GSE114090
ATAC-seq profiling of open chromatin with global epigenetic and transcriptional trends in two-line hybrid rice
The transcriptional regulatory switches responsible for the mechanism of fertility conversion in two-line system of hybrid rice remain unclear.  Here, we employed the ATAC-seq, combined with H3K9ac and H3K4me2 and gene expression analyses, in a rice PTGMS Line Wuxiang S to delineate an integrative chromatin accessibility profiling to uncover the key new regulatory modules in response to temperature fluctuation, which can provide important hypotheses regarding the mechanisms of fertility conversion. Collectively, the potentially active genes with H3K4me2 mark under the permissive state of chromatin can easily be regulated by these transcription factors (TFs). Analyzing TF binding cis-regulatory motifs in differentially accessible chromatin regions identified an ERF-driven regulatory module, that acts as an active transcriptional repressor with temperature-dependent function, specially in WXS(F), which can switch into an activator to control both cell wall development, response to temperature fluctuation, and plant architecture. On the contrary, a MADS/ERF co-regulatory module is unique to the WXS(S) at meiosis period, which tends to directly or indirectly affect various metabolic pathways-related genes to coordinate plant development and growth with proper anther development. Meanwhile, there was a unique accessibility of chromatin on the promoter of UbL40 mRNA in WXS(F), which were found to be regulated by the MADS/ERF module. Our analyses uncovered new TF control modules involved in fertility conversion and shed light on the transcriptional mechanisms as fundamental for further study of genetic manipulations of these transcription factors, in order to prove and elaborate on the specific predictions made by the key model. Overall design: ATAC-seq was performed on nuclei of a novel PTGMS male sterile line Wuxiang S (WXS) generated by our laboratory, which is derived from a mutant tms5 locus in indica rice. All ATAC-seq experiments were performed in two biological replicates. Genome-wide integrated mapping of mRNA transcripts in three biological replicates and two select histone modifications (H3K4me2 and H3K9ac) were performed. All datasets used in the analysis were developed using the  panicle of WXS(F) and WXS(S) at meiosis period and uninucleate period.