The role of histone modification in gene expression in Brassica rapa vegetables

Shiraki, S; Kamiya, Y; Mehraj, H; Takahashi, S; Seki, M; Dennis, ES; Fujimoto, R

The role of histone modification in gene expression in Brassica rapa vegetables

Shiraki, S Kamiya, Y Mehraj, H Takahashi, S Seki, M Dennis, ES Fujimoto, R

Permalink

Publisher:: International Society for Horticultural Science (ISHS)
Publication Type:: Journal Article
Citation:: Acta Horticulturae, 2023, (1362), pp. 107-111
Issue Date:: 2023-01-01

Closed Access

	Filename	Description	Size
	22047121_12800581190005671.pdf	Published version	361.62 kB	Adobe PDF	View/Open

Copyright Clearance Process

Recently Added
In Progress
Closed Access

This item is closed access and not available.

Full metadata record

Field	Value	Language
dc.contributor.author	Shiraki, S
dc.contributor.author	Kamiya, Y
dc.contributor.author	Mehraj, H
dc.contributor.author	Takahashi, S
dc.contributor.author	Seki, M
dc.contributor.author	Dennis, ES
dc.contributor.author	Fujimoto, R
dc.date.accessioned	2024-02-19T21:51:32Z
dc.date.available	2024-02-19T21:51:32Z
dc.date.issued	2023-01-01
dc.identifier.citation	Acta Horticulturae, 2023, (1362), pp. 107-111
dc.identifier.issn	0567-7572
dc.identifier.issn	2406-6168
dc.identifier.uri	http://hdl.handle.net/10453/175738
dc.description.abstract	Histone modification is an epigenetic regulatory mechanism, which affects the transcriptional activity of chromatin without changing the DNA sequence, and is crucial for the development and adaptation of plants to changing environments. The application of high-throughput sequencing technologies provides an opportunity to identify genome-wide profiles of histone modification by a combination of chromatin immunoprecipitation (ChIP) and genome-wide sequencing (ChIP-seq). We investigated the distribution of two active histone marks, trimethylation of lysine 4 of histone H3 (H3K4me3) and trimethylation of lysine 36 of histone H3 (H3K36me3), in Brassica rapa L. by ChIP-seq. H3K4me3 and H3K36me3 marks were enriched at the transcription start site of genes, and the transcription level of a gene was positively associated with the level of H3K4me3 and H3K36me3. In this study, we compared H3K4me3 and H3K36me3 levels between the two Chinese cabbage inbred lines in B. rapa var. pekinensis. Most H3K4me3-marked and H3K36me3-marked genes overlapped between the two lines, while 5 and 6% of genes showed a difference in H3K4me3 and H3K36me3 levels between the two lines. Among these genes showing a difference of H3K4me3 or H3K36me3 levels between the lines, 30 and 37% of genes showed a positive association between the level of H3K4me3 or H3K36me3 and the level of transcription. These results suggest that differences in the level of H3K4me3 and H3K36me3 between the lines determine the difference in the transcriptional levels, but did not account for the high percentage of differentially expressed genes seen between the two lines. It will be interesting to examine how histone modifications, which have been found to differ between the lines, are inherited in an F1 or cross-segregating population of these two lines.
dc.language	en
dc.publisher	International Society for Horticultural Science (ISHS)
dc.relation.ispartof	Acta Horticulturae
dc.relation.isbasedon	10.17660/ActaHortic.2023.1362.15
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 histone modification in gene expression 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	2024-02-19T21:51:31Z
pubs.issue	1362
pubs.publication-status	Published
utslib.citation.issue	1362

Abstract:

Histone modification is an epigenetic regulatory mechanism, which affects the transcriptional activity of chromatin without changing the DNA sequence, and is crucial for the development and adaptation of plants to changing environments. The application of high-throughput sequencing technologies provides an opportunity to identify genome-wide profiles of histone modification by a combination of chromatin immunoprecipitation (ChIP) and genome-wide sequencing (ChIP-seq). We investigated the distribution of two active histone marks, trimethylation of lysine 4 of histone H3 (H3K4me3) and trimethylation of lysine 36 of histone H3 (H3K36me3), in Brassica rapa L. by ChIP-seq. H3K4me3 and H3K36me3 marks were enriched at the transcription start site of genes, and the transcription level of a gene was positively associated with the level of H3K4me3 and H3K36me3. In this study, we compared H3K4me3 and H3K36me3 levels between the two Chinese cabbage inbred lines in B. rapa var. pekinensis. Most H3K4me3-marked and H3K36me3-marked genes overlapped between the two lines, while 5 and 6% of genes showed a difference in H3K4me3 and H3K36me3 levels between the two lines. Among these genes showing a difference of H3K4me3 or H3K36me3 levels between the lines, 30 and 37% of genes showed a positive association between the level of H3K4me3 or H3K36me3 and the level of transcription. These results suggest that differences in the level of H3K4me3 and H3K36me3 between the lines determine the difference in the transcriptional levels, but did not account for the high percentage of differentially expressed genes seen between the two lines. It will be interesting to examine how histone modifications, which have been found to differ between the lines, are inherited in an F1 or cross-segregating population of these two lines.

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

http://hdl.handle.net/10453/175738