Integrative analysis of reference epigenomes in 20 rice varieties

Abstract

Epigenomic modifications are instrumental for transcriptional regulation, but comprehensive reference epigenomes remain unexplored in rice. Here, we develop an enhanced chromatin immunoprecipitation (eChIP) approach for plants, and generate genome-wide profiling of five histone modifications and RNA polymerase II occupancy with it. By integrating chromatin accessibility, DNA methylation, and transcriptome datasets, we construct comprehensive epigenome landscapes across various tissues in 20 representative rice varieties. Approximately 81.8% of rice genomes are annotated with different epigenomic properties. Refinement of promoter regions using open chromatin and H3K4me3-marked regions provides insight into transcriptional regulation. We identify extensive enhancer-like promoters with potential enhancer function on transcriptional regulation through chromatin interactions. Active and repressive histone modifications and the predicted enhancers vary largely across tissues, whereas inactive chromatin states are relatively stable. Together, these datasets constitute a valuable resource for functional element annotation in rice and indicate the central role of epigenomic information in understanding transcriptional regulation.

Degradome sequencing-based identification of phasiRNAs biogenesis pathways in Oryza sativa

“…The result indicated a promoter of LOC_Os02g40860.1 gene was targeted by ve LOC_Os01g37325.1-derived phasiRNAs (Table 3). Since LOC_Os01g37325.1-derived phasiRNAs were detected in panicle rather than in root tissue (Figure 2), we used the bisul te-seq and RNA-seq datasets [41] of rice panicle and root for identi cation of the LOC_Os01g37325.1-derived phasiRNAs mediated DNA methylation on the target promoter and their role in transcriptional repression of target gene (LOC_Os02g40860.1), respectively. It is reported that CG and CHG methylation contexts are maintained by DNA methyltransferases and histone modi cations, while CHH methylation is associated with 24-nt siRNA guided RdDM [16].…”

“…ncbi.nlm.nih.gov/geo/). The bisul te-seq and RNA-seq datasets of panicle and root were contributed by Zhao et al [41]. All the HTS datasets employed for our study were listed in table 4.…”

“…The DNA methylation analysis of promoters were performed according to the method developed by Zhao et al [41]. The sequences of bisul te sequencing libraries were mapped to the potential promoter sequences, and the uniquely mapped sequences were used for further DNA methylation level analysis.…”

Degradome Sequencing-based Identification of PhasiRNAs Biogenesis Pathways in Oryza Sativa

“…CKIs have been identi ed highly conserved in eukaryotes, they are believed involving in a variety of important biological events, since they have a wide substrate speci city in vitro [26]. The expression level of LOC_Os02g40860.1 in root and panicle tissues of rice have been analyzed by utilizing the RNA-seq libraries (panicle: GSM4230036 and GSM4230037; root: GSM4230038 and GSM4230039) which contributed by Zhao et al [27]. As shown in Fig.…”

“…The DNA methylation analysis of promoters were performed according to the method of Zhao et al [27]. The sequences of bisul te sequencing libraries was processed by adapter cut and normalization in RPM (reads per million) as we described previously [40].…”