Genome-wide analysis of long noncoding RNAs, 24-nt siRNAs, DNA methylation and H3K27me3 marks in Brassica rapa

Mehraj, H; Shea, DJ; Takahashi, S; Miyaji, N; Akter, A; Seki, M; Dennis, ES; Fujimoto, R; Osabe, K

Genome-wide analysis of long noncoding RNAs, 24-nt siRNAs, DNA methylation and H3K27me3 marks in Brassica rapa

Mehraj, H Shea, DJ Takahashi, S Miyaji, N Akter, A Seki, M Dennis, ES Fujimoto, R Osabe, K

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Publisher:: Public Library of Science (PLoS)
Publication Type:: Journal Article
Citation:: PLoS One, 2021, 16, (3), pp. 1-18
Issue Date:: 2021-03-31

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Field	Value	Language
dc.contributor.author	Mehraj, H
dc.contributor.author	Shea, DJ
dc.contributor.author	Takahashi, S
dc.contributor.author	Miyaji, N
dc.contributor.author	Akter, A
dc.contributor.author	Seki, M
dc.contributor.author	Dennis, ES
dc.contributor.author	Fujimoto, R
dc.contributor.author	Osabe, K
dc.date.accessioned	2022-02-02T21:06:27Z
dc.date.available	2021-03-18
dc.date.available	2022-02-02T21:06:27Z
dc.date.issued	2021-03-31
dc.identifier.citation	PLoS One, 2021, 16, (3), pp. 1-18
dc.identifier.issn	1932-6203
dc.identifier.issn	1932-6203
dc.identifier.uri	http://hdl.handle.net/10453/154147
dc.description.abstract	Long noncoding RNAs (lncRNAs) are RNA fragments that generally do not code for a protein but are involved in epigenetic gene regulation. In this study, lncRNAs of Brassica rapa were classified into long intergenic noncoding RNAs, natural antisense RNAs, and intronic noncoding RNAs and their expression analyzed in relation to genome-wide 24-nt small interfering RNAs (siRNAs), DNA methylation, and histone H3 lysine 27 trimethylation marks (H3K27me3). More than 65% of the lncRNAs analyzed consisted of one exon, and more than 55% overlapped with inverted repeat regions (IRRs). Overlap of lncRNAs with IRRs or genomic regions encoding for 24-nt siRNAs resulted in increased DNA methylation levels when both were present. LncRNA did not overlap greatly with H3K27me3 marks, but the expression level of intronic noncoding RNAs that did coincide with H3K27me3 marks was higher than without H3K27me3 marks. The Brassica genus comprises important vegetables and oil seed crops grown across the world. B. rapa is a diploid (AA genome) thought to be one of the ancestral species of both B. juncea (AABB genome) and B. napus (AACC) through genome merging (allotetrapolyploidization). Complex genome restructuring and epigenetic alterations are thought to be involved in these allotetrapolyploidization events. Comparison of lncRNAs between B. rapa and B. nigra, B. oleracea, B. juncea, and B. napus showed the highest conservation with B. oleracea. This study presents a comprehensive analysis of the epigenome structure of B. rapa at multi-epigenetic levels (siRNAs, DNA methylation, H3K27me3, and lncRNAs) and identified a suite of candidate lncRNAs that may be epigenetically regulated in the Brassica genus.
dc.format	Electronic-eCollection
dc.language	eng
dc.publisher	Public Library of Science (PLoS)
dc.relation.ispartof	PLoS One
dc.relation.isbasedon	10.1371/journal.pone.0242530
dc.rights	info:eu-repo/semantics/openAccess
dc.subject.classification	General Science & Technology
dc.subject.mesh	Brassica rapa
dc.subject.mesh	DNA Methylation
dc.subject.mesh	Diploidy
dc.subject.mesh	Epigenesis, Genetic
dc.subject.mesh	Gene Ontology
dc.subject.mesh	Genome, Plant
dc.subject.mesh	Histones
dc.subject.mesh	Inverted Repeat Sequences
dc.subject.mesh	Plant Leaves
dc.subject.mesh	Plant Proteins
dc.subject.mesh	RNA, Long Noncoding
dc.subject.mesh	RNA, Plant
dc.subject.mesh	RNA, Small Interfering
dc.subject.mesh	Reverse Transcriptase Polymerase Chain Reaction
dc.subject.mesh	Brassica rapa
dc.subject.mesh	Plant Leaves
dc.subject.mesh	Histones
dc.subject.mesh	Plant Proteins
dc.subject.mesh	RNA, Small Interfering
dc.subject.mesh	RNA, Plant
dc.subject.mesh	Reverse Transcriptase Polymerase Chain Reaction
dc.subject.mesh	DNA Methylation
dc.subject.mesh	Epigenesis, Genetic
dc.subject.mesh	Diploidy
dc.subject.mesh	Genome, Plant
dc.subject.mesh	Inverted Repeat Sequences
dc.subject.mesh	RNA, Long Noncoding
dc.subject.mesh	Gene Ontology
dc.title	Genome-wide analysis of long noncoding RNAs, 24-nt siRNAs, DNA methylation and H3K27me3 marks in Brassica rapa
dc.type	Journal Article
utslib.citation.volume	16
utslib.location.activity	United States
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.consider-herdc	false
dc.date.updated	2022-02-02T21:06:22Z
pubs.issue	3
pubs.publication-status	Published
pubs.volume	16
utslib.citation.issue	3

Abstract:

Long noncoding RNAs (lncRNAs) are RNA fragments that generally do not code for a protein but are involved in epigenetic gene regulation. In this study, lncRNAs of Brassica rapa were classified into long intergenic noncoding RNAs, natural antisense RNAs, and intronic noncoding RNAs and their expression analyzed in relation to genome-wide 24-nt small interfering RNAs (siRNAs), DNA methylation, and histone H3 lysine 27 trimethylation marks (H3K27me3). More than 65% of the lncRNAs analyzed consisted of one exon, and more than 55% overlapped with inverted repeat regions (IRRs). Overlap of lncRNAs with IRRs or genomic regions encoding for 24-nt siRNAs resulted in increased DNA methylation levels when both were present. LncRNA did not overlap greatly with H3K27me3 marks, but the expression level of intronic noncoding RNAs that did coincide with H3K27me3 marks was higher than without H3K27me3 marks. The Brassica genus comprises important vegetables and oil seed crops grown across the world. B. rapa is a diploid (AA genome) thought to be one of the ancestral species of both B. juncea (AABB genome) and B. napus (AACC) through genome merging (allotetrapolyploidization). Complex genome restructuring and epigenetic alterations are thought to be involved in these allotetrapolyploidization events. Comparison of lncRNAs between B. rapa and B. nigra, B. oleracea, B. juncea, and B. napus showed the highest conservation with B. oleracea. This study presents a comprehensive analysis of the epigenome structure of B. rapa at multi-epigenetic levels (siRNAs, DNA methylation, H3K27me3, and lncRNAs) and identified a suite of candidate lncRNAs that may be epigenetically regulated in the Brassica genus.

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http://hdl.handle.net/10453/154147