Project description:RNA has been suggested to play a major role in the regulation of higher-order structures of chromatin. This study investigated chromatin-associated RNA (caRNA) in Drosophila melanogaster by applying high-throughput sequencing to RNA molecules that co-fractionate with chromatin. Using a cell-free in vitro chromatin assembly system (DREX), we demonstrated that caRNAs mainly comprise snoRNAs, snoRNA hosts and miRNAs.
Project description:Chromatin marks are associated with transcriptional regulatory activities. Here, We developed a method termed Chrom-seq to efficiently capture RNAs associated with various chromatin marks in living cells. Chrom-seq jointly applies highly specific chromatin-mark reader with APEX2 which catalyzes the oxidation of biotin-aniline to label the adjacent RNAs for isolation by streptavidin-coated beads. Using the readers of mCBX7/dPC, mCBX1 and mTAF3, we detected RNA species significantly associated with H3K27me3, H3K9me3 and H3K4me3, respectively. Chrom-seq provides an antibody-free approach to systematically map RNAs at chromatin marks with potential regulatory roles in different epigenetic events.
Project description:High-order rice chromatin contains numerous interactions among DNA, RNA and protein to regulate critical biological processes in various aspects of rice life. We developed an effective method for mapping histone-mediated chromatin associated RNA-DNA interactions, followed by paired-end-tag sequencing (ChRD-PET) in rice. With H3K4me3 ChRD-PET, H3 ChRD-PET and RNase H treated H3K4me3 ChRD-PET, we present a highly comprehensive map of RNA and chromatin interactions around promoters in rice MH63. Through integrating ChIA-PET (published data), ChRD-PET and ssDRIP-seq data analysis, we demonstrated the function of RNAs-chromatin interactions in different level. We also conducted ATAC-seq and integrative analysis uncovered the relationship of epigenetic modifications and ChRD-PET interactions. Our findings firstly revealed the map and features of RNAs-chromatin interactions in rice.
Project description:Chromatin-associated and RNA-dependent Chromatin-associated proteome from S. cerevisiae, obtained by a new method yChEFs(yeast Chromatin Enriched Fractions)
Project description:Chromatin-associated proteins are essential for maintaining chromatin structure, regulating gene expression, and epigenetic regulation. However, isolating nuclear proteins from plants with high purity is very difficult due to significant background contamination from cytoplasmic proteins, organelle proteins, and metabolites. In the present study, we build a method for isolating chromatin-associated proteins. This method does not need to isolating nuclei, and can directlty purify DNA-protein (DNP) complex.