Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MiRNA-seq of microRNAs from control or PARN depleted HeLa cells

ABSTRACT: PARN deficiency is linked to the inherited disease Dyskeratosis Congenita and Familial Pulmonary Fibrosis. The aim of this experiment is to identify miRNAs that are regulated by PARN in human cells, deficiency of which could explain the disease phenotype in patients.

INSTRUMENT(S): Illumina MiSeq

ORGANISM(S): Homo sapiens

SUBMITTER: Siddharth Shukla

PROVIDER: E-MTAB-7547 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Poly(A)-specific ribonuclease (PARN) mediates 3' end maturation of the telomerase RNA component

Project description:Mutations in the poly(A) ribonuclease (PARN) gene cause telomere diseases including familial idiopathic pulmonary fibrosis (IPF) and dyskeratosis congenita (DC)1,2, but how PARN deficiency impacts telomere maintenance is unclear. Here, using somatic cells and induced pluripotent stem (iPS) cells from DC patients with PARN mutations, we show that PARN is required for the 3′ end maturation of the telomerase RNA component (TERC). Patient cells as well as immortalized cells in which PARN is disrupted show decreased levels of TERC. Deep sequencing of TERC RNA 3′ termini reveals that PARN is required for removal of posttranscriptionally acquired oligo(A) tails that target nuclear RNAs for degradation. Diminished TERC levels and the increased oligo(A) forms of TERC are normalized by restoring PARN, which is limiting for TERC maturation in cells. Our results reveal a novel role for PARN in the biogenesis of TERC, and provide a mechanism linking PARN mutations to telomere diseases. mRNA sequencing of fibroblasts, induced pluripotent stem cells, and 293 cell line.

2015-09-08 | E-GEOD-71709 | biostudies-arrayexpress

Poly(A)-specific ribonuclease (PARN) mediates 3' end maturation of the telomerase RNA component

2015-09-08 | GSE71709 | GEO

microRNA-seq of miRNAs from control and DIS3L knockdown HeLa cells

Project description:DIS3L is a 3' to 5' exonuclease that plays a role in the degradation of cellular RNAs. The aim of this experiment was to identify miRNAs that are regulated by DIS3L in human cells.

2018-12-29 | E-MTAB-7548 | biostudies-arrayexpress

microRNA-seq of miRNAs isolated from control or DIS3L2 knockdown HeLa cells

Project description:DIS3L2 is a 3' to 5' exonuclease that plays a role in the degradation of specific non-coding RNAs in the cell. The aim of this experiment if to identify miRNAs regulated by DIS3L2 in HeLa cells.

2018-12-29 | E-MTAB-7549 | biostudies-arrayexpress

PARN is essential to GSIS in beta cells

Project description:To investigated the function of PARN in beta cells, we generated the specific deletion of Parn in beta cells.

2024-11-20 | GSE248559 | GEO

PARN is essential to GSIS in beta cell

Project description:To investigated the function of PARN in beta cells, we generated the specific deletion of Parn in beta cells.

2024-11-20 | GSE248389 | GEO

Screening of the targeted mRNAs of ER-anchored PARN by transcriptome sequencing.

Project description:The goals of this study are to identify the potential targets and then elucidate the function of ER-anchored PARN. After overexpressing the empty vector, PARN(wild type) or D28A(the enzyme-dead mutant of PARN) in HEK-293T cell respectively and the following fractionation of the cytosol and ER fraction, we performed the high-throughput RNA sequencing for each fraction. After comparing the abundance of detected transcripts in different samples we found ER-anchored PARN only affects a small subset of mRNAs in HEK-293T cell.

2021-09-19 | GSE120209 | GEO

Poly(A)-Specifc Ribonuclease 1 (PARN-1) Overexpression in Procyclic T. brucei

Project description:We sought to determine the effect of TbPARN-1 overexpression on global mRNA steady-state levels in T. brucei. The mRNA expression profile of tet-induced TbPARN-1 OvEx procyclic cells was compared to the mRNA profile of control cells (expressing tet-induced TAP tag alone) by microarray analysis. Since overexpression of TbPARN-1 showed increased deadenylation activity in cytoplasmic extracts, overexpressing PARN-1 in vivo should result in more rapid deadenylation and decay of mRNAs targeted by PARN-1. Thus, mRNAs with lower steady state levels in PARN-1 OvEx cells can be considered likely targets for PARN-1-dependent deadenylation.

2010-03-05 | GSE20593 | GEO

PARN and TOE1 constitute a 3′ end maturation module for nuclear non-coding RNAs

Project description:Poly(A)-specific ribonuclease (PARN) and target of EGR1 protein 1 (TOE1) are nuclear granule-associated deadenylases, whose mutations are linked to multiple human diseases. Here, we applied mTAIL-seq and RNA sequencing (RNA-seq) to systematically identify the substrates of PARN and TOE1 and elucidate their molecular functions. We found that PARN and TOE1 do not modulate the length of mRNA poly(A) tails. Rather, they promote the maturation of nuclear small non-coding RNAs (ncRNAs). PARN and TOE1 act redundantly on some ncRNAs, most prominently small Cajal body-specific RNAs (scaRNAs). scaRNAs are strongly downregulated when PARN and TOE1 are compromised together, leading to defects in small nuclear RNA (snRNA) pseudouridylation. They also function redundantly in the biogenesis of telomerase RNA component (TERC), which shares sequence motifs found in H/ACA box scaRNAs. Our findings extend the knowledge of nuclear ncRNA biogenesis, and they provide insights into the pathology of PARN/TOE1-associated genetic disorders whose therapeutic treatments are currently unavailable.

2018-03-30 | GSE111511 | GEO

Comparison of ribosomes between control and dyskerin-depleted human cells

Project description:Dyskerin is a pseudouridine synthase involved in fundamental cellular processes (including rRNA and snRNA modification and telomere stabilization), whose function is altered in X-linked dyskeratosis congenita and cancer. Dyskerin role in ribosome processing was suggested to underlie the alterations in mRNA translation described in cells lacking dyskerin function. We compared the protein contents of 5 replicates of ribosomal preparations from control or dyskerin-depleted human cells.

2015-05-07 | PXD001274 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data