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] |
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Organism | |
Number of Samples | 80 |
Release Date | 2021/08/06 00:00 |
Sequencing Types | |
Protocol Details |
Study Links
GWIPS-viz | Trips-Viz |
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Repository Details
SRA | SRP331348 |
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ENA | SRP331348 |
GEO | GSE181565 |
BioProject | PRJNA752584 |
Publication
Title | |
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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 | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359331 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359332 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359333 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359334 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359335 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359336 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359337 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359338 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359339 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359340 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359341 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359342 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359343 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359344 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359345 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359346 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359347 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359348 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359349 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359350 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359351 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359352 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359353 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359354 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359355 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359356 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359357 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359358 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359359 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359360 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359361 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359362 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359363 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359364 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359365 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359366 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359367 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359368 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359369 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359370 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359371 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359372 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359373 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359374 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359375 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359376 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359377 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359378 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359379 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359380 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359381 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359382 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359383 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359384 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359385 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359386 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359387 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359388 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359389 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359390 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359391 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359392 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359393 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359394 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359395 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359396 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359397 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359398 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359399 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359400 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359401 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359402 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359403 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359404 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359405 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359406 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359407 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359408 | PRJNA752584 | Neurospora crassa | 0.0 | Ribo-Seq | 0.0 | ||||||||
SRR15359409 | PRJNA752584 | Neurospora crassa | 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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