A comparison of transcriptome and epigenetic status between closely related species in the genus Arabidopsis

Kawanabe, T; Fujimoto, R; Sasaki, T; Taylor, JM; Dennis, ES

A comparison of transcriptome and epigenetic status between closely related species in the genus Arabidopsis

Kawanabe, T Fujimoto, R Sasaki, T Taylor, JM Dennis, ES

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Publication Type:: Journal Article
Citation:: Gene, 2012, 506 (2), pp. 301 - 309
Issue Date:: 2012-09-15

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Field	Value	Language
dc.contributor.author	Kawanabe, T	en_US
dc.contributor.author	Fujimoto, R	en_US
dc.contributor.author	Sasaki, T	en_US
dc.contributor.author	Taylor, JM	en_US
dc.contributor.author	Dennis, ES https://orcid.org/0000-0002-7850-591X	en_US
dc.date.available	2012-07-03	en_US
dc.date.issued	2012-09-15	en_US
dc.identifier.citation	Gene, 2012, 506 (2), pp. 301 - 309	en_US
dc.identifier.issn	0378-1119	en_US
dc.identifier.uri	http://hdl.handle.net/10453/28750
dc.description.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. © 2012 Elsevier B.V.	en_US
dc.relation.ispartof	Gene	en_US
dc.relation.isbasedon	10.1016/j.gene.2012.07.003	en_US
dc.subject.classification	Developmental Biology	en_US
dc.subject.mesh	Arabidopsis	en_US
dc.subject.mesh	Plant Proteins	en_US
dc.subject.mesh	Oligonucleotide Array Sequence Analysis	en_US
dc.subject.mesh	Gene Expression Profiling	en_US
dc.subject.mesh	Sequence Analysis, DNA	en_US
dc.subject.mesh	Phylogeny	en_US
dc.subject.mesh	Species Specificity	en_US
dc.subject.mesh	DNA Methylation	en_US
dc.subject.mesh	Epigenesis, Genetic	en_US
dc.subject.mesh	Gene Expression Regulation, Plant	en_US
dc.subject.mesh	Genomic Imprinting	en_US
dc.subject.mesh	Genes, Plant	en_US
dc.subject.mesh	Genetic Variation	en_US
dc.subject.mesh	Transcriptome	en_US
dc.title	A comparison of transcriptome and epigenetic status between closely related species in the genus Arabidopsis	en_US
dc.type	Journal Article
utslib.citation.volume	2	en_US
utslib.citation.volume	506	en_US
utslib.for	0604 Genetics	en_US
utslib.for	0606 Physiology	en_US
utslib.for	1108 Medical Microbiology	en_US
pubs.embargo.period	Not known	en_US
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Faculty of Science/School of Life Sciences
utslib.copyright.status	closed_access
pubs.issue	2	en_US
pubs.publication-status	Published	en_US
pubs.volume	506	en_US

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. © 2012 Elsevier B.V.

Please use this identifier to cite or link to this item:

http://hdl.handle.net/10453/28750