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E-GEOD-62031 - The DNMT1 associated lncRNA Dali is an epigenetic regulator of neural differentiation [1]

Status
Released on 3 December 2014, last updated on 2 January 2015
Organism
Mus musculus
Samples (6)
Array (1)
Protocols (7)
Description
Many intergenic long noncoding RNA (lncRNA) loci regulate the expression of adjacent protein coding genes. Less clear is whether intergenic lncRNAs commonly regulate transcription by modulating chromatin at genomically distant loci. Here, we report both genomically local and distal RNA-dependent roles of Dali, a conserved central nervous system expressed intergenic lncRNA. Dali is transcribed downstream of the Pou3f3 transcription factor gene and its depletion disrupts the differentiation of neuroblastoma cells. Locally, Dali transcript regulates transcription of the Pou3f3 locus. Distally, it preferentially targets active promoters and regulates expression of neural differentiation genes, in part through physical association with the POU3F3 protein. Dali interacts with the DNMT1 DNA methyltransferase in mouse and human and regulates DNA methylation status of CpG island-associated promoters in trans. These results demonstrate, for the first time, that a single intergenic lncRNA controls the activity and methylation of genomically distal regulatory elements to modulate large-scale transcriptional programmes. N2A cells transfected with a non-targeting control vector were compared to N2A cells transfected with a Dali knockdown construct. Three biological replicates of each condition were analysed on Affymetrix GeneChip Mouse Gene 1.0 ST Arrays.
Experiment type
transcription profiling by array 
Contacts
Vladislava Chalei <Vladislava.Chalei@gmail.com>, Chris P Ponting, Juan Montiel, Keith W Vance, Lesheng Kong, Sheena Lee, Stephen N Sansom
Citation
The long non-coding RNA <i>Dali</i> is an epigenetic regulator of neural differentiation. Chalei V, Sansom SN, Kong L, Lee S, Montiel J, Vance KW, Ponting CP. , PMID:25415054
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-62031.idf.txt
Sample and data relationshipE-GEOD-62031.sdrf.txt
Raw data (1)E-GEOD-62031.raw.1.zip
Processed data (1)E-GEOD-62031.processed.1.zip
Array designA-AFFY-130.adf.txt
Links