Genomics,Multiomics

Dataset Information

25

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


ABSTRACT: 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.

INSTRUMENT(S): Illumina HiSeq 2500 (Mus musculus)

ORGANISM(S): Mus musculus  

SUBMITTER: Andrea Cipriano  

PROVIDER: GSE94498 | GEO | 2018-09-04

REPOSITORIES: GEO

Dataset's files

Source:
Action DRS
GSE94498_chirpseq_merged_peaks.bed.gz Bed
GSE94498_gene_fpkm.txt.gz Txt
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Publications

Deficiency in the nuclear long noncoding RNA <i>Charme</i> causes myogenic defects and heart remodeling in mice.

Ballarino Monica M   Cipriano Andrea A   Tita Rossella R   Santini Tiziana T   Desideri Fabio F   Morlando Mariangela M   Colantoni Alessio A   Carrieri Claudia C   Nicoletti Carmine C   Musarò Antonio A   Carroll Dònal O' DO   Bozzoni Irene I  

The EMBO journal 20180903 18


Myogenesis is a highly regulated process that involves the conversion of progenitor cells into multinucleated myofibers. Besides proteins and miRNAs, long noncoding RNAs (lncRNAs) have been shown to participate in myogenic regulatory circuitries. Here, we characterize a murine chromatin-associated muscle-specific lncRNA, <i>Charme</i>, which contributes to the robustness of the myogenic program <i>in vitro</i> and <i>in vivo</i> In myocytes, <i>Charme</i> depletion triggers the disassembly of a  ...[more]

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