Thousands of human mobile element fragments undergo strong purifying selection near developmental genes.

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2007-05

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Abstract

At least 5% of the human genome predating the mammalian radiation is thought to have evolved under purifying selection, yet protein-coding and related untranslated exons occupy at most 2% of the genome. Thus, the majority of conserved and, by extension, functional sequence in the human genome seems to be nonexonic. Recent work has highlighted a handful of cases where mobile element insertions have resulted in the introduction of novel conserved nonexonic elements. Here, we present a genome-wide survey of 10,402 constrained nonexonic elements in the human genome that have all been deposited by characterized mobile elements. These repeat instances have been under strong purifying selection since at least the boreoeutherian ancestor (100 Mya). They are most often located in gene deserts and show a strong preference for residing closest to genes involved in development and transcription regulation. In particular, constrained nonexonic elements with clear repetitive origins are located near genes involved in cell adhesion, including all characterized cellular members of the reelin-signaling pathway. Overall, we find that mobile elements have contributed at least 5.5% of all constrained nonexonic elements unique to mammals, suggesting that mobile elements may have played a larger role than previously recognized in shaping and specializing the landscape of gene regulation during mammalian evolution.

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10.1073/pnas.0611223104

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Lowe, Craig B, Gill Bejerano and David Haussler (2007). Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. Proceedings of the National Academy of Sciences of the United States of America, 104(19). pp. 8005–8010. 10.1073/pnas.0611223104 Retrieved from https://hdl.handle.net/10161/17404.

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Lowe

Craig Lowe

Assistant Professor of Molecular Genetics and Microbiology

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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