RNA-Chrom: a manually curated analytical database of RNA-chromatin interactome

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Non-coding RNAs (ncRNAs) are increasingly recognized for their critical roles in cellular and organismal processes.
• Understanding ncRNA interactions with chromatin is essential for deciphering gene regulation and disease mechanisms.
• Existing data fragmentation hinders a systems-level study of ncRNA functions.

Purpose of the Study:

• To present the RNA-Chrom database, a manually curated resource for analyzing RNA-chromatin interactions.
• To provide a user-friendly web interface for querying and visualizing these interactions.
• To facilitate the study of the RNA-chromatin interactome in human and mouse systems.

Main Methods:

• Manual curation of RNA-chromatin contact data.
• Development of a comprehensive database storing billions of interaction coordinates.
• Implementation of a web interface for two distinct analytical approaches.
• Integration with the UCSC Genome Browser for enhanced visualization.

Main Results:

• The RNA-Chrom database contains billions of contacts between thousands of human and mouse RNAs and chromatin.
• The web interface allows users to identify chromatin targets of specific RNAs and RNAs interacting with specific DNA loci.
• Contact maps can be viewed and compared with other genomic data via the UCSC Genome Browser.

Conclusions:

• RNA-Chrom provides a valuable resource for exploring the RNA-chromatin interactome.
• The database supports systematic investigation into the regulatory roles of non-coding RNAs.
• This work advances the understanding of ncRNA involvement in biological processes and diseases.