The role of epigenetic modifications in the transcriptional regulation of long noncoding RNAs in Brassica rapa vegetables

Kamiya, Y; Shiraki, S; Mehraj, H; Akter, MA; Takahashi, S; Seki, M; Dennis, ES; Osabe, K; Fujimoto, R

The role of epigenetic modifications in the transcriptional regulation of long noncoding RNAs in Brassica rapa vegetables

Kamiya, Y Shiraki, S Mehraj, H Akter, MA Takahashi, S Seki, M Dennis, ES Osabe, K Fujimoto, R

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Publisher:: International Society for Horticultural Science (ISHS)
Publication Type:: Journal Article
Citation:: Acta Horticulturae, 2023, (1362), pp. 65-70
Issue Date:: 2023-01-01

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Field	Value	Language
dc.contributor.author	Kamiya, Y
dc.contributor.author	Shiraki, S
dc.contributor.author	Mehraj, H
dc.contributor.author	Akter, MA
dc.contributor.author	Takahashi, S
dc.contributor.author	Seki, M
dc.contributor.author	Dennis, ES
dc.contributor.author	Osabe, K
dc.contributor.author	Fujimoto, R
dc.date.accessioned	2024-02-13T22:08:11Z
dc.date.available	2024-02-13T22:08:11Z
dc.date.issued	2023-01-01
dc.identifier.citation	Acta Horticulturae, 2023, (1362), pp. 65-70
dc.identifier.issn	0567-7572
dc.identifier.issn	2406-6168
dc.identifier.uri	http://hdl.handle.net/10453/175651
dc.description.abstract	Plant transcriptome analyses have revealed RNAs devoid of protein-coding potential noncoding RNAs (ncRNAs). Long noncoding RNAs (lncRNAs) that are longer than 200 nucleotides (nt) are classified by their position and orientation of transcription. There are long intergenic noncoding RNAs (lincRNAs), intronic noncoding RNAs (incRNAs) derived from introns, and natural antisense transcripts (NATs) transcribed from the cDNA strand of their associated genes. Recent studies have shown that lncRNAs play crucial roles in abiotic and biotic stress responses. However, studies on the mechanism of lncRNA expression regulation are limited in plants. In this study, we identified lncRNAs with dimethylation of lysine 9 of histone H3 (H3K9me2) marks in their genomic region. There were fewer lncRNAs with H3K9me2 marks in their encoding regions than with the other histone modifications (H3K4me3, H3K36me3, H3K27me3). The encoding regions of lncRNAs with H3K9me2 marks tended to overlap inverted repeat regions (IRRs). LncRNAs with H3K9me2 marks in their encoding region showed no tendency to repress expression. The DNA methylation level in the encoding regions of lncRNAs with H3K9me2 marks was higher than that of lncRNAs with the other histone modifications, especially in lincRNAs encoding regions. This study presents a comprehensive analysis of the H3K9me2 in lncRNA encoding regions in Brassica rapa.
dc.language	en
dc.publisher	International Society for Horticultural Science (ISHS)
dc.relation.ispartof	Acta Horticulturae
dc.relation.isbasedon	10.17660/ActaHortic.2023.1362.10
dc.rights	info:eu-repo/semantics/closedAccess
dc.subject	0607 Plant Biology, 0706 Horticultural Production
dc.subject.classification	Plant Biology & Botany
dc.subject.classification	3008 Horticultural production
dc.subject.classification	3108 Plant biology
dc.title	The role of epigenetic modifications in the transcriptional regulation of long noncoding RNAs in Brassica rapa vegetables
dc.type	Journal Article
utslib.for	0607 Plant Biology
utslib.for	0706 Horticultural Production
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	*
dc.date.updated	2024-02-13T22:08:10Z
pubs.issue	1362
pubs.publication-status	Published
utslib.citation.issue	1362

Abstract:

Plant transcriptome analyses have revealed RNAs devoid of protein-coding potential noncoding RNAs (ncRNAs). Long noncoding RNAs (lncRNAs) that are longer than 200 nucleotides (nt) are classified by their position and orientation of transcription. There are long intergenic noncoding RNAs (lincRNAs), intronic noncoding RNAs (incRNAs) derived from introns, and natural antisense transcripts (NATs) transcribed from the cDNA strand of their associated genes. Recent studies have shown that lncRNAs play crucial roles in abiotic and biotic stress responses. However, studies on the mechanism of lncRNA expression regulation are limited in plants. In this study, we identified lncRNAs with dimethylation of lysine 9 of histone H3 (H3K9me2) marks in their genomic region. There were fewer lncRNAs with H3K9me2 marks in their encoding regions than with the other histone modifications (H3K4me3, H3K36me3, H3K27me3). The encoding regions of lncRNAs with H3K9me2 marks tended to overlap inverted repeat regions (IRRs). LncRNAs with H3K9me2 marks in their encoding region showed no tendency to repress expression. The DNA methylation level in the encoding regions of lncRNAs with H3K9me2 marks was higher than that of lncRNAs with the other histone modifications, especially in lincRNAs encoding regions. This study presents a comprehensive analysis of the H3K9me2 in lncRNA encoding regions in Brassica rapa.

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http://hdl.handle.net/10453/175651