title: Sequence Analysis and Characterization of Active Human Alu Subfamilies Based on the 1000 Genomes Pilot Project.
abstract: 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.
authors: Department of Biological Sciences, Louisiana State University.
authors: Miriam K
authors: MK
authors: Konkel
authors: Department of Biological Sciences, Louisiana State University.
authors: Jerilyn A
authors: JA
authors: Walker
authors: Department of Biological Sciences, Louisiana State University.
authors: Ashley B
authors: AB
authors: Hotard
authors: Department of Biological Sciences, Louisiana State University.
authors: Megan C
authors: MC
authors: Ranck
authors: Department of Biological Sciences, Louisiana State University.
authors: Catherine C
authors: CC
authors: Fontenot
authors: Department of Biological Sciences, Louisiana State University Department of Molecular, Cellular and Developmental Biology, The Ohio State University.
authors: Jessica
authors: J
authors: Storer
authors: Department of Biology, Boston College Cancer Genome Computational Analysis, Cambridge, MA.
authors: Chip
authors: C
authors: Stewart
authors: Department of Biology, Boston College Eccles Institute of Human Genetics, University of Utah.
authors: Gabor T
authors: GT
authors: Marth
authors: Department of Biological Sciences, Louisiana State University mbatzer@lsu.edu.
authors: Mark A
authors: MA
authors: Batzer
mesh_terms: D020087:Alu Elements; D019143:Evolution, Molecular; D014644:Genetic Variation; D015894:Genome, Human; D016045:Human Genome Project; D006801:Humans; D017422:Sequence Analysis, DNA; D017384:Sequence Deletion
keywords: mobilome; retrotransposon; structural variation