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Genome-wide identification of physically clustered genes suggests chromatin-level co-regulation in male reproductive development in Arabidopsis thaliana

Co-expression of physically linked genes occurs surprisingly frequently in eukaryotes. Such chromosomal clustering may confer a selective advantage as it enables coordinated gene regulation at the chromatin level. We studied the chromosomal organization of genes involved in male reproductive develop...

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Autores principales: Reimegård, Johan, Kundu, Snehangshu, Pendle, Ali, Irish, Vivian F., Shaw, Peter, Nakayama, Naomi, Sundström, Jens F., Emanuelsson, Olof
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5389543/
https://www.ncbi.nlm.nih.gov/pubmed/28175342
http://dx.doi.org/10.1093/nar/gkx087
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author Reimegård, Johan
Kundu, Snehangshu
Pendle, Ali
Irish, Vivian F.
Shaw, Peter
Nakayama, Naomi
Sundström, Jens F.
Emanuelsson, Olof
author_facet Reimegård, Johan
Kundu, Snehangshu
Pendle, Ali
Irish, Vivian F.
Shaw, Peter
Nakayama, Naomi
Sundström, Jens F.
Emanuelsson, Olof
author_sort Reimegård, Johan
collection PubMed
description Co-expression of physically linked genes occurs surprisingly frequently in eukaryotes. Such chromosomal clustering may confer a selective advantage as it enables coordinated gene regulation at the chromatin level. We studied the chromosomal organization of genes involved in male reproductive development in Arabidopsis thaliana. We developed an in-silico tool to identify physical clusters of co-regulated genes from gene expression data. We identified 17 clusters (96 genes) involved in stamen development and acting downstream of the transcriptional activator MS1 (MALE STERILITY 1), which contains a PHD domain associated with chromatin re-organization. The clusters exhibited little gene homology or promoter element similarity, and largely overlapped with reported repressive histone marks. Experiments on a subset of the clusters suggested a link between expression activation and chromatin conformation: qRT-PCR and mRNA in situ hybridization showed that the clustered genes were up-regulated within 48 h after MS1 induction; out of 14 chromatin-remodeling mutants studied, expression of clustered genes was consistently down-regulated only in hta9/hta11, previously associated with metabolic cluster activation; DNA fluorescence in situ hybridization confirmed that transcriptional activation of the clustered genes was correlated with open chromatin conformation. Stamen development thus appears to involve transcriptional activation of physically clustered genes through chromatin de-condensation.
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spelling pubmed-53895432017-04-24 Genome-wide identification of physically clustered genes suggests chromatin-level co-regulation in male reproductive development in Arabidopsis thaliana Reimegård, Johan Kundu, Snehangshu Pendle, Ali Irish, Vivian F. Shaw, Peter Nakayama, Naomi Sundström, Jens F. Emanuelsson, Olof Nucleic Acids Res Genomics Co-expression of physically linked genes occurs surprisingly frequently in eukaryotes. Such chromosomal clustering may confer a selective advantage as it enables coordinated gene regulation at the chromatin level. We studied the chromosomal organization of genes involved in male reproductive development in Arabidopsis thaliana. We developed an in-silico tool to identify physical clusters of co-regulated genes from gene expression data. We identified 17 clusters (96 genes) involved in stamen development and acting downstream of the transcriptional activator MS1 (MALE STERILITY 1), which contains a PHD domain associated with chromatin re-organization. The clusters exhibited little gene homology or promoter element similarity, and largely overlapped with reported repressive histone marks. Experiments on a subset of the clusters suggested a link between expression activation and chromatin conformation: qRT-PCR and mRNA in situ hybridization showed that the clustered genes were up-regulated within 48 h after MS1 induction; out of 14 chromatin-remodeling mutants studied, expression of clustered genes was consistently down-regulated only in hta9/hta11, previously associated with metabolic cluster activation; DNA fluorescence in situ hybridization confirmed that transcriptional activation of the clustered genes was correlated with open chromatin conformation. Stamen development thus appears to involve transcriptional activation of physically clustered genes through chromatin de-condensation. Oxford University Press 2017-04-07 2017-02-08 /pmc/articles/PMC5389543/ /pubmed/28175342 http://dx.doi.org/10.1093/nar/gkx087 Text en © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Genomics
Reimegård, Johan
Kundu, Snehangshu
Pendle, Ali
Irish, Vivian F.
Shaw, Peter
Nakayama, Naomi
Sundström, Jens F.
Emanuelsson, Olof
Genome-wide identification of physically clustered genes suggests chromatin-level co-regulation in male reproductive development in Arabidopsis thaliana
title Genome-wide identification of physically clustered genes suggests chromatin-level co-regulation in male reproductive development in Arabidopsis thaliana
title_full Genome-wide identification of physically clustered genes suggests chromatin-level co-regulation in male reproductive development in Arabidopsis thaliana
title_fullStr Genome-wide identification of physically clustered genes suggests chromatin-level co-regulation in male reproductive development in Arabidopsis thaliana
title_full_unstemmed Genome-wide identification of physically clustered genes suggests chromatin-level co-regulation in male reproductive development in Arabidopsis thaliana
title_short Genome-wide identification of physically clustered genes suggests chromatin-level co-regulation in male reproductive development in Arabidopsis thaliana
title_sort genome-wide identification of physically clustered genes suggests chromatin-level co-regulation in male reproductive development in arabidopsis thaliana
topic Genomics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5389543/
https://www.ncbi.nlm.nih.gov/pubmed/28175342
http://dx.doi.org/10.1093/nar/gkx087
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