MiRNA-seq of microRNAs from control or PARN depleted HeLa cells
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina MiSeq
ORGANISM(S): Homo sapiens
SUBMITTER: Siddharth Shukla
PROVIDER: E-MTAB-7547 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
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
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.
2015-09-08 | GSE71709 | GEO
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
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
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
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
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
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. Three different clones of the PARN-1 OvEx and Control cell lines were used for analysis. Each experiment was run in duplicate, with the dye-labeling reversed between duplicates. The T. brucei version 3 microarray chip (PFGRC) was used for this experiment. Each gene on the microarray was represented in duplicate, so for each experiment, mRNA levels were obtained from both points and averaged. As a control between arrays, we used a control probe set obtained from PFGRC. "The probe set consists of Cy3 and Cy5 end labeled 40-mer probes that are complementary to a set of 500 Arabidopsis thaliana 70-mer targets on PFGRC DNA microarrays. The UMSS is supplied as a ready to use mix of the Cy3 and Cy5 labeled oligonucleotides. A small aliquot is spiked into Cy-dye labeled nucleic acid samples just prior to hybridization on PFGRC microarrays. The UMSS produces a set of reference fluorescent signal intensities and ratios that are generated independent of the user-specific experimental samples. Since PFGRC intentionally targeted a heavy representation of Cy3 and Cy5 signals in the mid-range of detection, the Cy3 and Cy5 signal intensities and ratios generated by the UMSS should be highly reproducible. These signals serve as a reference point to judge the success of microarray experiments, and troubleshoot potential problems."
2010-03-04 | E-GEOD-20593 | biostudies-arrayexpress
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
Project description:Almost all cellular mRNAs terminate in a 3M-bM-^@M-^Y poly(A) tail, the removal of which can induce both translational silencing and mRNA decay. Mammalian cells encode many poly(A)-specific exoribonucleases but their individual roles are poorly understood. Here, we undertook an analysis of the role of PARN deadenylase in mouse myoblasts using global measurements of mRNA decay rates. Our results reveal that a discrete set of mRNAs exhibit altered mRNA decay as a result of PARN depletion and that stabilization is associated with increased poly(A) tail length and translation. We determined that stabilization of mRNAs does not generally result in their increased abundance supporting the idea that mRNA decay is coupled to transcription. Importantly, PARN knockdown has wide ranging effects on gene expression that specifically impact the extracellular matrix and cell migration. Finally, although PARN has its own unique target transcripts it also influences some genes whose expression is modulated by other deadenylases. In order to investigate the role of PARN deadenyl on mRNA decay in mouse muscle cells , C2C12 cells were transfected by shRNA knockdown of PARN and treated with actinomycin D to inhibit transcription. Total RNA was isolated from three replicates at 0, 15, 30, 60, 120 and 240 minutes. The CTRL cell line stably transfected with LKO1 vector was described previously (GSE21233).
2012-08-31 | E-GEOD-35944 | biostudies-arrayexpress