A comparison of transcriptome and epigenetic status between closely related species in the genus Arabidopsis
Difference in the level of expression of genes is one of the factors contributing to plant phenotype. As well as being under genetic control, gene expression is regulated by epigenetic processes such as DNA methylation and histone modifications. We compared genome-wide gene expression between Arabid...
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| Veröffentlicht in: | Gene 2012-09, Vol.506 (2), p.301-309 |
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| creator | Kawanabe, Takahiro Fujimoto, Ryo Sasaki, Taku Taylor, Jennifer M. Dennis, Elizabeth S. |
| description | Difference in the level of expression of genes is one of the factors contributing to plant phenotype. As well as being under genetic control, gene expression is regulated by epigenetic processes such as DNA methylation and histone modifications. We compared genome-wide gene expression between Arabidopsis thaliana and the related species Arabidopsis lyrata subsp. lyrata and Arabidopsis halleri subsp. gemmifera to understand which genes might contribute to species differences. Genes categorized into response to stress tended to show differential expression between species, suggesting that divergence of expression in these genes contributes to adaptation to environmental conditions following the divergence of species. Regions methylated in A. lyrata were identified from Methylated-DNA immunoprecipitation, and this DNA methylation profile together with transcriptome data revealed that gene body methylation was not associated with differential gene expression between A. thaliana and A. lyrata. The DNA methylation status of four putative imprinted genes of A. lyrata was examined and found to be conserved in vegetative tissues between A. thaliana and A. lyrata in FIS2, HDG3, and HDG9, but not in HDG8.
► We compared gene expression between three Arabidopsis species. ► Genes of response to stress tended to show differential expression between species. ► Gene body methylation was not associated with differential gene expression. ► There are conservation and variation of imprinted genes between species. |
| doi_str_mv | 10.1016/j.gene.2012.07.003 |
| format | Article |
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► We compared gene expression between three Arabidopsis species. ► Genes of response to stress tended to show differential expression between species. ► Gene body methylation was not associated with differential gene expression. ► There are conservation and variation of imprinted genes between species.</description><identifier>ISSN: 0378-1119</identifier><identifier>EISSN: 1879-0038</identifier><identifier>DOI: 10.1016/j.gene.2012.07.003</identifier><identifier>PMID: 22796129</identifier><language>eng</language><publisher>Netherlands: Elsevier B.V</publisher><subject>Arabidopsis - genetics ; Arabidopsis - metabolism ; Arabidopsis lyrata subsp. lyrata ; Arabidopsis thaliana ; DNA Methylation ; environmental factors ; Epigenesis, Genetic ; epigenetics ; gene expression ; Gene Expression Profiling ; gene expression regulation ; Gene Expression Regulation, Plant ; genes ; Genes, Plant ; Genetic Variation ; Genomic Imprinting ; histones ; Imprinting ; interspecific variation ; Microarray ; Oligonucleotide Array Sequence Analysis ; phenotype ; Phylogeny ; Plant Proteins ; precipitin tests ; Sequence Analysis, DNA ; Species Specificity ; stress response ; Transcriptome ; Transposon</subject><ispartof>Gene, 2012-09, Vol.506 (2), p.301-309</ispartof><rights>2012 Elsevier B.V.</rights><rights>Copyright © 2012 Elsevier B.V. All rights reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c446t-66c8936e5401ab07adb39237f777b3b78a178f9a7176bee2ba56c4651bbf71643</citedby><cites>FETCH-LOGICAL-c446t-66c8936e5401ab07adb39237f777b3b78a178f9a7176bee2ba56c4651bbf71643</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.gene.2012.07.003$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,780,784,3550,27924,27925,45995</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/22796129$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Kawanabe, Takahiro</creatorcontrib><creatorcontrib>Fujimoto, Ryo</creatorcontrib><creatorcontrib>Sasaki, Taku</creatorcontrib><creatorcontrib>Taylor, Jennifer M.</creatorcontrib><creatorcontrib>Dennis, Elizabeth S.</creatorcontrib><title>A comparison of transcriptome and epigenetic status between closely related species in the genus Arabidopsis</title><title>Gene</title><addtitle>Gene</addtitle><description>Difference in the level of expression of genes is one of the factors contributing to plant phenotype. As well as being under genetic control, gene expression is regulated by epigenetic processes such as DNA methylation and histone modifications. We compared genome-wide gene expression between Arabidopsis thaliana and the related species Arabidopsis lyrata subsp. lyrata and Arabidopsis halleri subsp. gemmifera to understand which genes might contribute to species differences. Genes categorized into response to stress tended to show differential expression between species, suggesting that divergence of expression in these genes contributes to adaptation to environmental conditions following the divergence of species. Regions methylated in A. lyrata were identified from Methylated-DNA immunoprecipitation, and this DNA methylation profile together with transcriptome data revealed that gene body methylation was not associated with differential gene expression between A. thaliana and A. lyrata. The DNA methylation status of four putative imprinted genes of A. lyrata was examined and found to be conserved in vegetative tissues between A. thaliana and A. lyrata in FIS2, HDG3, and HDG9, but not in HDG8.
► We compared gene expression between three Arabidopsis species. ► Genes of response to stress tended to show differential expression between species. ► Gene body methylation was not associated with differential gene expression. ► There are conservation and variation of imprinted genes between species.</description><subject>Arabidopsis - genetics</subject><subject>Arabidopsis - metabolism</subject><subject>Arabidopsis lyrata subsp. lyrata</subject><subject>Arabidopsis thaliana</subject><subject>DNA Methylation</subject><subject>environmental factors</subject><subject>Epigenesis, Genetic</subject><subject>epigenetics</subject><subject>gene expression</subject><subject>Gene Expression Profiling</subject><subject>gene expression regulation</subject><subject>Gene Expression Regulation, Plant</subject><subject>genes</subject><subject>Genes, Plant</subject><subject>Genetic Variation</subject><subject>Genomic Imprinting</subject><subject>histones</subject><subject>Imprinting</subject><subject>interspecific variation</subject><subject>Microarray</subject><subject>Oligonucleotide Array Sequence Analysis</subject><subject>phenotype</subject><subject>Phylogeny</subject><subject>Plant Proteins</subject><subject>precipitin tests</subject><subject>Sequence Analysis, DNA</subject><subject>Species Specificity</subject><subject>stress response</subject><subject>Transcriptome</subject><subject>Transposon</subject><issn>0378-1119</issn><issn>1879-0038</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kc1u3CAURlGVqpmkfYEuGpbZ2OXHBlvKZhSlTaVIXbRZI8DXKSPbuFymUd6-jGaaZdnA4nwflwMhHzmrOePq865-ggVqwbioma4Zk2_Ihne6r8qxOyMbJnVXcc77c3KBuGNlta14R86F0L3iot-QaUt9nFebAsaFxpHmZBf0Kaw5zkDtMlBYw-GeHDzFbPMeqYP8DLBQP0WE6YUmmGyGgeIKPgDSsND8C2hJFXibrAtDXDHge_J2tBPCh9N-SR6_3P28va8evn_9drt9qHzTqFwp5bteKmgbxq1j2g5O9kLqUWvtpNOd5bobe6u5Vg5AONsq36iWOzdqrhp5Sa6PvWuKv_eA2cwBPUyTXSDu0XAmhZataPqCiiPqU0RMMJo1hdmmlwKZg2WzM4fXm4Nlw7Qpakvo06l_72YYXiP_tBbg6giMNhr7VOSaxx-loS0_0EgtRCFujgQUD38CJINF3eJhCAl8NkMM_5vgL6nwmDw</recordid><startdate>20120915</startdate><enddate>20120915</enddate><creator>Kawanabe, Takahiro</creator><creator>Fujimoto, Ryo</creator><creator>Sasaki, Taku</creator><creator>Taylor, Jennifer M.</creator><creator>Dennis, Elizabeth S.</creator><general>Elsevier B.V</general><scope>FBQ</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope></search><sort><creationdate>20120915</creationdate><title>A comparison of transcriptome and epigenetic status between closely related species in the genus Arabidopsis</title><author>Kawanabe, Takahiro ; Fujimoto, Ryo ; Sasaki, Taku ; Taylor, Jennifer M. ; Dennis, Elizabeth S.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c446t-66c8936e5401ab07adb39237f777b3b78a178f9a7176bee2ba56c4651bbf71643</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>Arabidopsis - genetics</topic><topic>Arabidopsis - metabolism</topic><topic>Arabidopsis lyrata subsp. lyrata</topic><topic>Arabidopsis thaliana</topic><topic>DNA Methylation</topic><topic>environmental factors</topic><topic>Epigenesis, Genetic</topic><topic>epigenetics</topic><topic>gene expression</topic><topic>Gene Expression Profiling</topic><topic>gene expression regulation</topic><topic>Gene Expression Regulation, Plant</topic><topic>genes</topic><topic>Genes, Plant</topic><topic>Genetic Variation</topic><topic>Genomic Imprinting</topic><topic>histones</topic><topic>Imprinting</topic><topic>interspecific variation</topic><topic>Microarray</topic><topic>Oligonucleotide Array Sequence Analysis</topic><topic>phenotype</topic><topic>Phylogeny</topic><topic>Plant Proteins</topic><topic>precipitin tests</topic><topic>Sequence Analysis, DNA</topic><topic>Species Specificity</topic><topic>stress response</topic><topic>Transcriptome</topic><topic>Transposon</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Kawanabe, Takahiro</creatorcontrib><creatorcontrib>Fujimoto, Ryo</creatorcontrib><creatorcontrib>Sasaki, Taku</creatorcontrib><creatorcontrib>Taylor, Jennifer M.</creatorcontrib><creatorcontrib>Dennis, Elizabeth S.</creatorcontrib><collection>AGRIS</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Gene</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Kawanabe, Takahiro</au><au>Fujimoto, Ryo</au><au>Sasaki, Taku</au><au>Taylor, Jennifer M.</au><au>Dennis, Elizabeth S.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>A comparison of transcriptome and epigenetic status between closely related species in the genus Arabidopsis</atitle><jtitle>Gene</jtitle><addtitle>Gene</addtitle><date>2012-09-15</date><risdate>2012</risdate><volume>506</volume><issue>2</issue><spage>301</spage><epage>309</epage><pages>301-309</pages><issn>0378-1119</issn><eissn>1879-0038</eissn><abstract>Difference in the level of expression of genes is one of the factors contributing to plant phenotype. As well as being under genetic control, gene expression is regulated by epigenetic processes such as DNA methylation and histone modifications. We compared genome-wide gene expression between Arabidopsis thaliana and the related species Arabidopsis lyrata subsp. lyrata and Arabidopsis halleri subsp. gemmifera to understand which genes might contribute to species differences. Genes categorized into response to stress tended to show differential expression between species, suggesting that divergence of expression in these genes contributes to adaptation to environmental conditions following the divergence of species. Regions methylated in A. lyrata were identified from Methylated-DNA immunoprecipitation, and this DNA methylation profile together with transcriptome data revealed that gene body methylation was not associated with differential gene expression between A. thaliana and A. lyrata. The DNA methylation status of four putative imprinted genes of A. lyrata was examined and found to be conserved in vegetative tissues between A. thaliana and A. lyrata in FIS2, HDG3, and HDG9, but not in HDG8.
► We compared gene expression between three Arabidopsis species. ► Genes of response to stress tended to show differential expression between species. ► Gene body methylation was not associated with differential gene expression. ► There are conservation and variation of imprinted genes between species.</abstract><cop>Netherlands</cop><pub>Elsevier B.V</pub><pmid>22796129</pmid><doi>10.1016/j.gene.2012.07.003</doi><tpages>9</tpages></addata></record> |
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| subjects | Arabidopsis - genetics Arabidopsis - metabolism Arabidopsis lyrata subsp. lyrata Arabidopsis thaliana DNA Methylation environmental factors Epigenesis, Genetic epigenetics gene expression Gene Expression Profiling gene expression regulation Gene Expression Regulation, Plant genes Genes, Plant Genetic Variation Genomic Imprinting histones Imprinting interspecific variation Microarray Oligonucleotide Array Sequence Analysis phenotype Phylogeny Plant Proteins precipitin tests Sequence Analysis, DNA Species Specificity stress response Transcriptome Transposon |
| title | A comparison of transcriptome and epigenetic status between closely related species in the genus Arabidopsis |
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