title: MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles.
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 epsilon/beta 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 epsilon is a 3.2-kb polyadenylated RNA, whereas Men beta is an approximately 20-kb transcript containing a genomically encoded poly(A)-rich tract at its 3'-end. The 3'-end of Men beta is generated by RNase P cleavage. The Men epsilon/beta transcripts are localized to nuclear paraspeckles and directly interact with NONO. Knockdown of MEN epsilon/beta 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 epsilon/beta-depleted cells. Our findings indicate that the MEN epsilon/beta non-coding RNAs are essential structural/organizational components of paraspeckles.
authors.affiliation: Molecular and Cellular Biology Graduate Program, Stony Brook University, Stony Brook, New York 11794, USA.
authors.forename: Hongjae
authors.initials: H
authors.lastname: Sunwoo
authors.forename: Marcel E
authors.initials: ME
authors.lastname: Dinger
authors.forename: Jeremy E
authors.initials: JE
authors.lastname: Wilusz
authors.forename: Paulo P
authors.initials: PP
authors.lastname: Amaral
authors.forename: John S
authors.initials: JS
authors.lastname: Mattick
authors.forename: David L
authors.initials: DL
authors.lastname: Spector
mesh_terms: D021581:Active Transport, Cell Nucleus; D000818:Animals; D001483:Base Sequence; D002454:Cell Differentiation / Q000235:genetics; D002467:Cell Nucleus / Q000378:metabolism; D002478:Cells, Cultured; D018507:Gene Expression Regulation, Developmental; D006367:HeLa Cells; D006801:Humans; D045586:Intranuclear Inclusion Bodies / Q000378:metabolism*; D051379:Mice; D008969:Molecular Sequence Data; D024510:Muscle Development / Q000235:genetics*; D018485:Muscle Fibers, Skeletal / Q000378:metabolism / Q000502:physiology; D020033:Protein Isoforms / Q000235:genetics / Q000378:metabolism; D011518:Proto-Oncogene Proteins / Q000235:genetics* / Q000378:metabolism*; D022661:RNA, Untranslated / Q000235:genetics* / Q000378:metabolism; D043262:Ribonuclease P / Q000378:metabolism; D015854:Up-Regulation
chemical_list: C484898:Men1 protein, mouse; D020033:Protein Isoforms; D011518:Proto-Oncogene Proteins; D022661:RNA, Untranslated; D043262:Ribonuclease P