RNA-seq and ChIRP-seq analysis performed on Charme muscle specific lnc-RNA. Mus musculus

The main function of chromatin-associated long non coding RNAs (lncRNA) is to tether specific combinations of regulatory factors to target genomic sites. Here we show the characterization of a conserved lncRNA, Charme, that acts as an architectural scaffold to bring together distantly located genomic loci. The functional knock-down of Charme revealed a direct link between the formation of chromosomal loops and the down-regulation of genes therein contained, which are crucial for the correct control of muscle homeostasis. Notably, several Charme-target genes were previously linked to human cardiomyopathies and Charme deficiency in mice indeed resulted in a very strong cardiac phenotype. Altogether, these data disclose that the chromosomal architecture controlled by Charme is relevant for fine tuning the myogenic programme and for proper tissue homeostasis in vivo. Overall design: Gene expression profile upon Charme Knock-down obtained through an RNA-Seq experiment with two biological replicates in each condition. We silenced Charme expression using separately two different sets of gapmers (GAP-2 GAP-2/3) and both conditions were compared with control cells treated with GAP-scr. ChIRP-Seq analysis was performed to identify genomic binding sites of Charme. The long non coding RNA was pulled down using two different sets of probes (even and odd) and co-purified genomic DNA was sequenced and compared with input genomic DNA. LacZ DNA probes were used as negative controls.