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. (March 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: March 2009
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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