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

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.

MS1, a direct target of MS188, regulates the expression of key sporophytic pollen coat protein genes in Arabidopsis

“…In ms1 mutants, abnormal exine bacula are observed, with a lack of vesicles associated with intine formation, suggesting that MS1 is involved in pollen wall and coat formation ( Wilson et al , 2001 ; Ito and Shinozaki, 2002 ; Vizcay-Barrena and Wilson, 2006 ; Ito et al , 2007 ). Reimegård et al (2017) found 17 physically converged gene clusters acting downstream of MS1; Clusters #7 and #15 contain the pollen coat extracellular lipase (EXL4–EXL6) proteins and the GRP–oleosin chimeric proteins, respectively ( Fig. 1a , b ).…”

“…Interestingly, these physically clustered and co-regulated genes include not only tandem duplicated genes, but also non-homologous genes. For instance, the ANTHER27/BETA GLUCOSIDASE 20 ( ATA27/BGLU20 ), which locates to Cluster #7, has no homology with any of the adjacent lipases, but shows co-expression with EXL4–EXL6 ( Reimegård et al , 2017 ). ATA27/BGLU20 has tapetum-specific expression and has been proposed as playing an indispensable role in pollen development ( Rubinelli et al , 1998 ; Dong et al , 2019 ).…”

“…ATA27/BGLU20 is predicted to be localized to the endoplasmic reticulum (ER) lumen, which makes this protein less likely to be a sporophytic pollen coat protein (sPCP); however, the co-regulation of this gene with the clustered EXLs may indicate an important role in pollen coat metabolism ( Rubinelli et al , 1998 ). Reimegård et al (2017) speculated that up-regulation of these genes during late tapetum development is due to chromatin conformation changes induced by MS1. However, the relationship between MS1 and these sPCP genes in the tapetum remains unresolved.…”

Chromatin domains in space and their functional implications

“…Earlier studies of gene expression in several plant species have pointed out that it is common to observe co-expression between neighboring genes [52][53][54][55]. An explanation of this phenomenon is that neighboring genes (especially those with overlapping divergent promoters) share some common cis-regulatory elements.…”

Evolclust: automated inference of evolutionary conserved gene clusters in eukaryotes

“…Despite this trend, certain groups of genes remain close in the genome over long evolutionary distances, which suggests that selection acts to maintain their genomic colocalization. Genes within such conserved clusters may have functional links (Lee and Sonnhammer, 2003;Wisecaver et al, 2014), and can be transcribed in a coordinated manner (Boutanaev et al, 2002;Reimegård et al, 2017). Comparative genomics can be used to uncover groups of genes that remain significantly closer than expected, despite extensive gene order shuffling.…”