Three periods of regulatory innovation during vertebrate evolution.
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2011-08
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The gain, loss, and modification of gene regulatory elements may underlie a substantial proportion of phenotypic changes on animal lineages. To investigate the gain of regulatory elements throughout vertebrate evolution, we identified genome-wide sets of putative regulatory regions for five vertebrates, including humans. These putative regulatory regions are conserved nonexonic elements (CNEEs), which are evolutionarily conserved yet do not overlap any coding or noncoding mature transcript. We then inferred the branch on which each CNEE came under selective constraint. Our analysis identified three extended periods in the evolution of gene regulatory elements. Early vertebrate evolution was characterized by regulatory gains near transcription factors and developmental genes, but this trend was replaced by innovations near extracellular signaling genes, and then innovations near posttranslational protein modifiers.
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Lowe, Craig B, Manolis Kellis, Adam Siepel, Brian J Raney, Michele Clamp, Sofie R Salama, David M Kingsley, Kerstin Lindblad-Toh, et al. (2011). Three periods of regulatory innovation during vertebrate evolution. Science (New York, N.Y.), 333(6045). pp. 1019–1024. 10.1126/science.1202702 Retrieved from https://hdl.handle.net/10161/17403.
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Craig Lowe
Craig Lowe is an Assistant Professor in the Department of Molecular Genetics and Microbiology. His research interests are in understanding how traits and characteristics of humans, and other vertebrates, are encoded in their genomes. He is especially focused on adaptations and disease susceptibilities that are unique to humans. To address these questions, Craig uses both computational and experimental approaches. Craig's recent research has been on differences in how genes are regulated between species, or between different individuals within a species, and how this causes traits to differ. All students in Craig's lab are exposed to an interdisciplinary environment; current lab members have backgrounds in mathematics, computer science, neuroscience, developmental biology, and genetics. Each year Craig teaches one or two courses on rotating topics of: ancient DNA, ethical issues in genomics, and software development for genetic analyses.
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