|
| Status |
Public on Nov 21, 2013 |
| Title |
The long non-coding RNA Paupar regulates the expression of both local and distal genes [Paupar KD] |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by array
|
| Summary |
Although some long noncoding RNAs (lncRNAs) have been shown to regulate gene expression in cis, it remains unclear whether lncRNAs can directly regulate transcription in trans by interacting with chromatin genome-wide independently of their sites of synthesis. Here, we describe the genomically local and more distal functions of Paupar, a vertebrate-conserved and central nervous system-expressed lncRNA transcribed from a locus upstream of the gene encoding the Pax6 transcription factor. Knockdown of Paupar disrupts the normal cell cycle profile of neuroblastoma cells and induces neuronal differentiation. Paupar acts in a transcript-dependent manner both locally, to regulate Pax6, as well as distally by binding and regulating genes on multiple chromosomes, in part through physical association with Pax6 protein. Paupar binding sites are enriched near promoters and can function as transcriptional regulatory elements whose activity is modulated by Paupar transcript levels. Our findings demonstrate that a lncRNA can function in trans at transcriptional regulatory elements distinct from its site of synthesis to control large-scale transcriptional programmes.
|
| |
|
| Overall design |
N2A cells transfected with a non-targeting control vector were compared to N2A cells transfected with a Paupar knockdown construct. Three biological replicates of each condition were analysed on Affymetrix GeneChip Mouse Gene 1.0 ST Arrays.
|
| |
|
| Contributor(s) |
Vance KW, Sansom SN, Lee S, Chalei V, Kong L, Cooper SE, Oliver PL, Ponting CP |
| Citation(s) |
24488179 |
| |
| Submission date |
Nov 20, 2013 |
| Last update date |
Mar 04, 2019 |
| Contact name |
Stephen Sansom |
| E-mail(s) |
stephen.sansom@kennedy.ox.ac.uk
|
| Organization name |
Kennedy Institute of Rheumatology
|
| Department |
NDORMS
|
| Lab |
Sansom
|
| Street address |
Roosevelt Drive
|
| City |
Oxford |
| State/province |
Oxfordshire |
| ZIP/Postal code |
OX3 7FY |
| Country |
United Kingdom |
| |
|
| Platforms (1) |
| GPL6246 |
[MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version] |
|
| Samples (6)
|
|
| This SubSeries is part of SuperSeries: |
| GSE52571 |
The long non-coding RNA Paupar regulates the expression of both local and distal genes |
|
| Relations |
| BioProject |
PRJNA229398 |
Less...
More...