MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles

Sunwoo, H., Dinger, M. E., Wilusz, J. E., Amaral, P. P., Mattick, J. S., Spector, D. L. (2009) MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Research, 19 (3). pp. 347-359. ISSN 10889051 (ISSN)

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URL: http://www.ncbi.nlm.nih.gov/pubmed/19106332
DOI: 10.1101/gr.087775.108

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 similar to 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.

Item Type: Paper
Uncontrolled Keywords: X-CHROMOSOME INACTIVATION X-Chromosome inactivation GENE-EXPRESSION gene expression MOUSE GENOME mouse genome CELLS cells TRANSCRIPTS transcripts IDENTIFICATION identification RETENTION retention ACID acid SEQUENCE sequence POLY(A)
Subjects: bioinformatics > genomics and proteomics > analysis and processing > microarray gene expression processing
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > ncRNA
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > transcription factor
CSHL Authors:
Communities: CSHL labs > Spector lab
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Watson School > Publications
Depositing User: Brian Soldo
Date Deposited: 30 Mar 2012 22:41
Last Modified: 28 Jan 2015 16:06
PMCID: PMC2661813
Related URLs:
URI: http://repository.cshl.edu/id/eprint/25769

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