Integration analysis of Pearl millet epigenomic 

scripts for "Integration analysis of Pearl millet epigenomic" ()

Lin Luo, Fangjie Zhu, Dongmei Lin, Haidong Yan, Yarong Jin, Linkai Huang, Guodong Lu, Jiajing Xiao

Genome analysis provided genetic variants contributing to agronomical traits, but few is known about the comprehensive epigenomic information in pearl millet. Here, we performed integrative analysis of seven histone modifications, chromatin accessibility, and transcriptomes in leaf of pearl millet and established global maps of chromatin states and regulatory elements for whole genome. While 83.89% of the genome was annotated without epigenetic signals, the other non-transposons regions were featured by different histone modifications and classified into 15 chromatin states. Two new intermediate chromatin states were identified and characterized between the extensively studied repressive state and poised state. Regulatory elements in promoters and enhancer were predicted and DNase footprint analysis suggested the core function of AP2 transcription factors in leaf. Additionally, we uncovered valuable regulatory elements through the integration of GWAS results, which enhance our understanding of the genetic and regulatory underpinnings of important agronomical traits. These findings contribute significantly to our knowledge of pearl millet's epigenetic landscape and its implications for crop improvement and agricultural practices.