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

Genome-wide analyses of XRN1-sensitive targets in osteosarcoma cells identifies disease-relevant transcripts containing G-rich motifs

ABSTRACT: RNA-seq of ribosome depleted RNA extracted from SAOS-2 cells following treatment with either XRN1 siRNA or a scrambled siRNA control

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Ben Towler

PROVIDER: E-MTAB-10808 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Genome-wide analyses of XRN1-sensitive targets in osteosarcoma cells identify disease-relevant transcripts containing G-rich motifs.

Pashler Amy L AL Towler Benjamin P BP Jones Christopher I CI Haime Hope J HJ Burgess Tom T Newbury Sarah F SF

RNA (New York, N.Y.) 20210715 10

XRN1 is a highly conserved exoribonuclease which degrades uncapped RNAs in a 5'-3' direction. Degradation of RNAs by XRN1 is important in many cellular and developmental processes and is relevant to human disease. Studies in <i>D. melanogaster</i> demonstrate that XRN1 can target specific RNAs, which have important consequences for developmental pathways. Osteosarcoma is a malignancy of the bone and accounts for 2% of all pediatric cancers worldwide. Five-year survival of patients has remained s ...[more]

PMID: 34266995

Similar Datasets

RNAi profiling of human SAOS-2 cells, RBP2 knockdown or pRB overexpression

Project description:RBP2 is downstream of pRB pathway; We used gene expression profiling experiments to investigate if gene expression changes in cells with RBP2 knockdown significantly overlap with gene expression changes in cells overexpressing pRB, consistent with the data that knockdown of RBP2 phenocopies reintroduction of pRB in SAOS-2 (RB-/-) cells Experiment Overall Design: Knockdown of RBP2 by siRNA to RBP2 (RBP2siRNA) in SAOS-2 (RB-/-) cells in comparison to overexpression of pRB in the SOAS-2 (RB-/-) cells and scrambled version of the RBP2 siRNA (RBP2scsiRNA)

2008-10-25 | E-GEOD-9690 | biostudies-arrayexpress

In-vivo and in-vitro RIP-seq of WT and Delta NLS1/2 mutant of Xrn1

Project description:To examine whether the mutations in NLS1/2 affect the interaction with mRNAs, we determined the in vitro and in vivo interaction of WT Xrn1 and Xrn1 Delta NLS1/2 mutant with cellular mRNAs.

2022-08-29 | E-MTAB-12110 | biostudies-arrayexpress

Transcriptome-wide mapping of cut sites of the viral endoribonuclease SOX from Kaposi's sarcoma-associated herpesvirus (KSHV)

Project description:Purpose: identify sites in endogenous mRNAs that are cut by KSHV SOX; Method: parallel analysis of RNA ends (PARE, following Zhai et al., 2014); Results: SOX cuts at discrete locations in mRNAs human Xrn1 was knocked down in HEK293T cells by shRNAs or siRNAs to stabilize degradation fragments with free 5' ends; GFP-SOX or GFP were transfected for ~24 hrs; total RNA samples were collected and subjected to PARE protocol (Zhai et al., 2014)

2015-11-07 | E-GEOD-70373 | biostudies-arrayexpress

Transcription profiling of yeast wild type, xrn1, xrn1 upf1, xrn1 nmd2, and xrn1 upf3 strains to investigate mRNA decay

Project description:To determine the effects of inactivation of both the nosense-mediated mRNA decay pathway and the general 5' to 3' decay pathway on yeast mRNA decay, we compared the expression profiles of the wild-type, xrn1, xrn1 upf1, xrn1 nmd2, and xrn1 upf3 strains.

2011-11-08 | E-MEXP-27 | biostudies-arrayexpress

3' UTR length and mRNP composition determine endocleavage efficiencies at termination codons

Project description:We aimed to study the cleavage sites of nonsense-mediated mRNA decay (NMD) substrates. Therefore, we depleted the major exoribonuclease XRN1 in human cell culture, which degrades the 3' fragments generated by SMG6-mediated endonucleolytic cleavage. Different reporter mRNAs or endogenous NMD targets were investigated and the 3' fragments were cloned, amplified and subsequently subjected to high throughput sequencing.

2014-11-11 | E-MTAB-2907 | biostudies-arrayexpress

RNA-controlled nucleocytoplasmic shuttling of mRNA decay factors regulates mRNA synthesis and a novel mRNA decay pathway

Project description:mRNA level is controlled by factors that mediate both mRNA synthesis and decay, including the 5’ to 3’ exonuclease Xrn1 - a major mRNA synthesis and decay factor. Here we show that nucleocytoplasmic shuttling of several mRNA decay factors plays a key role in determining both mRNA synthesis and decay. Shuttling is regulated by RNA-controlled binding of the karyopherin Kap120 to two nuclear localization sequences (NLSs) in Xrn1, location of one of which is conserved from yeast to human. The decaying RNA binds and masks NLS1, establishing a link between mRNA decay and Xrn1 shuttling. Preventing Xrn1 import, either by deleting KAP120 or mutating the two Xrn1 NLSs, compromise transcription and, unexpectedly, also the cytoplasmic decay, uncovering a cytoplasmic decay pathway that initiates in the nucleus. Most mRNAs are degraded by both the “classical” and the novel pathways, the ratio between them represents a full spectrum. Importantly, Xrn1 shuttling is required for proper adaptation to environmental changes, in particular to ever changing environmental fluctuations.

2022-09-19 | PXD036414 | Pride

Identification of target genes regulated by M-NM-^TNp63M-NM-1 in SaOS-2 cells stably expressed with M-NM-^TNp63M-NM-1

Project description:To identify the target gene of M-NM-^TNp63M-NM-1, in osteosarcoma cells, we performed the global gene expression profiling in SaOS- 2 cells stably overexpressing the M-NM-^TNp63M-NM-1 gene (SaOS- 2-M-NM-^TNp63M-NM-1). M-NM-^TNp63M-NM-1 target genes were identified by comparison with genes expressed from SaOS-2-EV transfected with an empty vector ( SaOS-2-EV). Total RNA was extracted from SaOS- 2-M-NM-^TNp63M-NM-1 and SaOS-2-EV cells cultured in three independent replicates for each condition. Cy3-labeled cRNA was synthesized and hybridized to Agilent human 8 x 60K microarrays. Raw data, obtained after array image analysis were normalized and used to retrieve differentially expressed genes in M-NM-^TNp63M-NM-1 overexpressing SaOS- 2 cells and genes from control SaOS-2-EV cells.

2014-02-27 | E-GEOD-54942 | biostudies-arrayexpress

Saos-2 vs. Saos-2-2 cells

Project description:Saos-2-2, a TSG101-deficient stable line, was dereived from Saos-2 cells. The goal of this experiment was to determine the effects of TSG101 down-regulation on global gene expression. Saoa-2 and Saos-2-2 samples were labeled with Cys-3 and Cys-5 respectively, and hybrided with microarray simutaneously to differentiate the up- and down-regulated genes.

2013-10-11 | E-GEOD-50808 | biostudies-arrayexpress

Affymetrix CytoscanHD data for genomic plasticity of osteosarcoma cell lines

Project description:To identify chromosomal aberrations during passaging of parental SAOS-2 osteosarcoma cells with low metastatic potential and of SAOS-2-derived LM5 cells with increased metastatic potential DNA of early and late passage SAOS-2 and LM5 cells was analyzed by Affymetrix Cytoscan HD genotyping arrays

2015-05-01 | E-GEOD-67125 | biostudies-arrayexpress

Global changes in mRNA abundance drive differential shuttling of RNA binding proteins, linking cytoplasmic RNA degradation to transcription

Project description:Alterations in global mRNA decay can broadly impact multiple upstream and downstream stages of gene expression. For example, accelerated cytoplasmic mRNA degradation can trigger a reduction in mammalian RNA polymerase II (RNAPII) transcription, although signals that connect these seemingly distal processes remain largely unknown. Here, we used tandem mass tag labeling with mass spectrometry to chart how changes in Xrn1-dependent mRNA degradation impact nuclear-cytoplasmic protein distribution in human cells. Notably, accelerating mRNA decay through expression of a gammaherpesviral endonuclease known to coordinate with Xrn1 drove nuclear relocalization of many RNA binding proteins. Particularly enriched in the relocalized subset were factors linked to the poly(A) tail. Conversely, cells lacking Xrn1 exhibited changes in the localization and/or abundance of numerous factors linked to mRNA turnover. Based on these data, we uncovered a new role for cytoplasmic poly(A) binding protein in repressing RNAPII transcription upon its mRNA decay-induced translocation to the nucleus.

2018-10-24 | PXD009487 | 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