Castillo et al. 2022 (PRJNA752584)

General Details

Title Circadian Clock-Controlled Translation of Specific mRNAs in Neurospora crassa Requires Rhythmic eIF2α Activity and P-body Sequestration [Ribo-seq]
Organism
Number of Samples 80
Release Date 2021/08/06 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP331348
ENA SRP331348
GEO
BioProject PRJNA752584

Publication

Title
Authors Castillo KD,Wu C,Ding Z,Lopez-Garcia OK,Rowlinson E,Sachs MS,Bell-Pedersen D
Journal Cell reports
Publication Date 2022 Dec 27
Abstract Phosphorylation of Neurospora crassa eukaryotic initiation factor 2 α (eIF2α), a conserved translation initiation factor, is clock controlled. To determine the impact of rhythmic eIF2α phosphorylation on translation, we performed temporal ribosome profiling and RNA sequencing (RNA-seq) in wild-type (WT), clock mutant Δfrq, eIF2α kinase mutant Δcpc-3, and constitutively active cpc-3 c cells. About 14% of mRNAs are rhythmically translated in WT cells, and translation rhythms for ∼30% of these mRNAs, which we named circadian translation-initiation-controlled genes (cTICs), are dependent on the clock and CPC-3. Most cTICs are expressed from arrhythmic mRNAs and contain a P-body (PB) localization motif in their 5' leader sequence. Deletion of SNR-1, a component of cytoplasmic messenger ribonucleoprotein granules (cmRNPgs) that include PBs and stress granules (SGs), and the PB motif on one of the cTIC mRNAs, zip-1, significantly alters zip-1 rhythmic translation. These results reveal that the clock regulates rhythmic translation of specific mRNAs through rhythmic eIF2α activity and cmRNPg metabolism. Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.
PMC PMC10241597
PMID 36577368
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR15359330 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359331 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359332 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359333 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359334 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359335 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359336 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359337 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359338 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359339 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359340 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359341 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359342 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359343 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359344 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359345 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359346 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359347 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359348 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359349 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359350 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359351 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359352 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359353 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359354 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359355 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359356 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359357 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359358 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359359 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359360 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359361 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359362 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359363 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359364 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359365 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359366 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359367 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359368 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359369 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359370 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359371 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359372 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359373 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359374 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359375 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359376 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359377 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359378 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359379 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359380 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359381 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359382 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359383 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359384 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359385 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359386 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359387 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359388 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359389 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359390 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359391 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359392 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359393 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359394 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359395 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359396 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359397 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359398 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359399 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359400 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359401 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359402 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359403 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359404 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359405 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359406 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359407 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359408 PRJNA752584 Neurospora crassa Ribo-Seq
SRR15359409 PRJNA752584 Neurospora crassa 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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