Genome-wide characterization of DNA methylation, small RNA expression, and histone H3 lysine nine di-methylation in Brassica rapa L.

Takahashi, S; Osabe, K; Fukushima, N; Takuno, S; Miyaji, N; Shimizu, M; Takasaki-Yasuda, T; Suzuki, Y; Dennis, ES; Seki, M; Fujimoto, R

Genome-wide characterization of DNA methylation, small RNA expression, and histone H3 lysine nine di-methylation in Brassica rapa L.

Takahashi, S Osabe, K Fukushima, N Takuno, S Miyaji, N Shimizu, M Takasaki-Yasuda, T Suzuki, Y Dennis, ES

Seki, M Fujimoto, R

Permalink

Publication Type:: Journal Article
Citation:: DNA Research, 2018, 25 (5), pp. 511 - 520
Issue Date:: 2018-01-01

Open Access

Copyright Clearance Process

Recently Added
In Progress
Open Access

This item is open access.

Adobe PDF

Download Published VersionAdobe PDF (370.66 kB)

View on publisher's site

View statistics

Full metadata record

Field	Value	Language
dc.contributor.author	Takahashi, S	en_US
dc.contributor.author	Osabe, K	en_US
dc.contributor.author	Fukushima, N	en_US
dc.contributor.author	Takuno, S	en_US
dc.contributor.author	Miyaji, N	en_US
dc.contributor.author	Shimizu, M	en_US
dc.contributor.author	Takasaki-Yasuda, T	en_US
dc.contributor.author	Suzuki, Y	en_US
dc.contributor.author	Dennis, ES https://orcid.org/0000-0002-7850-591X	en_US
dc.contributor.author	Seki, M	en_US
dc.contributor.author	Fujimoto, R	en_US
dc.date.available	2018-05-30	en_US
dc.date.issued	2018-01-01	en_US
dc.identifier.citation	DNA Research, 2018, 25 (5), pp. 511 - 520	en_US
dc.identifier.issn	1340-2838	en_US
dc.identifier.uri	http://hdl.handle.net/10453/131062
dc.description.abstract	© The Author(s) 2018. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. Epigenetic gene regulation is crucial to plant life and can involve dynamic interactions between various histone modifications, DNA methylation, and small RNAs. Detailed analysis of epigenome information is anticipated to reveal how the DNA sequence of the genome is translated into the plant’s phenotype. The aim of this study was to map the DNA methylation state at the whole genome level and to clarify the relationship between DNA methylation and transcription, small RNA expression, and histone H3 lysine 9 di-methylation (H3K9me2) in Brassica rapa. We performed whole genome bisulfite sequencing, small RNA sequencing, and chromatin immunoprecipitation sequencing using H3K9me2 antibody in a Chinese cabbage inbred line, RJKB-T24, and examined the impact of epigenetic states on transcription. Cytosine methylation in DNA was analysed in different sequence contexts (CG, CHG, and CHH) (where H could be A, C, or T) and position (promoter, exon, intron, terminator, interspersed repeat regions), and the H3K9me2 and 24 nucleotide small interfering RNAs (24nt-siRNA) were overlaid onto the B. rapa reference genome. The epigenome was compared with that of Arabidopsis thaliana and the relationship between the position of DNA methylation and gene expression, and the involvement of 24nt siRNAs and H3K9me2 are discussed.	en_US
dc.relation.ispartof	DNA Research	en_US
dc.relation.isbasedon	10.1093/dnares/dsy021	en_US
dc.subject.classification	Plant Biology & Botany	en_US
dc.subject.mesh	Brassica rapa	en_US
dc.subject.mesh	Histones	en_US
dc.subject.mesh	Chromatin Immunoprecipitation	en_US
dc.subject.mesh	Genomics	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	Genome, Plant	en_US
dc.subject.mesh	Genome-Wide Association Study	en_US
dc.subject.mesh	RNA, Small Untranslated	en_US
dc.subject.mesh	High-Throughput Nucleotide Sequencing	en_US
dc.title	Genome-wide characterization of DNA methylation, small RNA expression, and histone H3 lysine nine di-methylation in Brassica rapa L.	en_US
dc.type	Journal Article
utslib.citation.volume	5	en_US
utslib.citation.volume	25	en_US
utslib.for	0604 Genetics	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	open_access
pubs.issue	5	en_US
pubs.publication-status	Published	en_US
pubs.volume	25	en_US

Abstract:

© The Author(s) 2018. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. Epigenetic gene regulation is crucial to plant life and can involve dynamic interactions between various histone modifications, DNA methylation, and small RNAs. Detailed analysis of epigenome information is anticipated to reveal how the DNA sequence of the genome is translated into the plant’s phenotype. The aim of this study was to map the DNA methylation state at the whole genome level and to clarify the relationship between DNA methylation and transcription, small RNA expression, and histone H3 lysine 9 di-methylation (H3K9me2) in Brassica rapa. We performed whole genome bisulfite sequencing, small RNA sequencing, and chromatin immunoprecipitation sequencing using H3K9me2 antibody in a Chinese cabbage inbred line, RJKB-T24, and examined the impact of epigenetic states on transcription. Cytosine methylation in DNA was analysed in different sequence contexts (CG, CHG, and CHH) (where H could be A, C, or T) and position (promoter, exon, intron, terminator, interspersed repeat regions), and the H3K9me2 and 24 nucleotide small interfering RNAs (24nt-siRNA) were overlaid onto the B. rapa reference genome. The epigenome was compared with that of Arabidopsis thaliana and the relationship between the position of DNA methylation and gene expression, and the involvement of 24nt siRNAs and H3K9me2 are discussed.

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

http://hdl.handle.net/10453/131062