iMARGI

iMARGI maps interactions between chromatin-associated RNAs (caRNAs) and their genomic loci by converting proximal RNA–DNA pairs into chimeric RNA-linker-DNA sequences and decoding paired-end sequencing reads to identify caRNA–DNA contacts.

Key Features:

• In situ crosslinking and genome fragmentation: Crosslinking of RNA–DNA pairs within cells followed by genome fragmentation captures physical RNA–chromatin interactions.
• Chimeric sequence formation: Proximal RNA–DNA pairs are converted into chimeric RNA-linker-DNA molecules for sequencing.
• Sequencing library construction: Chimeric molecules are used to construct libraries suitable for paired-end sequencing.
• iMARGI-Docker software package: Processes paired-end sequencing reads to identify and map caRNA–DNA interactions from sequencing data.
• Reduced input requirements: Requires approximately 100-fold fewer input cells compared to MARGI (mapping RNA–genome interactions).
• Time efficiency: Library construction is performed over eight days with a few hours per day, and data processing with iMARGI-Docker can be completed in one day.
• Experimental checkpoints: Established checkpoints are included to ensure accuracy and reproducibility.

Scientific Applications:

• Discovery of chromatin-associated RNAs (caRNAs): Enables identification of caRNAs and their genomic interaction sites.
• Genomic interaction loci mapping: Reveals specific genomic loci that interact with caRNAs to inform studies of chromatin organization and transcriptional regulation.

Methodology:

iMARGI-Docker processes paired-end sequencing reads to identify and map caRNA–DNA interactions.