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 2 fold 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 a ~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. Knock-down 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.