Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 101, Issue 28, Pages 10349-10354Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.0403727101
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- NCI NIH HHS [5T32CA09311, 5R01CA81152, R01 CA081152, 5P30CA45508, 2R01CA078544, R01 CA078544, T32 CA009311, P30 CA045508] Funding Source: Medline
- NHGRI NIH HHS [5R21HG02606] Funding Source: Medline
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Mammalian genomes are densely populated with long duplicated sequences. In this paper, we demonstrate the existence of doublets, short duplications between 25 and 100 bp, distinct from previously described repeats. Each doublet is a pair of exact matches, separated by some distance. The distribution of these intermatch distances is strikingly nonrandom. An unexpectedly high number of doublets have matches either within 100 bp (adjacent) or at distances tightly concentrated approximate to1,000 bp apart (nearby). We focus our study on these proximate doublets. First, they tend to have both matches on the same strand. By comparing nearby doublets shared in human and chimpanzee, we can also see that these doublets seem to arise by an insertion event that produces a copy without markedly affecting the surrounding sequence. Most doublets in humans are shared with chimpanzee, but many new pairs arose after the divergence of the species. Doublets found in human but not chimpanzee are most often composed of almost tandem matches, whereas older doublets (found in both species) are more likely to have matches spaced by approximate to1 kb, indicating that the nearly tandem doublets may be ore dynamic. The spacing of doublets is highly conserved. So far, we have found clearly recognizable doublets in the followin genomes: Homo sapiens, Mus musculus, Arabidopsis thaliana, and Caenorhabditis elegans, indicating that the mechanism generating these doublets is widespread. A mechanism that generates short local duplications while conserving polarity could have a profound impact on the evolution of regulatory and proteincoding sequences.
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