Dynamic epigenome changes in response to light in Brachypodium distachyon

Light plays an important role in many plant biological processes such as photosynthesis and photomorphogenesis. In this study, we applied RNA-seq, ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) as well as histone modification and transcription factor ChIP-seq (Chromatin Immunoprecipitation Sequencing) to study how transcriptional regulation could be affected by epigenome in B. distachyon under controlled light and extended darkness conditions. We have identified 8,400 differentially expressed genes (DEGs), and they are enriched in photosynthesis Gene Ontology (GO) terms. Over 20% of the open chromatin regions of the total genes decreased after extended darkness treatment, and the distribution of ATAC-seq peaks was away from the transcription start site (TSS), indicating that light has a dramatic impact on chromatin accessibility. We also found that differential H3K4me3 andH3K9ac modifications enriched in gene loci associated with photosynthesis and other light-dependent reactions. We further identified a candidate transcription factor BdHY5 that targets these light reaction genes. Together, our results indicated the light-induced changes of chromatin accessibility and two histone modifications contributes to the transcriptional regulation of BdHY5 in photosynthesis.