Berthold ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

HELIX LOOP HELIX PROTEIN; LYASE; SELENOCYSTEINE LYASE;

ANIMAL; ARTICLE; BINDING SITE; BIOINFORMATICS; COMPARATIVE STUDY; CONTROLLED STUDY; DATA BASE; DOG; ENZYMOLOGY; GENE CONTROL; GENE FUNCTION; GENE LOCUS; GENE SEQUENCE; GENETIC DATABASE; GENETIC MARKER; GENETICS; GENOME; GENOMICS; HUMAN; INTERNET; LEUKEMIA; MAMMAL; METHODOLOGY; MOLECULAR GENETICS; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; ONLINE SYSTEM; PRIORITY JOURNAL; RAT; REGULATORY SEQUENCE; SEQUENCE ALIGNMENT; SIGNAL NOISE RATIO; STRUCTURAL GENE; VERTEBRATE;

ANIMALS; DATABASES, GENETIC; DOGS; GENES, NEOPLASM; GENETIC MARKERS; GENOME; GENOME, HUMAN; GENOMICS; HUMANS; INTERNET; LEUKEMIA; LYASES; MICE; MOLECULAR SEQUENCE DATA; ONLINE SYSTEMS; RATS; RESEARCH DESIGN; SEQUENCE ALIGNMENT;

ANIMALIA; CANIS FAMILIARIS; MAMMALIA; VERTEBRATA;

EID: 1242296821     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.1759004     Document Type: Article

References (36)

1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403-410.
2. Barton, L.M., Göttgens, B., Gering, M., Gilbert, J.G., Grafham, D., Rogers, J., Bentley, D., Patient, R., and Green, A.R. 2001. Regulation of the stem cell leukemia (SCL) gene: A tale of two fishes. Proc. Natl. Acad. Sci. 98: 6747-6752.
3. Begley, C.G. and Green, A.R. 1999. The SCL gene: From case report to critical hematopoietic regulator. Blood 93: 2760-2770.
4. Boffelli, D., McAuliffe, J., Ovcharenko, D., Lewis, K.D., Ovcharenko, I., Pachter, I., and Rubin, E.M. 2003. Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science 299: 1391-1394.
5. Brudno, M., Do, C.B., Cooper, G.M., Kim, M.F., Davydov, E., Green, E.D., Sidow, A., and Batzoglou, S. 2003. LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA. Genome Res. 13: 721-731.
6. Brudno, M., Chapman, M., Göttgens, B., Batzoglou, S., and Morgenstern, B. 2004. Fast and sensitive multiple alignment of large genomic sequences. BMC Bioinformatics (in press).
7. Chapman, M.A., Charchar, F.J., Kinston, S., Bird, C.P., Grafham, D., Rogers, J., Grutzner, F., Marshall Graves, J.A., Green, A.R., and Gottgens, B. 2003. Comparative and functional analyses of LYL1 loci establish marsupial sequences as a model for phylogenetic footprinting. Genomics 81: 249-259.
8. Cioffi, C.C., Middleton, D.L., Wilson, M.R., Miller, N.W., Clem, L.W., and Warr, G.W. 2001. An IgH enhancer that drives transcription through basic helix-loop-helix and Oct transcription factor binding motifs. Functional analysis of the E(mu)3′ enhancer of the catfish. J. Biol. Chem. 276: 27825-27830.
9. 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.
10. 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.
11. Elnitski, L., Hardison, R.C., Li, J., Yang, S., Kolbe, D., Eswara, P., O'Connor, M.J., Schwartz, S., Miller, W., and Chiaromonte, F. 2003. Distinguishing regulatory DNA from neutral sites. Genome Res. 13: 64-72.
12. Flint, J., Tufarelli, C., Peden, J., Clark, K., Daniels, R.J., Hardison, R., Miller, W., Philipsen, S., Tan-Un, K.C., McMorrow, T., et al. 2001. Comparative genome analysis delimits a chromosomal domain and identifies key regulatory elements in the α lobin cluster. Hum. Mol. Genet. 10: 371-382.
13. Fordham, J.I., Göttgens, B., McLaughlin, F., and Green, A.R. 1999. Chromatin structure and transcriptional regulation of the stem cell leukaemia (SCL) gene in mast cells. Leukemia 13: 750-759.
14. Frazer, K.A., Elnitski, L., Church, D.M., Dubchak, I., and Hardison, R.C. 2003. Cross-species sequence comparisons: A review of methods and available resources. Genome Res. 13: 1-12.
15. Gilligan, P., Brenner, S., and Venkatesh, B. 2002. Fugu and human sequence comparison identifies novel human genes and conserved non-coding sequences. Gene 294: 35.
16. Göttgens, B., Barton, L.M., Gilbert, J.G., Bench, A.J., Sanchez, M.J., Bahn, S., Mistry, S., Grafham, D., McMurray, A., Vaudin, M., et al. 2000. Analysis of vertebrate SCL loci identifies conserved enhancers. Nat. Biotechnol. 18: 181-186.
17. Göttgens, B., Gilbert, J.G., Barton, L.M., Grafham, D., Rogers, J., Bentley, D.R., and Green, A.R. 2001. Long-range comparison of human and mouse SCL loci: Localized regions of sensitivity to restriction endonucleases correspond precisely with peaks of conserved noncoding sequences. Genome Res. 11: 87-97.
18. 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. 2002a. Transcriptional regulation of the stem cell leukemia gene (SCL)-Comparative analysis of five vertebrate SCL loci. Genome Res. 12: 749-759.
19. Göttgens, B., Nastos, A., Kinston, S., Piltz, S., Delabesse, E.C., Stanley, M., Sanchez, M.J., Ciau-Uitz, A., Patient, R., and Green, A.R. 2002b. Establishing the transcriptional programme for blood: The SCL stem cell enhancer is regulated by a multiprotein complex containing Ets and GATA factors. EMBO J. 21: 3039-3050.
20. Gumucio, D.L., Shelton, D.A., Bailey, W.J., Slightom, J.L., and Goodman, M. 1993. Phylogenetic footprinting reveals unexpected complexity in trans factor binding upstream from the E-globin gene. Proc. Natl. Acad. Sci. 90: 6018-6022.
21. 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.
22. Li, R., Mignot, E., Faraco, J., Kadotani, H., Cantanese, J., Zhao, B., Lin, X., Hinton, L., Ostrander, E.A., Patterson, D.F., et al. 1999. Construction and characterization of an eightfold redundant dog genomic bacterial artificial chromosome library. Genomics 58: 9-17.
23. Loots, G.G., Locksley, R.M., Blankespoor, C.M., Wang, Z.E., Miller, W., Rubin, E.M., and Frazer, K.A. 2000. Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. Science 288: 136-140.
24. Miles, C., Elgar, G., Coles, E., Kleinjan, D.J., van Heyningen, V., and Hastie, N. 1998. Complete sequencing of the Fugu WAGR region from WT1 to PAX6: Dramatic compaction and conservation of synteny with human chromosome 11p13. Proc. Natl. Acad. Sci. 95: 13068-13072.
25. Miller, W. 2001. Comparison of genomic DNA sequences: Solved and unsolved problems. Bioinformatics 17: 391-397.
26. Sanchez, M., Göttgens, B., Sinclair, A.M., Stanley, M., Begley, C.G., Hunter, S., and Green, A.R. 1999. An SCL 3′ enhancer targets developing endothelium together with embryonic and adult haematopoietic progenitors. Development 126: 3891-3904.
27. Sanchez, M.J., Bockamp, E.O., Miller, J., Gambardella, L., and Green, A.R. 2001. Selective rescue of early haematopoietic progenitors in Scl(-/-) mice by expressing Scl under the control of a stem cell enhancer. Development 128: 4815-4827.
28. Schwartz, S., Zhang, Z., Frazer, K.A., Smit, A., Riemer, C., Bouck, J., Gibbs, R., Hardison, R., and Miller, W. 2000. PipMaker-A web server for aligning two genomic DNA sequences. Genome Res. 10: 577-586.
29. Schwartz, S., Elnitski, L., Li, M., Weirauch, M., Riemer, C., Smit, A., Green, E.D., Hardison, R.C., and Miller, W. 2003. MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences. Nucleic Acids Res. 31: 3518-3524.
30. Shelton, D.A., Stegman, L., Hardison, R., Miller, W., Bock, J.H., Slightom, J.L., Goodman, M., and Gumucio, D.L. 1997. Phylogenetic footprinting of hypersensitive site 3 of the β-globin locus control region. Blood 89: 3457-3469.
31. Sinclair, A.M., Göttgens, B., Barton, L.M., Stanley, M.L., Pardanaud, L., Klaine, M., Gering, M., Bahn, S., Sanchez, M., Bench, A.J., et al. 1999. Distinct 5′ SCL enhancers direct transcription to developing brain, spinal cord, and endothelium: Neural expression is mediated by GATA factor binding sites. Dev. Biol. 209: 128-142.
32. Sinclair, A.M., Bench, A.J., Bloor, A.J., Li, J., Göttgens, B., Stanley, M.L., Miller, J., Piltz, S., Hunter, S., Nacheva, E.P., et al. 2002. Rescue of the lethal scl-(-/-) phenotype by the human SCL locus. Blood 99: 3931-3938.
33. Stojanovic, N., Florea, L., Riemer, C., Gumucio, D., Slightom, J., Goodman, M., Miller, W., and Hardison, R. 1999. Comparison of five methods for finding conserved sequences in multiple alignments of gene regulatory regions. Nucleic Acids Res. 27: 3899-3910.
34. Tagle, D.A., Koop, B.F., Goodman, M., Slightom, J.L., Hess, D.L., and Jones, R.T. 1988. Embryonic ε and γ globin genes of a prosimian primate (Galago crassicaudatus). Nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints. J. Mol. Biol. 203: 439-455.
35. 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.
36. Wasserman, W.W., Palumbo, M., Thompson, W., Fickett, J.W., and Lawrence, C.E. 2000. Human-mouse genome comparisons to locate regulatory sites. Nat. Genet. 26: 225-228.