Aeschimann et al. 2017 (PRJNA318054)

General Details

Title Post-transcriptional regulation by the let-7 microRNA and the TRIM-NHL protein LIN41 [RNA-seq]
Organism
Number of Samples 50
Release Date 2016/04/11 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP073117
ENA SRP073117
GEO GSE80157
BioProject PRJNA318054

Publication

Title
Authors Aeschimann F, Kumari P, Bartake H, Gaidatzis D, Xu L, Ciosk R, Großhans H
Journal Molecular cell
Publication Date 2017 Feb 2
Abstract The RNA-binding protein (RBP) LIN41, also known as LIN-41 or TRIM71, is a key regulator of animal development, but its physiological targets and molecular mechanism of action are largely elusive. Here we find that this RBP has two distinct mRNA-silencing activities. Using genome-wide ribosome profiling, RNA immunoprecipitation, and in vitro-binding experiments, we identify four mRNAs, each encoding a transcription factor or cofactor, as direct physiological targets of C. elegans LIN41. LIN41 silences three of these targets through their 3' UTRs, but it achieves isoform-specific silencing of one target, lin-29A, through its unique 5' UTR. Whereas the 3' UTR targets mab-10, mab-3, and dmd-3 undergo transcript degradation, lin-29A experiences translational repression. Through binding site transplantation experiments, we demonstrate that it is the location of the LIN41-binding site that specifies the silencing mechanism. Such position-dependent dual activity may, when studied more systematically, emerge as a feature shared by other RBPs. Copyright © 2017 Elsevier Inc. All rights reserved.
PMC
PMID 28111013
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR3356596 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356597 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356598 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356599 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356600 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356601 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356602 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356603 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356604 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356605 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356606 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356607 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356608 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356609 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356610 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356611 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356613 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356615 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356617 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356619 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356621 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356623 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356625 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356627 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356629 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356631 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356632 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356633 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356634 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356635 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356636 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356637 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356638 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356639 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356640 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356641 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356642 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356643 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356644 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356645 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356646 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356647 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356648 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356649 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356650 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356651 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356652 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356653 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356654 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
SRR3356655 PRJNA318054 Caenorhabditis elegans 0.0 RNA-Seq 0.0
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)

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