Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Non-coding RNAs Associated With Prader-Willi Syndrome Regulate Transcription Of Neurodevelopmental Genes In Human Induced Pluripotent Stem Cells

ABSTRACT: We generated knockdowns (KD) of long non-coding RNAs (lncRNAs) arising from locus 15q11-q13, deletions in which result in Prader-Willi syndrome, in induced pluripotent stem cells. We extracted chromatin-associated RNA (chRNA) and total RNA and sequenced those using Illumina platform. There were four conditions for chRNA: control, KD of sno-lncRNAs, KD of SPA-lncRNAs, KD of both sno/SPA-lncRNAs, in biological duplicate. There were only two conditions for the total RNA seq: control and sno/SPA-lncRNAs. We found differential expression of genes relating to neurodevelopment and cell death between control and sno/SPA-lncRNAs only in chRNA samples.

ORGANISM(S): Homo sapiens

PROVIDER: GSE174043 | GEO | 2021/05/08

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Human PA-1 cells treated with scrambled or specific ASOs

Project description:We describe the discovery of sno-lncRNAs, a class of nuclear-enriched intron-derived long noncoding RNAs (lncRNAs) that are processed on both ends by the snoRNA machinery. During exonucleolytic trimming, the sequences between the snoRNAs are not degraded, leading to the accumulation of lncRNAs flanked by snoRNA sequences but lacking 5' caps and 3' poly(A) tails. Such RNAs are widely expressed in cells and tissues and can be produced by either box C/D or box H/ACA snoRNAs. Importantly, the genomic region encoding one abundant class of sno-lncRNAs (15q11-q13) is specifically deleted in Prader-Willi Syndrome (PWS). The PWS region sno-lncRNAs do not colocalize with nucleoli or Cajal bodies, but rather accumulate near their sites of synthesis. These sno-lncRNAs associate strongly with Fox family splicing regulators and alter patterns of splicing. These results thus implicate a previously unannotated class of lncRNAs in the molecular pathogenesis of PWS. We have used deep sequencing to explore the gene expression from poly(A)+ RNAs in embryonal carcinoma (EC) line PA-1 cells treated with scrambled or specific antisense oligodeoxynucleotides (ASOs).

2013-04-26 | E-GEOD-38541 | biostudies-arrayexpress

Human PA-1 cells treated with scrambled or specific ASOs

2013-04-26 | GSE38541 | GEO

Prader-Willi Syndrome Microbiota

Project description:Prader-Willi Syndrome Microbiota Targeted loci environmental

| PRJNA669563 | ENA

Differential Gene Expression and Mitochondrial Dysfunction in Imprinting center deletion (PWS- IC del) Mouse model of Prader-Willi Syndrome

Project description:Prader-Willi syndrome (PWS) is a genetic disorder caused by deficiency of imprinted gene expression from the paternal chromosome 15q11-15q13 and clinically characterized by neonatal hypotonia, short stature, cognitive impairment, hypogonadism, hyperphagia, morbid obesity and diabetes. Previous clinical studies suggest that a defect in energy metabolism may be involved in the pathogenesis of PWS. Assessment of enzyme activities of mitochondrial oxidative phosphorylation (OXPHOS) complexes in the brain, heart, liver and muscle were assessed. We used microarrays to detail the global programme of gene expression underlyingthe PWS and identified distinct classes of disregulated genes during this process.

2013-04-19 | GSE41759 | GEO

Differential Gene Expression and Mitochondrial Dysfunction in Imprinting center deletion (PWS- IC del) Mouse model of Prader-Willi Syndrome

2013-04-19 | E-GEOD-41759 | biostudies-arrayexpress

Insulin secretion deficits in a Prader-Willi syndrome β-cell model are associated with a concerted downregulation of multiple endoplasmic reticulum chaperones [ncRNA-Seq]

Project description:A Prader-willi syndrome (PWS) model of β-cell dysfunction

2022-06-01 | GSE190336 | GEO

Insulin secretion deficits in a Prader-Willi syndrome β-cell model are associated with a concerted downregulation of multiple endoplasmic reticulum chaperones [RNA-seq]

Project description:A Prader-willi syndrome (PWS) model of β-cell dysfunction

2022-06-01 | GSE190334 | GEO

The noncoding RNA IPW regulates the imprinted DLK1-DIO3 locus in an induced pluripotent stem cell model of Prader-Willi syndrome

Project description:Parental imprinting is a form of epigenetic regulation that results in parent-of-origin differential gene expression. To study Prader-Willi syndrome (PWS), a developmental imprinting disorder, we generated patient-derived induced pluripotent stem cells (iPSCs) harboring distinct deletions in the affected region on chromosome 15. Studying PWS-iPSCs and human parthenogenetic iPSCs unexpectedly revealed substantial upregulation of virtually all maternally expressed genes (MEGs) in the imprinted DLK1-DIO3 locus on chromosome 14. Subsequently, we identified IPW, a long noncoding RNA in the critical region of the PWS locus, as a regulator of the DLK1-DIO3 region, as its over-expression in PWS and parthenogenetic iPSCs results in downregulation of the MEGs in this locus. We further show that gene expression changes in the DLK1-DIO3 region coincide with chromatin modifications, rather than DNA methylation levels. Our results suggest that a subset of PWS phenotypes may arise from dysregulation of an imprinted locus distinct from the PWS region. Gene expression analysis was performed on a total of 4 human cell lines, including 3 Prader-Willi Syndrome indcued pluripotent stem cell lines - derived from 3 affected individuals and one of their parental fibroblast cell line.

2014-04-03 | E-GEOD-56136 | biostudies-arrayexpress

A Prader-Willi locus lncRNA cloud modulates diurnal genes and energy expenditure.

Project description: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.

2013-06-20 | GSE43575 | GEO

Predictors for OWOB in children with Prader Willi Syndrome

Project description:Predictors for OWOB in children with Prader Willi Syndrome

| PRJEB34790 | ENA