PIRCh-seq

PIRCh-seq (Polymerase Inhibiting RNA Chromatin sequencing) maps chromatin-associated RNAs, including long non-coding RNAs (lncRNAs) and other non-coding RNAs (ncRNAs), to specific histone modifications to study RNA–chromatin interactions.

Key Features:

• Histone Modification-Specific Analysis: maps RNA associations with distinct histone modifications to resolve epigenetic mark–specific interactions.
• Reduction in Contamination: minimizes contamination by nascent transcripts to enrich for RNAs that are genuinely chromatin-associated.
• Functional Classification: classifies non-coding RNAs into functional groups based on their patterns of association with histone modifications.

Scientific Applications:

• Identification of Chromatin-Associated RNAs: detects hundreds of chromatin-associated RNAs across various cell types.
• Elucidation of Single-Stranded RNA Associations: reveals that single-stranded RNA bases are more frequently associated with chromatin.
• Discovery of Allele-Specific Interactions: uncovers allele-specific RNA–chromatin interactions relevant to genetic variation and chromatin dynamics.

Methodology:

PIRCh-seq uses sequencing technologies combined with bioinformatics analyses to map RNAs associated with specific histone modifications and to classify them into functional categories.