Accessible chromatin regions and their functional interrelations with gene transcription and epigenetic modifications in sorghum genome

Accessible chromatin regions (ACRs) provide physical scaffolds to recruit transcriptional co-regulators and displace their nearby nucleosomes in multiple plant species. Characterization of ACRs and investigation of their biological effects in Sorghum bicolor has lagged behind. Regulation of gene expression relies on the transcriptional co-regulators that are recruited to ACRs to affect epigenomic modifications of surrounding nucleosomes. In this study, we employed transposase-accessible chromatin sequencing to identify ACRs and decipher how the presence of ACRs affects gene expression and epigenetic signatures in the Sorghum genome. As a result, 21 077 ACRs, which are mapped to 22.9% of genes and 2.7% of repeats, were identified. The profiling of ACRs on gene structures reveals a narrow and sharp peak around the transcription start site, with relatively weak and broad signals covering the entire gene body and an explicit but wide peak from the transcription termination site to its downstream regions. We discovered that the correlations between gene expression levels and profiled ACR densities are dependent on the positions of ACRs. The occurrence of genic ACRs cumulatively enhances the transcriptional activity of intergenic ACR-associated genes. In addition, an intricate crosstalk among ACRs, gene expression, and epigenetic marks has been unveiled by integrating multiple-omics analyses of whole-genome bisulfite sequencing, 6mA immunoprecipitation followed by sequencing, RNA sequencing, chromatin immunoprecipitation sequencing, and DNase I hypersensitive sites sequencing datasets. Our study provides a genome-wide landscape of ACRs in sorghum, decrypts their interrelations with various epigenetic marks, and sheds new light on their roles in transcriptional regulation.