The Contribution of Alu Elements to Mutagenic DNA Double-Strand Break Repair

Alu elements make up the largest family of human mobile elements, numbering 1.1 million copies and comprising 11% of the human genome. As a consequence of evolution and genetic drift, Alu elements of various sequence divergence exist throughout the human genome. Alu/Alu recombination has been shown...

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Main Authors:	Morales, Maria E., White, Travis B., Streva, Vincent A., DeFreece, Cecily B., Hedges, Dale J., Deininger, Prescott L.
Format:	Online
Language:	English
Published:	Public Library of Science 2015
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4356517/

id	pubmed-4356517
recordtype	oai_dc
spelling	pubmed-43565172015-03-17 The Contribution of Alu Elements to Mutagenic DNA Double-Strand Break Repair Morales, Maria E. White, Travis B. Streva, Vincent A. DeFreece, Cecily B. Hedges, Dale J. Deininger, Prescott L. Research Article Alu elements make up the largest family of human mobile elements, numbering 1.1 million copies and comprising 11% of the human genome. As a consequence of evolution and genetic drift, Alu elements of various sequence divergence exist throughout the human genome. Alu/Alu recombination has been shown to cause approximately 0.5% of new human genetic diseases and contribute to extensive genomic structural variation. To begin understanding the molecular mechanisms leading to these rearrangements in mammalian cells, we constructed Alu/Alu recombination reporter cell lines containing Alu elements ranging in sequence divergence from 0%-30% that allow detection of both Alu/Alu recombination and large non-homologous end joining (NHEJ) deletions that range from 1.0 to 1.9 kb in size. Introduction of as little as 0.7% sequence divergence between Alu elements resulted in a significant reduction in recombination, which indicates even small degrees of sequence divergence reduce the efficiency of homology-directed DNA double-strand break (DSB) repair. Further reduction in recombination was observed in a sequence divergence-dependent manner for diverged Alu/Alu recombination constructs with up to 10% sequence divergence. With greater levels of sequence divergence (15%-30%), we observed a significant increase in DSB repair due to a shift from Alu/Alu recombination to variable-length NHEJ which removes sequence between the two Alu elements. This increase in NHEJ deletions depends on the presence of Alu sequence homeology (similar but not identical sequences). Analysis of recombination products revealed that Alu/Alu recombination junctions occur more frequently in the first 100 bp of the Alu element within our reporter assay, just as they do in genomic Alu/Alu recombination events. This is the first extensive study characterizing the influence of Alu element sequence divergence on DNA repair, which will inform predictions regarding the effect of Alu element sequence divergence on both the rate and nature of DNA repair events. Public Library of Science 2015-03-11 /pmc/articles/PMC4356517/ /pubmed/25761216 http://dx.doi.org/10.1371/journal.pgen.1005016 Text en © 2015 Morales et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Morales, Maria E. White, Travis B. Streva, Vincent A. DeFreece, Cecily B. Hedges, Dale J. Deininger, Prescott L.
spellingShingle	Morales, Maria E. White, Travis B. Streva, Vincent A. DeFreece, Cecily B. Hedges, Dale J. Deininger, Prescott L. The Contribution of Alu Elements to Mutagenic DNA Double-Strand Break Repair
author_facet	Morales, Maria E. White, Travis B. Streva, Vincent A. DeFreece, Cecily B. Hedges, Dale J. Deininger, Prescott L.
author_sort	Morales, Maria E.
title	The Contribution of Alu Elements to Mutagenic DNA Double-Strand Break Repair
title_short	The Contribution of Alu Elements to Mutagenic DNA Double-Strand Break Repair
title_full	The Contribution of Alu Elements to Mutagenic DNA Double-Strand Break Repair
title_fullStr	The Contribution of Alu Elements to Mutagenic DNA Double-Strand Break Repair
title_full_unstemmed	The Contribution of Alu Elements to Mutagenic DNA Double-Strand Break Repair
title_sort	contribution of alu elements to mutagenic dna double-strand break repair
description	Alu elements make up the largest family of human mobile elements, numbering 1.1 million copies and comprising 11% of the human genome. As a consequence of evolution and genetic drift, Alu elements of various sequence divergence exist throughout the human genome. Alu/Alu recombination has been shown to cause approximately 0.5% of new human genetic diseases and contribute to extensive genomic structural variation. To begin understanding the molecular mechanisms leading to these rearrangements in mammalian cells, we constructed Alu/Alu recombination reporter cell lines containing Alu elements ranging in sequence divergence from 0%-30% that allow detection of both Alu/Alu recombination and large non-homologous end joining (NHEJ) deletions that range from 1.0 to 1.9 kb in size. Introduction of as little as 0.7% sequence divergence between Alu elements resulted in a significant reduction in recombination, which indicates even small degrees of sequence divergence reduce the efficiency of homology-directed DNA double-strand break (DSB) repair. Further reduction in recombination was observed in a sequence divergence-dependent manner for diverged Alu/Alu recombination constructs with up to 10% sequence divergence. With greater levels of sequence divergence (15%-30%), we observed a significant increase in DSB repair due to a shift from Alu/Alu recombination to variable-length NHEJ which removes sequence between the two Alu elements. This increase in NHEJ deletions depends on the presence of Alu sequence homeology (similar but not identical sequences). Analysis of recombination products revealed that Alu/Alu recombination junctions occur more frequently in the first 100 bp of the Alu element within our reporter assay, just as they do in genomic Alu/Alu recombination events. This is the first extensive study characterizing the influence of Alu element sequence divergence on DNA repair, which will inform predictions regarding the effect of Alu element sequence divergence on both the rate and nature of DNA repair events.
publisher	Public Library of Science
publishDate	2015
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4356517/
_version_	1613197595645050880

The Contribution of Alu Elements to Mutagenic DNA Double-Strand Break Repair

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