Sequence Analysis and Characterization of Active Human Alu Subfamilies Based on the 1000 Genomes Pilot Project.

Autor:	Konkel MK; Department of Biological Sciences, Louisiana State University., Walker JA; Department of Biological Sciences, Louisiana State University., Hotard AB; Department of Biological Sciences, Louisiana State University., Ranck MC; Department of Biological Sciences, Louisiana State University., Fontenot CC; Department of Biological Sciences, Louisiana State University., Storer J; Department of Biological Sciences, Louisiana State University Department of Molecular, Cellular and Developmental Biology, The Ohio State University., Stewart C; Department of Biology, Boston College Cancer Genome Computational Analysis, Cambridge, MA., Marth GT; Department of Biology, Boston College Eccles Institute of Human Genetics, University of Utah., Batzer MA; Department of Biological Sciences, Louisiana State University mbatzer@lsu.edu.
Jazyk:	angličtina
Zdroj:	Genome biology and evolution [Genome Biol Evol] 2015 Aug 29; Vol. 7 (9), pp. 2608-22. Date of Electronic Publication: 2015 Aug 29.
DOI:	10.1093/gbe/evv167
Abstrakt:	The goal of the 1000 Genomes Consortium is to characterize human genome structural variation (SV), including forms of copy number variations such as deletions, duplications, and insertions. Mobile element insertions, particularly Alu elements, are major contributors to genomic SV among humans. During the pilot phase of the project we experimentally validated 645 (611 intergenic and 34 exon targeted) polymorphic "young" Alu insertion events, absent from the human reference genome. Here, we report high resolution sequencing of 343 (322 unique) recent Alu insertion events, along with their respective target site duplications, precise genomic breakpoint coordinates, subfamily assignment, percent divergence, and estimated A-rich tail lengths. All the sequenced Alu loci were derived from the AluY lineage with no evidence of retrotransposition activity involving older Alu families (e.g., AluJ and AluS). AluYa5 is currently the most active Alu subfamily in the human lineage, followed by AluYb8, and many others including three newly identified subfamilies we have termed AluYb7a3, AluYb8b1, and AluYa4a1. This report provides the structural details of 322 unique Alu variants from individual human genomes collectively adding about 100 kb of genomic variation. Many Alu subfamilies are currently active in human populations, including a surprising level of AluY retrotransposition. Human Alu subfamilies exhibit continuous evolution with potential drivers sprouting new Alu lineages. (© The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)
Databáze:	MEDLINE
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