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| Content Provider | World Health Organization (WHO)-Global Index Medicus |
|---|---|
| Author | Bergmann, Jan H. Li, Jingjing Eckersley-Maslin, Mélanie A. Rigo, Frank Freier, Susan M. Spector, David L. |
| Description | Author Affiliation: Bergmann JH ( Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA); Li J ( Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA); Eckersley-Maslin MA ( Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA); Rigo F ( Isis Pharmaceuticals, Inc., Carlsbad, California 92010, USA.); Freier SM ( Isis Pharmaceuticals, Inc., Carlsbad, California 92010, USA.); Spector DL ( Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA) |
| 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 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. |
| File Format | HTM / HTML |
| ISSN | 10889051 |
| e-ISSN | 15495469 |
| DOI | 10.1101/gr.189027.114 |
| Journal | Genome Research |
| Issue Number | 9 |
| Volume Number | 25 |
| Language | English |
| Publisher | Cold Spring Harbor Laboratory Press |
| Publisher Date | 2015-09-01 |
| Publisher Place | United States |
| Access Restriction | Open |
| Subject Keyword | Discipline Genetics Discipline Genomics Embryonic Stem Cells Metabolism Gene Expression Regulation Rna, Long Noncoding Genetics Transcriptome Animals Cell Differentiation Cell Nucleus Cluster Analysis Cytology Gene Expression Profiling Mice Neural Stem Cells Research Support, N.i.h., Extramural Research Support, Non-u.s. Gov't |
| Content Type | Text |
| Resource Type | Article |
| Subject | Genetics Genetics (clinical) |
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