Aeschimann et al. 2017 (PRJNA318047)

General Details

Title Post-transcriptional regulation by the let-7 microRNA and the TRIM-NHL protein LIN41 [Ribosome footprinting]
Organism
Number of Samples 46
Release Date 2016/04/11 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP073115
ENA SRP073115
GEO GSE80133
BioProject PRJNA318047

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)
SRR3356477 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356478 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356479 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356480 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356481 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356482 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356483 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356484 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356485 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356486 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356487 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356488 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356489 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356490 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356491 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356492 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356493 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356494 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356495 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356496 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356497 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356498 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356499 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356500 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356501 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356502 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356503 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356504 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356505 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356506 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356507 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356508 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356509 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356510 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356511 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356512 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356513 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356514 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356515 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356516 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356517 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356518 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356519 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356520 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356521 PRJNA318047 Caenorhabditis elegans Ribo-Seq
SRR3356522 PRJNA318047 Caenorhabditis elegans Ribo-Seq
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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