ScienceDaily (June 1, 2010) — Using high-throughput sequencing to map the locations of a common type of jumping gene within a person's entire genome, researchers at the University of Pennsylvania School of Medicine found extensive variation in these locations among the individuals they studied, further underscoring the role of these errant genes in maintaining genetic diversity.
Schematic drawing of a composite (or complex) transposon. It is composed of two insertion sequence, which codify genes for transposition, flanking structural genes which codify for various proteins or enzymes, i.e. for antibiotic or viral resistance. (Credit: Jacek FH / Courtesy of Wikipedia)
Jumping genes -- also called transposons -- are sequences of DNA that move to different areas of the genome within the same cell.
"The significance of this work is that there is much more diversity in our genome due to insertions by this family of transposons than previously thought," said co-author Haig Kazazian, MD, Seymour Gray Professor of Molecular Medicine, in the Penn Department of Genetics. "This movement of genetic material provides the raw material of genetic evolution, and it doesn't take into account the insertions that we believe occur outside of the sperm and egg cells studied in this project."
Transposons are a source of diversity within a species' gene pool, with implications on many levels. For example, slight changes in genes help organisms adapt and survive in new environments, and populations with genetic diversity are less vulnerable to disease and problems with reproduction.
Insertions into certain spots in the genome can also cause cell function to go awry, so understanding their placement and variation in the human genome is important for a fundamental understanding of disease. Insertions can cause many genetic diseases, such as hemophilia and Duchenne muscular dystrophy, and may play a role in the development of cancer.
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High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes
Adam D Ewing and Haig H Kazazian1
-Author Affiliations
University of Pennsylvania
* Corresponding author; email: kazazian@mail.med.upenn.edu
Abstract
Utilizing high-throughput sequencing, we devised a technique to determine the insertion sites of virtually all members of the human-specific L1 retrotransposon family in any human genome. Using diagnostic nucleotides, we were able to locate the ~800 L1Hs copies corresponding specifically to the pre-Ta, Ta-0, and Ta-1 L1Hs subfamilies, with over 90% of sequenced reads corresponding to human-specific elements. We find that any two individual genomes differ at an average of 285 sites with respect to L1 insertion presence or absence. In total, we assayed 25 individuals, 15 of which are unrelated, at 1139 sites including 772 shared with the reference genome and 367 non-reference L1 insertions. We show that L1Hs profiles recapitulate genetic ancestry, and determine the chromosomal distribution of these elements. Using these data, we estimate that the rate of L1 retrotransposition in humans is between 1/95 and 1/270 births, and the number of dimorphic L1 elements in the human population with gene frequencies >.05 is between 3,000 and 10,000.
Genomics LINE-1 Retrotransposition
Footnotes
Footnotes
Received February 10, 2010.
Accepted May 6, 2010.
Copyright © 2010, Cold Spring Harbor Laboratory Press
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