Regulation of the ESC transcriptome by nuclear long non-coding RNAs

Bergmann, J. H., Li, J., Eckersley-Maslin, M. A., Rigo, F., Freier, S. M., Spector, D. L. (2015) Regulation of the ESC transcriptome by nuclear long non-coding RNAs. Genome Res, 25 (9). pp. 1336-1346. ISSN 1549-5469 (Electronic)1088-9051 (Linking)

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URL: http://www.ncbi.nlm.nih.gov/pubmed/26048247
DOI: 10.1101/gr.189027.114

Abstract

Long noncoding (lnc)RNAs have recently emerged as key regulators of gene expression. Here, we performed high-depth poly(A)+ RNA sequencing across multiple clonal populations of mouse embryonic stem cells (ESCs) and neural progenitor cells (NPCs) to comprehensively identify differentially regulated lncRNAs. We establish a biologically robust profile of lncRNA expression in these two cell types and further confirm that the majority of these lncRNAs are enriched in the nucleus. Applying weighted gene co-expression network analysis, we define a group of lncRNAs that are tightly associated with the pluripotent state of ESCs. Among these, we show that acute depletion of PAT-14 using antisense oligonucleotides impacts the differentiation- and development-associated gene expression program of ESCs. Furthermore, we demonstrate that Firre, a lncRNA highly enriched in the nucleoplasm and previously reported to mediate chromosomal contacts in ESCs, controls a network of genes related to RNA processing. Together, we provide a comprehensive, up-to-date and high resolution compilation of lncRNA expression in ESCs and NPCs and show that nuclear lncRNAs are tightly integrated into the regulation of ESC gene expression.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > long non-coding RNA
organs, tissues, organelles, cell types and functions > cell types and functions > cell types > stem cells
organs, tissues, organelles, cell types and functions > cell types and functions > cell types > stem cells
organs, tissues, organelles, cell types and functions > cell types and functions > cell types > stem cells

bioinformatics > genomics and proteomics > genetics & nucleic acid processing > transcriptomes
CSHL Authors:
Communities: CSHL Cancer Center Program > Gene Regulation and Cell Proliferation
CSHL Cancer Center Shared Resources > Microscopy Service
CSHL labs > Spector lab
CSHL Cancer Center Shared Resources > DNA Sequencing Service
Highlight: Spector, David L.
Depositing User: Matt Covey
Date Deposited: 09 Jun 2015 19:34
Last Modified: 06 Nov 2017 17:10
PMCID: PMC4561492
Related URLs:
URI: http://repository.cshl.edu/id/eprint/31568

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