RNA-Chrom

RNA-Chrom catalogs genome-wide RNA–chromatin interactions to enable analysis of non-coding RNA influences on gene expression, chromatin structure, and disease-related processes.

Key Features:

• Extensive Data Collection: Aggregates billions of contact points between thousands of human and mouse RNAs and chromatin, providing genome-wide interaction coordinates.
• RNA-centric Contact Identification: Identifies chromatin contacts formed by specific RNAs and reports associated genes and DNA loci.
• Locus-centric RNA Discovery: Identifies RNAs interacting with specified DNA loci and characterizes the nature of these interactions.
• Contact Maps and Coordinates: Provides precise interaction coordinates and contact maps for detailed analysis of RNA–chromatin associations.
• UCSC Genome Browser Integration: Formats interaction data for visualization of contact maps within the UCSC Genome Browser for comparative genomic analysis.
• Curated Dataset: Consolidates and curates diverse interaction datasets to produce a unified, structured resource for downstream analysis.

Scientific Applications:

• Gene Expression Regulation: Maps RNA–chromatin contacts to genes to support studies of non-coding RNA roles in transcriptional regulation.
• Chromatin Structure and Remodeling: Enables investigation of RNA-associated chromatin remodeling and maintenance using interaction coordinates and contact maps.
• Transposon Suppression: Facilitates study of co-transcriptional suppression of transposons mediated by RNA–chromatin interactions.
• RNA Modification Context: Supports analysis of post-transcriptional RNA modifications in the context of chromatin interactions.
• Disease and Development Studies: Links interactions to genomic loci and genes to investigate roles of non-coding RNAs in development, aging, cancer, and cardiovascular diseases.

Methodology:

Manual curation and unification of diverse datasets into a structured database, aggregating contact points and providing precise interaction coordinates and contact maps formatted for UCSC Genome Browser visualization.