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 0.0 Ribo-Seq 0.0
SRR3356478 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356479 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356480 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356481 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356482 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356483 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356484 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356485 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356486 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356487 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356488 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356489 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356490 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356491 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356492 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356493 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356494 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356495 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356496 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356497 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356498 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356499 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356500 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356501 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356502 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356503 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356504 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356505 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356506 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356507 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356508 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356509 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356510 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356511 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356512 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356513 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356514 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356515 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356516 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356517 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356518 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356519 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356520 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356521 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR3356522 PRJNA318047 Caenorhabditis elegans 0.0 Ribo-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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