Phylogenetic shadowing of primate sequences to find functional regions of the human genome

Science

Volumn 299, Issue 5611, 2003, Pages 1391-1394

  Boffelli, Dario ^a,b   McAuliffe, Jon ^c   Ovcharenko, Dmitriy ^b   Lewis, Keith D ^b   Ovcharenko, Ivan ^a,b   Pachter, Lior ^c   Rubin, Edward M ^a,b  

^a U S DEPARTMENT OF ENERGY   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENES; HUMAN ENGINEERING;

HOMO SAPIENS;

GENETIC ENGINEERING;

GENOME; PHYLOGENETICS; PRIMATE;

ARTICLE; EVALUATION; EXON; GENE FUNCTION; GENE SEQUENCE; GENETIC CONSERVATION; HUMAN; MAMMAL; NONHUMAN; PHYLOGENY; PRIMATE; PRIORITY JOURNAL; REGULATOR GENE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SPECIES DIFFERENTIATION;

ANIMALS; APOLIPOPROTEINS A; CEBIDAE; CERCOPITHECIDAE; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; DNA-BINDING PROTEINS; ELECTROPHORETIC MOBILITY SHIFT ASSAY; EVOLUTION; EXONS; GENE EXPRESSION REGULATION; GENOME; GENOME, HUMAN; HOMINIDAE; HUMANS; HYLOBATES; LIKELIHOOD FUNCTIONS; PHYLOGENY; PRIMATES; REGULATORY SEQUENCES, NUCLEIC ACID; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY; TUMOR CELLS, CULTURED;

HOMO; HOMO SAPIENS; MAMMALIA; PLATYRRHINI; PRIMATES;

EID: 0242418246     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.1081331     Document Type: Article

References (19)

1. G. G. Loots et al., Science 288, 136 (2000).
2. L. A. Pennacchio et al., Science 294, 169 (2001).
3. L. A. Pennacchio, E. M. Rubin, Nature Rev. Genet. 2, 100 (2001).
4. M. Goodman, Am. J. Hum. Genet. 64, 31 (1999).
5. D. A. Tagle et al., J. Mol. Biol. 203, 439 (1988).
6. D. L. Gumucio et al., Mol. Cell. Biol. 12, 4919 (1992).
7. Genomic DNA from the following species was analyzed in this study: Pan troglodytes (*), Pan paniscus (*), Gorilla gorilla (*), Pongo pygmaeus (*), Hylobates lar lar (#), Hylobates syndactylus (#), Papio hamadryas, Macaca nemestrina (*), Macaca mulatta (*), Mandrillus leucophaeus (#), Cercopithecus hamlyni (#), Lophocebus albigena (#), Allenopithecus nigroviridis (#), Miopithecus talapoin (#), Cercopithecus aethiops (#), Erythrocebus patas (*), Colobus guereza kikuyuensis (#), Pygathrix nemaeus (#), Trachypithecus francoisi (#), Presbytis entellus Nasatis larvatus (#), Ateles geoffrey (#), Callicebus moloch (#), Alouatta seniculus (#), Saimiri sciureus (#), Aotus trivirgatus (#), Callithrix (#), and Saguinus labiatus (#). DNA for Papio hamadryas was from the RPCI-41 Baboon BAC Library (www.chori.org). DNA for species marked with * was from the Coriell Cell Repositories (http://locus.umdnj.edu). DNA for species marked with # was provided by the San Diego Zoo/Center for the Reproduction of Endangered Species.
8. Materials and Methods are available as supporting material on Science Online.
9. E. S. Lander et al., Nature 409, 860 (2001).
10. I. Ebersberger, D. Metzler, C. Schwarz, S. Paabo, Am. J. Hum. Genet. 70, 1490 (2002).
11. Mouse Genome Sequencing Consortium, Nature 420, 520 (2002).
12. R. M. Lawn et al., J. Biol. Chem. 270, 24004 (1995).
13. J. Danesh, R. Collins, R. Peto, Circulation 102, 1082 (2000).
14. G. Luc et al., Atherosclerosis 163, 377 (2002).
15. This region was used to learn the mutation rates for "conserved" and "nonconserved" regimes used in this paper.
16. D. P. Wade, G. E. Lindahl, R. M. Lawn, J. Biol. Chem. 269, 19757 (1994).
17. Deletion of region 9, containing the promoter's TATA box, reduces expression by only 30%, likely attributable to the presence of one of the several cryptic TATA boxes further upstream.
18. C. Notredame, Bioinformatics 17, 373 (2001).
19. We thank J.-F. Cheng for support with the sequencing infrastructure, the Zoological Society of San Diego for providing primate DNA samples, and I. Udalova and L. Pennacchio for useful discussions. M. Jordan contributed useful suggestions concerning statistical methods. This work was performed under the auspices of the U.S. Department of Energy's Office of Science, Biological and Environmental Research; by the University of California, Lawrence Berkeley National Laboratory under Contract No. DEAC0376SF00098; supported by Grant #HL66728, Berkeley-PGA, under the Programs for Genomic Application, funded by National Heart, Lung, and Blood Institute, USA. L.P. was partially supported by a grant from NIH (R01-HG02362-01).