Metastable differentially methylated regions within Arabidopsis inbred populations are associated with modified expression of non-coding transcripts
Individual plants within a population may vary at both genetic and epigenetic levels. The rate of genetic divergence and its underlying mechanisms is well understood. Less is known about the factors contributing to epigenetic divergence among isogenic populations except that, despite the presence of...
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| description | Individual plants within a population may vary at both genetic and epigenetic levels. The rate of genetic divergence and its underlying mechanisms is well understood. Less is known about the factors contributing to epigenetic divergence among isogenic populations except that, despite the presence of mechanisms that faithfully maintain epigenetic marks, epigenetic differences are more frequent than genetic variation. Epigenetically divergent stretches of isogenic DNA sequence are called epialleles. Currently, it is not clear why certain regions exhibit variable epigenetic status. We identified and characterised two long RNA transcripts with altered expression and DNA methylation in an ago5 mutant. However, further investigation revealed that these changes were not dependent upon AGO5. Rather, the variable transcription of these loci in Arabidopsis mutant and wild-type populations corresponds to spontaneous differential methylated regions (DMRs) or epialleles. These two DMRs are delineated by RNAs which are highly expressed when the DMR is hypomethylated. Furthermore, they control the expression of 5' transcriptional start site mRNA variants of nearby protein coding genes. Our data support the recent observations that meiotically stable DMRs exist within inbred populations. We further demonstrate that DMR boundaries can be defined by putative non-coding promoter-associated transcripts. |
| doi_str_mv | 10.1371/journal.pone.0045242 |
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The rate of genetic divergence and its underlying mechanisms is well understood. Less is known about the factors contributing to epigenetic divergence among isogenic populations except that, despite the presence of mechanisms that faithfully maintain epigenetic marks, epigenetic differences are more frequent than genetic variation. Epigenetically divergent stretches of isogenic DNA sequence are called epialleles. Currently, it is not clear why certain regions exhibit variable epigenetic status. We identified and characterised two long RNA transcripts with altered expression and DNA methylation in an ago5 mutant. However, further investigation revealed that these changes were not dependent upon AGO5. Rather, the variable transcription of these loci in Arabidopsis mutant and wild-type populations corresponds to spontaneous differential methylated regions (DMRs) or epialleles. These two DMRs are delineated by RNAs which are highly expressed when the DMR is hypomethylated. Furthermore, they control the expression of 5' transcriptional start site mRNA variants of nearby protein coding genes. Our data support the recent observations that meiotically stable DMRs exist within inbred populations. We further demonstrate that DMR boundaries can be defined by putative non-coding promoter-associated transcripts.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0045242</identifier><identifier>PMID: 23028873</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Alleles ; Arabidopsis ; Arabidopsis - genetics ; Arabidopsis Proteins - genetics ; Arabidopsis thaliana ; Bioinformatics ; Biology ; Deoxyribonucleic acid ; Divergence ; DNA ; DNA Methylation ; DNA, Plant - genetics ; Epigenesis, Genetic ; Epigenetic inheritance ; Epigenetics ; Gene expression ; Genes ; Genetic aspects ; Genetic divergence ; Genetic diversity ; Genetic Loci ; Genetic Variation ; Genetics, Population ; Genomes ; Genotype ; Inbreeding ; Methylation ; Mutation ; Nucleotide sequence ; Physiological aspects ; Plant sciences ; Populations ; Promoter Regions, Genetic ; Ribonucleic acid ; RNA ; RNA polymerase ; RNA, Messenger - genetics ; RNA, Untranslated - genetics ; RNA-Binding Proteins - genetics ; Transcription</subject><ispartof>PloS one, 2012-09, Vol.7 (9), p.e45242-e45242</ispartof><rights>COPYRIGHT 2012 Public Library of Science</rights><rights>Havecker et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2012 Havecker et al 2012 Havecker et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-249ff963faca1ea2dee52a6d8bf602ac64d98b46ebeb31191cf6fd916a59c4583</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3447930/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3447930/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79342,79343</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/23028873$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Havecker, Ericka R</creatorcontrib><creatorcontrib>Wallbridge, Laura M</creatorcontrib><creatorcontrib>Fedito, Paola</creatorcontrib><creatorcontrib>Hardcastle, Thomas J</creatorcontrib><creatorcontrib>Baulcombe, David C</creatorcontrib><title>Metastable differentially methylated regions within Arabidopsis inbred populations are associated with modified expression of non-coding transcripts</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Individual plants within a population may vary at both genetic and epigenetic levels. The rate of genetic divergence and its underlying mechanisms is well understood. Less is known about the factors contributing to epigenetic divergence among isogenic populations except that, despite the presence of mechanisms that faithfully maintain epigenetic marks, epigenetic differences are more frequent than genetic variation. Epigenetically divergent stretches of isogenic DNA sequence are called epialleles. Currently, it is not clear why certain regions exhibit variable epigenetic status. We identified and characterised two long RNA transcripts with altered expression and DNA methylation in an ago5 mutant. However, further investigation revealed that these changes were not dependent upon AGO5. Rather, the variable transcription of these loci in Arabidopsis mutant and wild-type populations corresponds to spontaneous differential methylated regions (DMRs) or epialleles. These two DMRs are delineated by RNAs which are highly expressed when the DMR is hypomethylated. 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We further demonstrate that DMR boundaries can be defined by putative non-coding promoter-associated transcripts.</description><subject>Alleles</subject><subject>Arabidopsis</subject><subject>Arabidopsis - genetics</subject><subject>Arabidopsis Proteins - genetics</subject><subject>Arabidopsis thaliana</subject><subject>Bioinformatics</subject><subject>Biology</subject><subject>Deoxyribonucleic acid</subject><subject>Divergence</subject><subject>DNA</subject><subject>DNA Methylation</subject><subject>DNA, Plant - genetics</subject><subject>Epigenesis, Genetic</subject><subject>Epigenetic inheritance</subject><subject>Epigenetics</subject><subject>Gene expression</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genetic divergence</subject><subject>Genetic diversity</subject><subject>Genetic Loci</subject><subject>Genetic Variation</subject><subject>Genetics, Population</subject><subject>Genomes</subject><subject>Genotype</subject><subject>Inbreeding</subject><subject>Methylation</subject><subject>Mutation</subject><subject>Nucleotide sequence</subject><subject>Physiological aspects</subject><subject>Plant sciences</subject><subject>Populations</subject><subject>Promoter Regions, Genetic</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>RNA polymerase</subject><subject>RNA, Messenger - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Havecker, Ericka R</au><au>Wallbridge, Laura M</au><au>Fedito, Paola</au><au>Hardcastle, Thomas J</au><au>Baulcombe, David C</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Metastable differentially methylated regions within Arabidopsis inbred populations are associated with modified expression of non-coding transcripts</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2012-09-20</date><risdate>2012</risdate><volume>7</volume><issue>9</issue><spage>e45242</spage><epage>e45242</epage><pages>e45242-e45242</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Individual plants within a population may vary at both genetic and epigenetic levels. The rate of genetic divergence and its underlying mechanisms is well understood. Less is known about the factors contributing to epigenetic divergence among isogenic populations except that, despite the presence of mechanisms that faithfully maintain epigenetic marks, epigenetic differences are more frequent than genetic variation. Epigenetically divergent stretches of isogenic DNA sequence are called epialleles. Currently, it is not clear why certain regions exhibit variable epigenetic status. We identified and characterised two long RNA transcripts with altered expression and DNA methylation in an ago5 mutant. However, further investigation revealed that these changes were not dependent upon AGO5. Rather, the variable transcription of these loci in Arabidopsis mutant and wild-type populations corresponds to spontaneous differential methylated regions (DMRs) or epialleles. These two DMRs are delineated by RNAs which are highly expressed when the DMR is hypomethylated. Furthermore, they control the expression of 5' transcriptional start site mRNA variants of nearby protein coding genes. Our data support the recent observations that meiotically stable DMRs exist within inbred populations. We further demonstrate that DMR boundaries can be defined by putative non-coding promoter-associated transcripts.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>23028873</pmid><doi>10.1371/journal.pone.0045242</doi><tpages>e45242</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Alleles Arabidopsis Arabidopsis - genetics Arabidopsis Proteins - genetics Arabidopsis thaliana Bioinformatics Biology Deoxyribonucleic acid Divergence DNA DNA Methylation DNA, Plant - genetics Epigenesis, Genetic Epigenetic inheritance Epigenetics Gene expression Genes Genetic aspects Genetic divergence Genetic diversity Genetic Loci Genetic Variation Genetics, Population Genomes Genotype Inbreeding Methylation Mutation Nucleotide sequence Physiological aspects Plant sciences Populations Promoter Regions, Genetic Ribonucleic acid RNA RNA polymerase RNA, Messenger - genetics RNA, Untranslated - genetics RNA-Binding Proteins - genetics Transcription |
| title | Metastable differentially methylated regions within Arabidopsis inbred populations are associated with modified expression of non-coding transcripts |
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