Ontology highlight
ABSTRACT:
PROVIDER: PRJNA113187 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This SuperSeries is composed of the following subset Series: GSE12351: mRNAs associated with human PUM1 protein GSE12352: mRNAs associated with human PUM2 protein Refer to individual Series
2008-09-08 | E-GEOD-12357 | biostudies-arrayexpress
Project description:The functions of human PUM1 and PUM2 are considered to be redundant given that both PUF1 and PUF2 recognize the same PBE motif UGUANAUA. However pools of mRNAs published so far for PUM1 and PUM2 do not overlap. Therefore we sought to investigate the issue of redundancy in human cells. The both PUM proteins are less conserved in the region that is outside the PUM domain. We sought that interactors could be different. We identified mRNA pools binding separately PUM1 and PUM2 by RIP-Seq approach, normalized them using the whole TCam-2 cells transcriptome and aligned them with mRNA pools activated or repressed as tested by siRNA PUM1 and PUM2 knockdown.
2018-11-28 | GSE123016 | GEO
Project description:mRNAs associated with human Pumilio2 protein (PUM2)
| PRJNA136441 | ENA
Project description:we employ crosslinking immunoprecipitation (iCLIP) to reveal Pum1 and Pum2 binding mRNAs
2017-08-15 | GSE95195 | GEO
Project description:PUF family proteins are among the best characterized regulatory RNA-binding proteins in non-mammalian species, but relatively little is known about mRNA targets or functions of mammalian PUF proteins. In this study, we used ribonomic analysis to identify and analyze mRNAs associated with ribonucleoproteins containing an endogenous human PUF protein, Pum1. Pum1 associated mRNAs were highly enriched for genes encoding proteins that function in transcriptional regulation and cell cycle/proliferation, results consistent with the post-transcriptional RNA regulon model and the proposed ancestral functions of PUF proteins in stem cell biology. Analysis of 3’UTR sequences of Pum1 associated mRNAs revealed a core Pum1 consensus sequence, UGUAHAUA. Pum1 knockdown demonstrated that Pum1 enhances decay of associated mRNAs, and re-localization of Pum1 to stress granules suggested that Pum1 functions in repression of translation. This study is the first in vivo genome-wide mRNA target identification of a mammalian PUF protein and provides direct evidence that human PUF proteins regulate stability of associated mRNAs. Comparison of Pum1 associated mRNAs to mRNA targets of PUF proteins from S. cerevisiae and Drosophila demonstrates how a well conserved RNA-binding domain and cognate binding sequence have been evolutionarily rewired to regulate the collective expression of different sets of functionally related genes. Pum1 IP, negative IP, and total IP samples were analyzed for each of 3 biological replicates. Each IP or total RNA sample was run on a separate array versus a common reference sample
2008-05-01 | E-GEOD-11301 | biostudies-arrayexpress
Project description:We employ Mass spectrum to investigate proteome of Pum1-Knockout, Pum2-Knockout and WT conditions in human colorectal cancer cell line Hct116. Overall design: In order to investigate whether Pum1 and Pum2 regulate their targets at their protein levels, we used Pum1-Knockout, Pum2-Knockout and WT Hct116 cell line to extract total protein for Mass spectrum.
2021-07-23 | PXD027513 |
Project description:The human members of the PUF family of proteins, PUM1 and PUM2, are RNA-binding proteins that post-transcriptionally regulate gene expression through binding to a PUM recognition element (PRE) in the 3′ UTR of target mRNAs, promoting RNA decay. Recent RNA-seq experiments in PUM1/2 knockdown conditions have identified hundreds of known and new human PUM targets through measurement of changes in steady state RNA levels. However, steady-state RNA levels do not allow for measurement of changes in RNA stability between conditions and do not allow for the differentiation between the contributions of changes in transcription rates and changes in RNA decay. Here, we identify hundreds of human PUM1/2 targets that have changes in RNA stability following PUM1/2 knockdown. We separate the contributions of changes in transcription rate and RNA stability and find that human PUM proteins almost exclusively modulate RNA abundance through changing RNA stability and not transcription. In addition, we find that the sequence preferences for all possible 8mers are largely similar between PUM1 and PUM2, suggesting that PUM1 and PUM2 recognize similar targets. We identify an ideal PRE “rulebook” by determining key contextual features around PREs, including local AU content, location of a PRE within a 3′ UTR, clustering of PREs, and number of miRNA sites near a PRE, that help differentiate functional PREs from non-functional ones as measured by our decay dataset. Consistent with previously identified functional roles of mammalian PUMs, we find that human PUM1 and PUM2 modulate the decay of genes related to signaling cascades and neuronal function. Finally, we train machine learning models to predict functional regulation of RNA targets by the human PUM proteins and find that contextual features around PREs contribute meaningful information to our models.
2020-08-05 | GSE145237 | GEO
Project description:Pumilio paralogs, PUM1 and PUM2, are sequence-specific RNA-binding proteins that are essential for vertebrate development and neurological functions. PUM1&2 function to negatively regulate gene expression by accelerating degradation of specific mRNAs. Here, we determined the repression mechanism and impact of human PUM1&2 on the transcriptome. We identified subunits of the CCR4-NOT (CNOT) deadenylase complex required for stable interaction with PUM1&2 and to elicit CNOT-dependent repression. Isoform-level RNA sequencing revealed broad co-regulation of target mRNAs through the PUM-CNOT repression mechanism. Functional dissection of the domains of PUM1&2 identified a conserved N-terminal region that confers the predominant repressive activity via direct interaction with CNOT. In addition, we show that the DCP2 mRNA decapping enzyme has an important role in repression by PUM1&2 N-terminal regions. Our results support a molecular model of repression by human PUM1&2 via direct recruitment of CNOT deadenylation machinery in a decapping-dependent pathway.
2021-09-09 | GSE159510 | GEO