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Nucleic Acids Res. 2017 Apr 7;45(6):3253-3265. doi: 10.1093/nar/gkx087.

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

Author information

1
Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, KTH Royal Institute of Technology, Solna SE-171 65, Sweden.
2
Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden.
3
Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
4
Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA.
5
Institute of Molecular Plant Science, SynthSys Centre for Synthetic and Systems Biology, and Centre for Science at Extreme Conditions, University of Edinburgh, King's Buildings, Edinburgh, UK.

Abstract

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.

PMID:
28175342
PMCID:
PMC5389543
DOI:
10.1093/nar/gkx087
[Indexed for MEDLINE]
Free PMC Article

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