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

<jats:p>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 <jats:italic>Men ε/β</jats:italic> 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. <jats:italic>Men ε</jats:italic> is a 3.2-kb polyadenylated RNA, whereas <jats:italic>Men β</jats:italic> is an ∼20-kb transcript containing a genomically encoded poly(A)-rich tract at its 3′-end. The 3′-end of <jats:italic>Men β</jats:italic> is generated by RNase P cleavage. The <jats:italic>Men ε/β</jats:italic> transcripts are localized to nuclear paraspeckles and directly interact with NONO. Knockdown of <jats:italic>MEN ε/β</jats:italic> expression results in the disruption of nuclear paraspeckles. Furthermore, the formation of paraspeckles, after release from transcriptional inhibition by DRB treatment, was suppressed in <jats:italic>MEN ε/β</jats:italic>-depleted cells. Our findings indicate that the <jats:italic>MEN ε/β</jats:italic> non-coding RNAs are essential structural/organizational components of paraspeckles.</jats:p>