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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling time series of S. cerevisiae wild type and upf1 mutant strains following transcription inhibition by thiolutin

ABSTRACT: Isogenic UPF1+ or upf1- yeast strains were treated with 10 ug/ml thiolutin to inhibit global transcription. Targets were obtained from 16 time points: 0, 2, 4, 6, 8, 10, 12, 15, 20, 25, 30, 35, 40, 45, 50, 60 minutes after transcription inhibition. Three biological replicates of each were generated and the expression profiles were determined using Affymetrix YG-S98 arrays. Comparisons between the sample groups allow the identification of genes with differential expression over time between UPF1+ and upf1-. Experiment Overall Design: Sample from 2 genotypes, 16 time points, 3 biological replicates were analyzed

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Michael Culbertson

PROVIDER: E-GEOD-3076 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Impact of nonsense-mediated mRNA decay on the global expression profile of budding yeast.

Guan Qiaoning Q Zheng Wei W Tang Shijie S Liu Xiaosong X Zinkel Robert A RA Tsui Kam-Wah KW Yandell Brian S BS Culbertson Michael R MR

PLoS genetics 20061018 11

Nonsense-mediated mRNA decay (NMD) is a eukaryotic mechanism of RNA surveillance that selectively eliminates aberrant transcripts coding for potentially deleterious proteins. NMD also functions in the normal repertoire of gene expression. In Saccharomyces cerevisiae, hundreds of endogenous RNA Polymerase II transcripts achieve steady-state levels that depend on NMD. For some, the decay rate is directly influenced by NMD (direct targets). For others, abundance is NMD-sensitive but without any eff ...[more]

PMID: 17166056

Similar Datasets

Impact of Nonsense-mediated mRNA Decay on the Global Expression Profile of Budding Yeast

Project description:Isogenic UPF1+ or upf1- yeast strains were treated with 10 ug/ml thiolutin to inhibit global transcription. Targets were obtained from 16 time points: 0, 2, 4, 6, 8, 10, 12, 15, 20, 25, 30, 35, 40, 45, 50, 60 minutes after transcription inhibition. Three biological replicates of each were generated and the expression profiles were determined using Affymetrix YG-S98 arrays. Comparisons between the sample groups allow the identification of genes with differential expression over time between UPF1+ and upf1-. Keywords: time course

2006-08-31 | GSE3076 | GEO

Transcription profiling of S. cerevisiae to identify Upf1p-associated transcripts in S. cerevisiae

Project description:The goal of this experiment was to identify transcripts associated with the S. cerevisiae Upf1 protein. Experiment Overall Design: The RNA population from four independent pairs of Upf1p-TAP and mock affinity selections were analyzed by using Affymetrix Yeast Genome S98 Arrays.

2008-06-16 | E-GEOD-9486 | biostudies-arrayexpress

Phosphorylated UPF1 (p-UPF1) RIP-seq using mouse Neuro-2A (N2A) neuroblastoma cells

Project description:To identify high-confidence NMD targets in mouse N2A neuroblastoma cells, we used our established transcriptome-wide RNA sequencing (RNA-seq) methodologies. Through parallel analyses of RNA-seq upon UPF1-knockdown (KD) and RNA immunoprecipitation (RIP-seq) footprinting of p-UPF1-bound RNAs, we identified 1027 high-confidence neuronal NMD targets.

2021-10-25 | GSE180134 | GEO

The RNA helicase UPF1 associates with mRNAs cotranscriptionally

Project description:UPF1 is an ATP-driven RNA helicase required for efficient nonsense mediated mRNA decay in eukaryotes. Although it is currently understood that UPF1 primarily acts on the 3’UTR of translating mRNAs in the cytoplasm, our data indicates that this is a highly dynamic protein that is rapidly shuttling between nucleus and cytoplasm in Drosophila. Additionally, ChIP-seq analysis in different cell types demonstrates genome-wide association of UPF1 with nascent RNAs at most of the active Pol II transcription sites, and at some specific Pol III genes. Notably, intron recognition appears to interfere with association and translocation of UPF1 on nascent transcripts. Cells depleted of UPF1 show defects in nuclear processes such as mRNA export and transcription site retention. These data, thus redefine UPF1 as a global player in mRNA based processes in the nucleus as well as the cytoplasm.

2019-04-01 | GSE116808 | GEO

A post-translational regulatory switch on UPF1 controls targeted mRNA degradation.

Project description:Nonsense-mediated mRNA decay (NMD) controls the quality of eukaryotic gene expression and also degrades physiologic mRNAs. How NMD targets are identified is incompletely understood. A central NMD factor is the ATP-dependent RNA helicase UPF1. Neither the distance in space between the termination codon and the poly(A) tail nor the binding of steady-state, largely hypophosphorylated UPF1 is a discriminating marker of cellular NMD targets, unlike for PTC-containing reporter mRNAs when compared to their PTC-free counterparts. Here, we map phosphorylated UPF1 (p-UPF1) binding sites using transcriptome-wide footprinting or DNA oligonucleotide-directed mRNA cleavage to report that p-UPF1 provides the first reliable cellular NMD-target marker. p-UPF1 is enriched on NMD target 3'UTRs along with SMG5 and SMG7 but not SMG1 or SMG6. Immunoprecipitations of UPF1 variants deficient in various aspects of the NMD process in parallel with FRET experiments reveal that ATPase/helicase-deficient UPF1 manifests high levels of RNA binding and disregulated hyperphosphorylation, whereas wild-type UPF1 releases from nonspecific RNA interactions in an ATP hydrolysis-dependent mechanism until an NMD target is identified. 3'UTR-associated UPF1 undergoes regulated phosphorylation on NMD targets, providing a binding platform for mRNA degradative activities. p-UPF1 binding to NMD target 3'UTRs is stabilized by SMG5 and SMG7. Our results help to explain why steady-state UPF1 binding is not a marker for cellular NMD substrates and how this binding is transformed to induce mRNA decay. RIP-seq experiments for p-UPF1, control IPs using rabbit IgG and additional control sample without IP were performed in duplicates

2014-08-15 | E-GEOD-60045 | biostudies-arrayexpress

AP-MS of helicase Upf1 in PC12 cells

Project description:DNA/RNA helicase Upf1 seems to interact with axonal transcripts in response to nerve growth factor (NGF, A. Ludanyi, M. Gaspari and A. Riccio, unpublished data). In order to shed light on Upf1 mechanism of action and to identify potential associations with molecules having cleavage activity, we performed an AP-MS experiment comprising Upf1 immunoprecipitation, on-beads digestion, isotopic labelling (18O) and quantitative LC-MS/MS analysis.

2021-09-10 | PXD023586 | Pride

A post-translational regulatory switch on UPF1 controls targeted mRNA degradation.

2014-08-15 | GSE60045 | GEO

Role of UPF1-LIN28A interaction during early differentiation of pluripotent stem cells

Project description:Two RNA binding proteins, UPF1 and LIN28A, have well-known functions in posttranscriptional regulations and stem cell differentiation. Most studies on UPF1 and LIN28A have focused on the molecular mechanism in differentiated cells and stem cell differentiation, respectively. We revealed that LIN28A directly interacts with UPF1, which happens before UPF1 forms a complex with UPF2, thereby resulting in the reduction of UPF1 phosphorylation and inhibition of nonsense-mediated mRNA decay (NMD). Our studies reveal that cell fate is determined by transcriptome regulation through UPF1-LIN28A interaction in hPSCs.

2023-12-12 | GSE224358 | GEO

Genome-wide mapping of UPF1 and Pol II [ChIP-seq]

Project description:ChIP with NMD core componenet UPF1 antibody in normal S2 cells and ChIP with Pol II Ser2 antibodies in S2 cells. UPF1 is an ATP-driven RNA helicase required for efficient nonsense mediated mRNA decay in eukaryotes. Although it is currently understood that UPF1 primarily acts on the 3’UTR of translating mRNAs in the cytoplasm, our data indicates that this is a highly dynamic protein that is rapidly shuttling between nucleus and cytoplasm in Drosophila. Additionally, ChIP-seq analysis in different cell types demonstrates genome-wide association of UPF1 with nascent RNAs at most of the active Pol II transcription sites, and at some specific Pol III genes. Notably, intron recognition appears to interfere with association and translocation of UPF1 on nascent transcripts. Cells depleted of UPF1 show defects in nuclear processes such as mRNA export and transcription site retention. These data, thus redefine UPF1 as a global player in mRNA based processes in the nucleus as well as the cytoplasm.

2019-04-01 | GSE116806 | GEO

UPF1/SMG7-dependent MicroRNA-mediated Gene Regulation

Project description:A majority of metazoan mRNAs are under microRNA (miRNA)/Argonaute (Ago)-mediated control of RNA stability at the post-transcriptional level. Although the molecular mechanism of the miRNA-mediated repression of target mRNAs through Ago/TNRC6 pathway have been largely elucidated, however, the existence of alternative TNRC6-independent miRNA-mediated post-transcriptional gene regulation pathway remains unknown. Here, we suggest that endogenous miRNAs (endo-miRNAs) can downregulate the target mRNAs via the alternative molecular pathway, Ago-associated UPF1/SMG7, core mediators of nonsense-mediated mRNA decay. Global analyses of mRNAs in a response to UPF1 RNA interference in miRNA-deficient cells reveal that 3’UTR-length-dependent mRNA decay by UPF1 requires endo-miRNA targeting via CUG motif. The repression of miRNA targets is more additively or synergistically accomplished by combination of Ago2 and UPF1 through UPF1-associated SMG7, recruiting CCR4-NOT deadenylase complex, in TNRC6-independent manner. We expect that the new miRNA-mediated mRNA decay pathway enables the miRNA targeting to become more predictable and expand the miRNA-mRNA regulatory network.

2019-06-30 | GSE99169 | GEO

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