Deep genome-wide measurement of meiotic gene conversion using tetrad analysis in Arabidopsis thaliana

Gene conversion, the non-reciprocal exchange of genetic information, is one of the potential products of meiotic recombination. It can shape genome structure by acting on repetitive DNA elements, influence allele frequencies at the population level, and is known to be implicated in human disease. Bu...

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Published in	PLoS genetics Vol. 8; no. 10; p. e1002968
Main Authors	Sun, Yujin, Ambrose, Jonathan H, Haughey, Brena S, Webster, Tyler D, Pierrie, Sarah N, Muñoz, Daniela F, Wellman, Emily C, Cherian, Shalom, Lewis, Scott M, Berchowitz, Luke E, Copenhaver, Gregory P
Format	Journal Article
Language	English
Published	United States Public Library of Science 01.10.2012 Public Library of Science (PLoS)
Subjects	Alleles Arabidopsis - genetics Arabidopsis thaliana Biology Chromosomes Deoxyribonucleic acid DNA Gene Conversion Genetic aspects Genetic recombination Genome, Plant Genomics Meiosis Models, Genetic Physiological aspects Plant genetics Plants, Genetically Modified Polymorphism, Single Nucleotide Proteins Quantitative Trait Loci Recombination, Genetic Yeast United States
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Abstract	Gene conversion, the non-reciprocal exchange of genetic information, is one of the potential products of meiotic recombination. It can shape genome structure by acting on repetitive DNA elements, influence allele frequencies at the population level, and is known to be implicated in human disease. But gene conversion is hard to detect directly except in organisms, like fungi, that group their gametes following meiosis. We have developed a novel visual assay that enables us to detect gene conversion events directly in the gametes of the flowering plant Arabidopsis thaliana. Using this assay we measured gene conversion events across the genome of more than one million meioses and determined that the genome-wide average frequency is 3.5×10(-4) conversions per locus per meiosis. We also detected significant locus-to-locus variation in conversion frequency but no intra-locus variation. Significantly, we found one locus on the short arm of chromosome 4 that experienced 3-fold to 6-fold more gene conversions than the other loci tested. Finally, we demonstrated that we could modulate conversion frequency by varying experimental conditions.
AbstractList	Gene conversion, the non-reciprocal exchange of genetic information, is one of the potential products of meiotic recombination. It can shape genome structure by acting on repetitive DNA elements, influence allele frequencies at the population level, and is known to be implicated in human disease. But gene conversion is hard to detect directly except in organisms, like fungi, that group their gametes following meiosis. We have developed a novel visual assay that enables us to detect gene conversion events directly in the gametes of the flowering plant Arabidopsis thaliana. Using this assay we measured gene conversion events across the genome of more than one million meioses and determined that the genome-wide average frequency is 3.5×10(-4) conversions per locus per meiosis. We also detected significant locus-to-locus variation in conversion frequency but no intra-locus variation. Significantly, we found one locus on the short arm of chromosome 4 that experienced 3-fold to 6-fold more gene conversions than the other loci tested. Finally, we demonstrated that we could modulate conversion frequency by varying experimental conditions. Gene conversion, the non-reciprocal exchange of genetic information, is one of the potential products of meiotic recombination. It can shape genome structure by acting on repetitive DNA elements, influence allele frequencies at the population level, and is known to be implicated in human disease. But gene conversion is hard to detect directly except in organisms, like fungi, that group their gametes following meiosis. We have developed a novel visual assay that enables us to detect gene conversion events directly in the gametes of the flowering plant Arabidopsis thaliana . Using this assay we measured gene conversion events across the genome of more than one million meioses and determined that the genome-wide average frequency is 3.5×10 −4 conversions per locus per meiosis. We also detected significant locus-to-locus variation in conversion frequency but no intra-locus variation. Significantly, we found one locus on the short arm of chromosome 4 that experienced 3-fold to 6-fold more gene conversions than the other loci tested. Finally, we demonstrated that we could modulate conversion frequency by varying experimental conditions. During the production of gametes, most sexually reproducing organisms undergo meiotic recombination. The most familiar form of meiotic recombination is crossing-over, which results in the reciprocal exchange of DNA between parental chromosomes and is important for chromosome segregation as well as generating new allelic combinations in progeny. The same molecular mechanisms that facilitate crossing-over can also enable the non-reciprocal exchange of genetic information between chromosomes in the process called gene conversion. Understanding gene conversion is important because it influences allele frequencies and has been implicated in human diseases. Unfortunately, it has been difficult until now to measure directly except in organisms, like fungi, that group their gametes after meiosis. In this study we have developed a novel assay system that enables us to measure gene conversion directly in the model multi-cellular eukaryote A. thaliana (a flowering plant). Using this assay system we measured gene conversion frequencies across the Arabidopsis genome in more than 1 million meioses and also demonstrated that we can manipulate those frequencies by varying experimental conditions. Gene conversion, the non-reciprocal exchange of genetic information, is one of the potential products of meiotic recombination. It can shape genome structure by acting on repetitive DNA elements, influence allele frequencies at the population level, and is known to be implicated in human disease. But gene conversion is hard to detect directly except in organisms, like fungi, that group their gametes following meiosis. We have developed a novel visual assay that enables us to detect gene conversion events directly in the gametes of the flowering plant Arabidopsis thaliana. Using this assay we measured gene conversion events across the genome of more than one million meioses and determined that the genome-wide average frequency is 3.5×10-4 conversions per locus per meiosis. We also detected significant locus-to-locus variation in conversion frequency but no intra-locus variation. Significantly, we found one locus on the short arm of chromosome 4 that experienced 3-fold to 6-fold more gene conversions than the other loci tested. Finally, we demonstrated that we could modulate conversion frequency by varying experimental conditions. Gene conversion, the non-reciprocal exchange of genetic information, is one of the potential products of meiotic recombination. It can shape genome structure by acting on repetitive DNA elements, influence allele frequencies at the population level, and is known to be implicated in human disease. But gene conversion is hard to detect directly except in organisms, like fungi, that group their gametes following meiosis. We have developed a novel visual assay that enables us to detect gene conversion events directly in the gametes of the flowering plant Arabidopsis thaliana. Using this assay we measured gene conversion events across the genome of more than one million meioses and determined that the genome-wide average frequency is 3.5 x[10.sup.-4] conversions per locus per meiosis. We also detected significant locus-to-locus variation in conversion frequency but no intra-locus variation. Significantly, we found one locus on the short arm of chromosome 4 that experienced 3-fold to 6-fold more gene conversions than the other loci tested. Finally, we demonstrated that we could modulate conversion frequency by varying experimental conditions.
Audience	Academic
Author	Sun, Yujin Berchowitz, Luke E Muñoz, Daniela F Ambrose, Jonathan H Pierrie, Sarah N Webster, Tyler D Wellman, Emily C Cherian, Shalom Lewis, Scott M Copenhaver, Gregory P Haughey, Brena S
AuthorAffiliation	The Pennsylvania State University, United States of America 3 Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America 2 Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America 1 Department of Biology and the Carolina Center for Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
AuthorAffiliation_xml	– name: 3 Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America – name: 1 Department of Biology and the Carolina Center for Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America – name: 2 Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America – name: The Pennsylvania State University, United States of America
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Copyright	COPYRIGHT 2012 Public Library of Science Sun et al. 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 credited: Sun Y, Ambrose JH, Haughey BS, Webster TD, Pierrie SN, et al. (2012) Deep Genome-Wide Measurement of Meiotic Gene Conversion Using Tetrad Analysis in Arabidopsis thaliana. PLoS Genet 8(10): e1002968. doi:10.1371/journal.pgen.1002968 2012 Sun et al 2012 Sun et al
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Snippet	Gene conversion, the non-reciprocal exchange of genetic information, is one of the potential products of meiotic recombination. It can shape genome structure... Gene conversion, the non-reciprocal exchange of genetic information, is one of the potential products of meiotic recombination. It can shape genome structure...
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StartPage	e1002968
SubjectTerms	Alleles Arabidopsis - genetics Arabidopsis thaliana Biology Chromosomes Deoxyribonucleic acid DNA Gene Conversion Genetic aspects Genetic recombination Genome, Plant Genomics Meiosis Models, Genetic Physiological aspects Plant genetics Plants, Genetically Modified Polymorphism, Single Nucleotide Proteins Quantitative Trait Loci Recombination, Genetic Yeast
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Title	Deep genome-wide measurement of meiotic gene conversion using tetrad analysis in Arabidopsis thaliana
URI	https://www.ncbi.nlm.nih.gov/pubmed/23055940 https://www.proquest.com/docview/1313569021 https://search.proquest.com/docview/1111858188 https://pubmed.ncbi.nlm.nih.gov/PMC3464199 https://doaj.org/article/c78fe35aad4f4d4790963c13b68c5e88 http://dx.doi.org/10.1371/journal.pgen.1002968
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