Project description:Cis-regulatory elements coordinate the regulation of their targeted genes’ expression. However, the joint measurement of cis-regulatory elements’ activities and their interactions in spatial proximity is limited by the current sequencing approaches. We describe a method, NOMe-HiC, which simultaneously captures single nucleotide polymorphisms, DNA methylation, chromatin accessibility (GpC methyltransferase footprints), and chromosome conformation changes from the same DNA molecule, together with the transcriptome, in a single assay. NOMe-HiC shows high concordance with state-of-the-art mono-omic assays across different molecular measurements and reveals coordinated chromatin accessibility at distal genomic segments in spatial proximity and novel types of long-range allele-specific chromatin accessibility.
Project description:We performed Hi-C, Micro-C, and capture Micro-C in human prostate cancer cells and compared chromatin interactions called using different methods. By integrating Micro-C with NOMe-seq, ChIP-seq, and RNA-seq, we investigated the relationships among nucleosome positioning of regulatory elements, chromatin interactions, and transcription. This work provides a framework for understanding the chromatin interactions among regulatory elements, nucleosome-depleted regions, and transcription.
