Functional characterization of open chromatin in bidirectional promoters of rice

Bidirectional gene pairs tend to be highly coregulated and function in similar biological processes in eukaryotic genomes. Structural features and functional consequences of BDPs have received considerable attention among diverse species. However, the underlying mechanisms responsible for bidirectional transcription and coexpression of BDPs remain poorly understood in plants. In this study, we integrated DNase-seq, RNA-seq, ChIP-seq and nucleosome positioning data and investigated the effect of DHSs on transcription of rice BDPs. We found that the physical localization of DHSs can affect the expression of the corresponding genes, closer to TSS, higher expression level of genes. Most importantly, we observed that distribution of DHS plays a significant role in regulation of transcription and coexpression of gene pairs, which is possibly mediated by orchestrating the positioning of histone marks and canonical nucleosomes around BPDs. 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 regulation of bidirectional transcription or coexpression in rice BDPs. Our findings may help to enhance the understanding of DHSs in regulation of bidirectional gene pairs. Overall design: Examination of 6 different histone modifications in rice leaves tissue.