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Regulation of the ESC transcriptome by nuclear long noncoding RNAs
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...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Cold Spring Harbor Laboratory Press
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4561492/ https://www.ncbi.nlm.nih.gov/pubmed/26048247 http://dx.doi.org/10.1101/gr.189027.114 |
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author | Bergmann, Jan H. Li, Jingjing Eckersley-Maslin, Mélanie A. Rigo, Frank Freier, Susan M. Spector, David L. |
author_facet | Bergmann, Jan H. Li, Jingjing Eckersley-Maslin, Mélanie A. Rigo, Frank Freier, Susan M. Spector, David L. |
author_sort | Bergmann, Jan H. |
collection | PubMed |
description | 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 coexpression 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 Platr14 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. |
format | Online Article Text |
id | pubmed-4561492 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Cold Spring Harbor Laboratory Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-45614922016-03-01 Regulation of the ESC transcriptome by nuclear long noncoding RNAs Bergmann, Jan H. Li, Jingjing Eckersley-Maslin, Mélanie A. Rigo, Frank Freier, Susan M. Spector, David L. Genome Res Research 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 coexpression 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 Platr14 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. Cold Spring Harbor Laboratory Press 2015-09 /pmc/articles/PMC4561492/ /pubmed/26048247 http://dx.doi.org/10.1101/gr.189027.114 Text en © 2015 Bergmann et al.; Published by Cold Spring Harbor Laboratory Press http://creativecommons.org/licenses/by-nc/4.0/ This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/. |
spellingShingle | Research Bergmann, Jan H. Li, Jingjing Eckersley-Maslin, Mélanie A. Rigo, Frank Freier, Susan M. Spector, David L. Regulation of the ESC transcriptome by nuclear long noncoding RNAs |
title | Regulation of the ESC transcriptome by nuclear long noncoding RNAs |
title_full | Regulation of the ESC transcriptome by nuclear long noncoding RNAs |
title_fullStr | Regulation of the ESC transcriptome by nuclear long noncoding RNAs |
title_full_unstemmed | Regulation of the ESC transcriptome by nuclear long noncoding RNAs |
title_short | Regulation of the ESC transcriptome by nuclear long noncoding RNAs |
title_sort | regulation of the esc transcriptome by nuclear long noncoding rnas |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4561492/ https://www.ncbi.nlm.nih.gov/pubmed/26048247 http://dx.doi.org/10.1101/gr.189027.114 |
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