Phylogenetic Shadowing of Primate Sequences to Find Functional Regions of the Human Genome
Open accessAbstract
Nonhuman primates represent the most relevant model organisms to understand the biology of Homo sapiens . The recent divergence and associated overall sequence conservation between individual members of this taxon have nonetheless largely precluded the use of primates in comparative sequence studies. We used sequence comparisons of an extensive set of Old World and New World monkeys and hominoids to identify functional regions in the human genome. Analysis of these data enabled the discovery of primate-specific gene regulatory elements and the demarcation of the exons of multiple genes. Much of the information content of the comprehensive primate sequence comparisons could be captured with a small subset of phylogenetically close primates. These results demonstrate the utility of intraprimate sequence comparisons to discover common mammalian as well as primate-specific functional elements in the human genome, which are unattainable through the evaluation of more evolutionarily distant species.
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Only the phylogenetic shadowing method makes use of branch lengths of the phylogeny, allows multiple substitutions per site on single branches, and considers the pattern of substitution.
“only the “phylogenetic shadowing” method (Boffelli et al. 2003) (to our knowledge) makes use of the branch lengths of the phylogeny, allows for multiple substitutions per site on single branches of the tree, and considers the “pattern” of substitution”
From Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes (2005) · cites this paper as Boffelli et al. 2003
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- Authors
- Boffelli, D., McAuliffe, J., Ovcharenko, D., Lewis, K. D., Ovcharenko, I., Pachter, L., & Rubin, E. M.
- Affiliations
- Lawrence Berkeley National Laboratory (US)
- Department of Statistics,
- University of California, Berkeley (US)
- Corresponding author
- Rubin, Edward M.
- Venue
- Science
- Published
- 2003-02-28
- Volume
- 299
- Issue
- 5611
- Pages
- 1391-1394
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- OpenAlex
- W2087892194
- Cited by
- 516
- References
- 1
- Citations by year
- 2026: 3 · 2025: 4 · 2024: 6 · 2023: 3 · 2022: 2 · 2021: 4 · 2020: 4 · 2019: 4 · 2018: 9 · 2017: 5 · 2016: 8 · 2015: 9 · 2014: 11 · 2013: 18 · 2012: 14
- FWCI
- 23.91
- Type
- journal article
- Language
- en
- Open access
- green
- www.osti.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- University of North Texas Digital Library (University of North Texas) (submittedVersion)
- CaltechAUTHORS (California Institute of Technology) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Heart, Lung, and Blood Institute (HL 66728, U01HL066728)
- National Human Genome Research Institute (R01-HG02362-01, R01HG002362)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- gene regulatory elements, exon prediction, hominoids, Old World monkeys, New World monkeys, comparative genomics, sequence conservation
- MeSH terms
- Animals, Apolipoproteins A, Cebidae, Cercopithecidae, DNA-Binding Proteins, Biological Evolution, Exons, Gene Expression Regulation, Humans, Hylobates, Phylogeny, Primates, Regulatory Sequences, Nucleic Acid, Species Specificity, Tumor Cells, Cultured, Hominidae, Genome, Human, Likelihood Functions, Genome, Conserved Sequence, Sequence Analysis, DNA, Computational Biology, Electrophoretic Mobility Shift Assay
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