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Research article2017Peer reviewedOpen access

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

Reimegard, Johan; Kundu, Snehangshu; Pendle, Ali; Irish, Vivian F.; Shaw, Peter; Nakayama, Naomi; Sundstrom, Jens F.; Emanuelsson, Olof

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 downregulated 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 decondensation.

Published in

Nucleic Acids Research
2017, Volume: 45, number: 6, pages: 3253-3265
Publisher: OXFORD UNIV PRESS

        SLU Authors

      • Kundu, Snehangshu

        • Department of Plant Biology, Swedish University of Agricultural Sciences

        • UKÄ Subject classification

        Developmental Biology
        Bioinformatics (Computational Biology)
        Genetics and Breeding

        Publication identifier

        DOI: https://doi.org/10.1093/nar/gkx087

        Permanent link to this page (URI)

        https://res.slu.se/id/publ/83511