Welcome to MARGI’s portal!

Although only 5% of the genome encode protein-coding genes, most of it is actively transcribed. We know that several of these non-coding RNAs bind distal genomic regions, but how pervasive is this situation, and what are the loci involved in these interactions are questions that remain elusive. Using MARGI –a novel technology to identify RNA-chromatin interactions in an unbias way– we have identified thousands of chromatin-associated RNAs (caRNAs) along with their associated chromatin target loci.

We designed two MARGI protocols: pxMARGI and diMARGI. Whereas pxMARGI is designed to not differentiate passive and direct interactions, diMARGI is aimed to reveal protein tethered interactions. For the former, this was achieved by a combination of formaldehyde crosslinking and complete genome fragmentation, by overnight HaeIII digestion to ensure all genomic regions including heterochromatin were fragmented before the subsequent DNA ligation step. For the second, after crosslinking with formaldehyde and DSG, the chromatin was fragmented by sonication, and only the soluble fraction was passed onto the subsequent ligation steps.

In the following sections you will find the procedure used to analysed pxMARGI and diMARGI libraries of human embryonic (H9) and adult (HEK) cells.

• Reads processing
• Mapping
• Identified caRNAs
• Identified RNA-DNA associations