RDD reveals the landscape of RNA-associated chromatin DNA-DNA interactome and gene regulation

ABSTRACT: Although non-coding RNAs (ncRNAs) have been proposed to play important roles in nuclear organization with three-dimensional (3D) conformation and gene transcription regulation, exploring the targeting and diffusion patterns of ncRNAs on chromatin has been challenging because it requires a technique that can simultaneously detect high-affinity sites and their higher-order contacts in 3D structures. Here we developed a new method, RNA-associated chromatin DNA-DNA interactions (RDD) in solution, which enables genome-wide detection of genomic binding sites and high-resolution chromatin interactions for a specific ncRNA. Using RDD to investigate the well-known ncRNA roX2 that involved in Drosophila dosage compensation, we not only recapitulate roX2 targeting chromatin sites but also reveal the landscape of chromatin DNA-DNA contacts at various resolutions from loops, domains to territories. We further show that roX2 anchors at the target gene TES and spreads around as a 'boot-like' structure for maintaining gene activity, where tethered daisy-chain chromatin loops, bridging to TSS to dock RNAPII-related contact hubs to achieve a precise twofold expression of male X-linked genes, further crossing active domains to form distinct hubs to exhibit the condensed properties of roX2 in high-throughput sequencing. These results provide a genome-wide 3D model for explaining the mechanism of ncRNA roX2 involved dosage compensation in Drosophila. Together, we demonstrate the high specificity and robustness of the RDD method to capture RNA-associated chromatin DNA-DNA interactome, which provides topological insights into the mechanism of gene transcription regulation by ncRNAs.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE207720 | GEO | 2024/05/21

REPOSITORIES: GEO