<i>MEN ε/β</i> nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles

TLDR

The human and mouse genomes produce many more transcripts than predicted protein‑coding genes, indicating extensive non‑coding transcription. The study investigates the Men ε/β locus, which is up‑regulated 3.3‑fold during muscle differentiation. A custom microarray identified 184 non‑coding RNAs that change more than twofold during differentiation of C2C12 myoblasts into myotubes. Men ε and Men β, two isoforms from a single promoter, localize to paraspeckles, bind NONO, and are essential for paraspeckle structure, as knockdown disrupts paraspeckles and blocks their re‑formation after transcriptional release.

Abstract

Studies of the transcriptional output of the human and mouse genomes have revealed that there are many more transcripts produced than can be accounted for by predicted protein-coding genes. Using a custom microarray, we have identified 184 non-coding RNAs that exhibit more than twofold up- or down-regulation upon differentiation of C2C12 myoblasts into myotubes. Here, we focus on the Men ε/β locus, which is up-regulated 3.3-fold during differentiation. Two non-coding RNA isoforms are produced from a single RNA polymerase II promoter, differing in the location of their 3′ ends. Men ε is a 3.2-kb polyadenylated RNA, whereas Men β is an ∼20-kb transcript containing a genomically encoded poly(A)-rich tract at its 3′-end. The 3′-end of Men β is generated by RNase P cleavage. The Men ε/β transcripts are localized to nuclear paraspeckles and directly interact with NONO. Knockdown of MEN ε/β expression results in the disruption of nuclear paraspeckles. Furthermore, the formation of paraspeckles, after release from transcriptional inhibition by DRB treatment, was suppressed in MEN ε/β -depleted cells. Our findings indicate that the MEN ε/β non-coding RNAs are essential structural/organizational components of paraspeckles.