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The RNA exosome nuclease complex regulates human embryonic stem cell differentiation [PAR-iCLIP]

ABSTRACT: This work shows that the exosome modulates the levels of LINE-1 retrotransposons, miRNAs, lncRNAs and specific mRNAs that encode developmental regulators or affect their expression. The exosome restrains differentiation in part by degrading transcripts encoding FOXH1, a transcription factor crucial for mesendoderm formation.

ORGANISM(S): Homo sapiens

PROVIDER: GSE132466 | GEO | 2019/07/11

REPOSITORIES: GEO

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The RNA exosome nuclease complex regulates human embryonic stem cell differentiation [HITS-CLIP]

Project description:This work shows that the exosome modulates the levels of LINE-1 retrotransposons, miRNAs, lncRNAs and specific mRNAs that encode developmental regulators or affect their expression. The exosome restrains differentiation in part by degrading transcripts encoding FOXH1, a transcription factor crucial for mesendoderm formation.

2019-07-11 | GSE132360 | GEO

The RNA exosome nuclease complex regulates human embryonic stem cell differentiation [RNA-Seq SS]

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The RNA exosome nuclease complex regulates human embryonic stem cell differentiation [PAR-iCLIP]

Project description:The RNA exosome nuclease complex regulates human embryonic stem cell differentiation [PAR-iCLIP]

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iCLIP analysis of RNA substrates of the archaeal exosome (iCLIP)

Project description:In this study, an exoribonuclease was analyzed by iCLIP. The data documents the role of the archaeal exosome as an exoribonuclease and RNA-tailing enzyme interacting with all RNA classes. Mapping of most reads to mRNAs underlines the role of exosome in mRNA turnover, which is important for adaptation of prokaryotic cells to changing environmental conditions. The clustering of crosslink sites near 5’-ends of genes suggests simultaneous binding of both RNA ends by the S. solfataricus exosome. This may serve to prevent translation of mRNAs designated to degradation in 3’-5’ direction.

2020-11-24 | GSE149140 | GEO

Expression data from Drosophila S2 cells depleted of exosome subunits

Project description:The exosome complex and its' subunits are vital for proccessing and or degrading many cellular RNAs. We used microarrays to detail the global changes in mRNA levels in response to exosome subunit depletion. RNA was extracted from dsRNA treated S2 cells and hybridized using Affymetrix microarrays. We aimed to obtain a master set of mRNAs surveyed by exosme subunits in vivo.

2010-04-12 | E-GEOD-17874 | biostudies-arrayexpress

Expression data from Drosophila S2 cells depleted of exosome subunits

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HEB and E2A function as SMAD/FOXH1 cofactors

Project description:Nodal signaling, mediated through SMAD transcription factors, is necessary for pluripotency maintenance and endoderm commitment. We have identified a new motif, termed SMAD Complex Associated (SCA) that is bound by SMAD2/3/4 and FOXH1 in human embryonic stem cells (hESCs) and derived endoderm. We demonstrate that two bHLH proteins - HEB and E2A - bind the SCA motif at regions overlapping SMAD2/3 and FOXH1. Further, we show that HEB and E2A associate with SMAD2/3 and FOXH1, suggesting they form a complex at critical target regions. This association is biologically important, as E2A is critical for mesendoderm specification, gastrulation, and Nodal signal transduction in Xenopus tropicalis embryos. Taken together, E2A is a novel Nodal signaling cofactor that associates with SMAD2/3 and FOXH1 and is necessary for mesendoderm differentiation. ChIP-seq of Smad2/3 and Input in X.tropicalis, stage 10.5 embryo.

2011-08-23 | E-GEOD-30146 | biostudies-arrayexpress

Genome-wide view of TGFb/Foxh1 regulation of the early mesendoderm program [ChIP-seq]

Project description:We defined the genome-wide binding regions of Smad2/3 and Foxh1 at mid-gastrula stage Xenopus tropicalis embryos, at which Nodal signaling and Foxh1 are critical in mesendoderm specification program.

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iCLIP analysis of RNA substrates of the archaeal exosome (RNA-Seq)

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