GSE196604
Genomic variations combined with epigenetic modifications rewire open chromatin in rice
Cis-regulatory elements (CREs) fine-tune gene transcription during normal growth and development and environmental stress responses in eukaryotes. CREs with sequence variations play vital roles in driving plant or crop domestication. However, how global genomic sequence and structural variations causative for multi-level changes between Indica and Japonica are still less studied. To answer this question, we here conducted MH-seq (MNase hypersensitive sequencing) for global profiling of open chromatin (MNase hypersensitive sites, MHSs) between two typical Oryza sativa cultivars, Nipponbare (NIP) and 93-11. We found that differential MHSs exhibited some distinct intrinsic genomic sequence features between NIP and 93-11. Moreover, MHSs can coordinate with DNA sequence or genomic structural variations in the regulation of differential gene expression between NIP and 93-11. Importantly, by applying MHS-GWAS association analyses, we found that CREs with sequence variations may act as the key determinant for controlling expression of genes responsible for some biological relevance in NIP and 93-11. Therefore, this study provides new insights into how sequence and genomic structural variations function in differential biological relevance and key crop agronomic traits between Indica and Japonica. It also provides some promising genomic editing targets for molecular breeding to improve favorable agronomic trait. Overall design: Differential MHSs can regulate differential expression of overlapping genes, thereby affecting some biological processes in NIP and 93-11.