Functional characterization of open chromatin in bidirectional promoters of rice

Abstract

Bidirectional gene pairs tend to be highly coregulated and function in similar biological processes in eukaryotic genomes. Structural features and functional consequences of bidirectional promoters (BDPs) have received considerable attention among diverse species. However, the underlying mechanisms responsible for the bidirectional transcription and coexpression of BDPs remain poorly understood in plants. In this study, we integrated DNase-seq, RNA-seq, ChIP-seq and MNase-seq data and investigated the effect of physical DNase I hypersensitive site (DHS) positions on the transcription of rice BDPs. We found that the physical position of a DHS relative to the TSS of bidirectional gene pairs can affect the expression of the corresponding genes: the closer a DHS is to the TSS, the higher is the expression level of the genes. Most importantly, we observed that the distribution of DHSs plays a significant role in the regulation of transcription and the coexpression of gene pairs, which are possibly mediated by orchestrating the positioning of histone marks and canonical nucleosomes around BDPs. Our results demonstrate that the combined actions of chromatin structures with DHSs, which contain functional cis-elements for interaction with transcriptional machinery, may play an important role in the regulation of the bidirectional transcription or coexpression in rice BDPs. Our findings may help to enhance the understanding of DHSs in the regulation of bidirectional gene pairs.

Histone modifications facilitate the coexpression of bidirectional promoters in rice

“…In addition, the percentage of coexpressed gene pairs decreased with increasing BDP size (Additional file 6 : Table S6). The highest frequency of coexpression was previously found in gene pairs separated by 200 bp [ 32 ], here we further observed that gene pairs were generally more frequently coexpressed when the intergenic distance was less than 500 bp. (Additional file 7 : Figure S1).…”

“…To comprehensively characterize the DNA sequence profiles of the BDPs in rice, we first identified bidirectional gene pairs with head-to-head orientations using the updated version of the rice genome (The Institute for Genomic Research (TIGR), rice subsp. Japonica version 7.0) as described previously [ 32 ], which contains a total of 55,801 annotated genes. We identified a total of 290 type I BDPs, 294 type II BDPs (BDPs II) and 627 type III BDPs (BDPs III), with TSS intergenic distances of 0–250 bp (BDPs I), 250–500 bp (BDPs II) and 500–1000 bp (BDPs III), respectively.…”

“…However, the effect of the intergenic distance between the TSSs of a gene pair on the coexpression of the corresponding genes was unclear. We calculated the Pearson correlation coefficients for all bidirectional gene pairs using eleven total gene expression datasets extracted from the Rice Genome Annotation Project ( http://rice.plantbiology.msu.edu/expression.shtml ) as described previously [ 32 ]. We observed that the median coexpression values of bidirectional gene pairs were significantly higher than those of randomly selected two adjacent unidirectional genes (Fig.…”

“…In this study, we continued to perform a comprehensive analysis of chromatin-based epigenetic features in rice BDPs. BDPs were classified into three types (I, II and III with sizes of 0–250 bp, 250–500 bp and 500–1000 bp, respectively) as described previously [ 32 ]. The BDP size was defined as the intergenic distance between the transcription start sites (TSSs) of the corresponding gene pairs.…”

Global Quantitative Mapping of Enhancers in Rice Genome by STARR-seq

“…Histone modification data, including H3K4me3, H3K27me3 were retrieved from GSE19602 [38], and the H3K27ac, H3K9me3 were retrieved from GSE79033 [39], the H3K4me1 was retrieved from GSA under accession no. PRJCA000387 [40].…”