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Series GSE52570 Query DataSets for GSE52570
Status Public on Nov 21, 2013
Title The long non-coding RNA Paupar regulates the expression of both local and distal genes [CHART-seq]
Organism Mus musculus
Experiment type Other
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 The genome-wide binding profile of Paupar was determined using Capture Hybridisation Analysis of RNA Targets (CHART)-Seq technique (Simon et al, Proc Natl Acad Sci U S A 108: 20497-20502, 2011) in N2A cells. Following the CHART-seq protocol, we used RNase H elution to recover genomic DNA associated with endogenous Paupar transcripts and genomic DNA associated with a control oligonucleotide (corresponding to the E.coli LacZ sequence). We identified Paupar binding sites in comparison both to DNA recovered using the control LacZ oligonucleotide and to an input DNA sample from N2A cells.
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 May 15, 2019
Contact name Stephen Sansom
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)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (5)
GSM1269955 n2a-lacZ-R1
GSM1269956 n2a-lacZ-R2
GSM1269957 n2a-paupar-R1
This SubSeries is part of SuperSeries:
GSE52571 The long non-coding RNA Paupar regulates the expression of both local and distal genes
BioProject PRJNA229399
SRA SRP033202

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Supplementary file Size Download File type/resource
GSE52570_paupar_peaks.bed.gz 38.8 Kb (ftp)(http) BED
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