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Series GSE43575 Query DataSets for GSE43575
Status Public on Jun 20, 2013
Title A Prader-Willi locus lncRNA cloud modulates diurnal genes and energy expenditure.
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary Prader-Willi syndrome (PWS), a genetic cause of childhood obesity, is characterized by intellectual disabilities and sleep abnormalities. PWS-causing deletions include a neuronal long, non-coding RNA (lncRNA) processed into small nucleolar RNAs and a spliced lncRNA,116HG. We show that 116HG forms a subnuclear RNA cloud that co-purifies with the transcriptional activator RBBP5 and active metabolic genes, remains tethered to the site of its transcription and increases in size in postnatal neurons. Snord116del mice lacking 116HG exhibited increased energy expenditure corresponding to dysregulation of diurnally expressed Mtor and circadian genes Clock, Cry1, and Per2. Genomic and metabolic analyses demonstrate altered diurnal energy regulation in the Snord116del mouse cortex and link the loss of 116HG to the energy imbalance observed in PWS.
Overall design Examination of lncRNA binding sites by ChIRP-seq using an oligo-based purification method from WT and Snord116del (+/-) mouse brain with specific and nonspecific control oligos. Transcript abundance levels by RNA-seq analysis of 3 adult WT and 2 adult Snord116del (+/-) mouse brain cortices at Zt+6 and 2 adult WT and 2 adult Snord116del (+/-) mouse brain cortices at Zt+16.
Contributor(s) Powell WT
Citation(s) 23771028
Submission date Jan 17, 2013
Last update date May 15, 2019
Contact name Weston Powell
Organization name UC Davis
Department MMI
Lab LaSalle Lab
Street address 3426 Tupper Hall
City Davis
State/province CA
ZIP/Postal code 95616
Country USA
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (15)
GSM1065671 WT_116HG_ChIRP-seq rep1
GSM1065672 WT_NSC_ChIRP-seq
GSM1065673 WT_116HG_ChIRP-seq rep2
BioProject PRJNA186743
SRA SRP018013

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Supplementary file Size Download File type/resource
GSE43575_RAW.tar 910.0 Kb (http)(custom) TAR (of BED)
GSE43575_RNAseq030113.txt.gz 870.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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