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Why are young and old repetitive elements distributed differently in the human genome?
Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi. (Molecular evolution)
2005 (English)In: J Mol Evol, ISSN 0022-2844, Vol. 60, no 3, 290-6 p.Article in journal (Refereed) Published
Abstract [en]

Alu elements are not distributed homogeneously throughout the human genome: old elements are preferentially found in the GC-rich parts of the genome, while young Alus are more often found in the GC-poor parts of the genome. The process giving rise to this differential distribution remains poorly understood. Here we investigate whether this pattern could be due to a preferential degradation of Alu elements integrated in GC-poor regions by small indel mutations. We aligned 5.1 Mb of human and chimpanzee sequences and examined whether the rate of insertion and deletion inside Alu elements differed according to the base composition surrounding them. We found that Alu elements are not preferentially degraded in GC-poor regions by indel events. We also looked at whether very young L1 elements show the same change in distribution compared to older ones. This analysis indicated that L1 elements also show a shift in their distribution, although we could not assess it as precisely as for Alu elements. We propose that the differential distribution of Alu elements is likely to be due to a change in their pattern of insertion or their probability of fixation through evolutionary time.

Place, publisher, year, edition, pages
2005. Vol. 60, no 3, 290-6 p.
Keyword [en]
Alu Elements/*genetics, Animals, Comparative Study, Computational Biology, Databases; Nucleic Acid, Evolution; Molecular, GC Rich Sequence/*genetics, Genome; Human, Humans, Pan troglodytes/*genetics, Sequence Alignment, Species Specificity, Time Factors
National Category
Genetics
Identifiers
URN: urn:nbn:se:uu:diva-76385PubMedID: 15871040OAI: oai:DiVA.org:uu-76385DiVA: diva2:104297
Available from: 2006-03-02 Created: 2006-03-02 Last updated: 2011-01-11

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Webster, Matthew T

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