Chou et al. 2017 (PRJNA392312)

General Details

Title Transcriptome-wide analysis of roles for tRNA modifications in translational regulation
Organism
Number of Samples 165
Release Date 2017/06/28 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP110707
ENA SRP110707
GEO GSE100626
BioProject PRJNA392312

Publication

Title
Authors Chou HJ, Donnard E, Gustafsson HT, Garber M, Rando OJ
Journal Molecular cell
Publication Date 2017 Dec 7
Abstract Covalent nucleotide modifications in noncoding RNAs affect a plethora of biological processes, and new functions continue to be discovered even for well-known modifying enzymes. To systematically compare the functions of a large set of noncoding RNA modifications in gene regulation, we carried out ribosome profiling in budding yeast to characterize 57 nonessential genes involved in tRNA modification. Deletion mutants exhibited a range of translational phenotypes, with enzymes known to modify anticodons, or non-tRNA substrates such as rRNA, exhibiting the most dramatic translational perturbations. Our data build on prior reports documenting translational upregulation of the nutrient-responsive transcription factor Gcn4 in response to numerous tRNA perturbations, and identify many additional translationally regulated mRNAs throughout the yeast genome. Our data also uncover unexpected roles for tRNA-modifying enzymes in regulation of TY retroelements, and in rRNA 2'-O-methylation. This dataset should provide a rich resource for discovery of additional links between tRNA modifications and gene regulation. Copyright © 2017 Elsevier Inc. All rights reserved.
PMC PMC5728682
PMID 29198561
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR5766382 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766383 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766384 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766385 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766386 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766387 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766388 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766389 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766390 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766391 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766392 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766393 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766394 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766395 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766396 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766397 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766398 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766399 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766400 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766401 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766402 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766403 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766404 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766405 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766406 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766407 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766408 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766409 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766410 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766411 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766412 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766413 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766414 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766415 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766416 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766417 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766418 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766419 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766420 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766421 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766422 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766423 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766424 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766425 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766426 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766427 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766428 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766429 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766430 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766431 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766432 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766433 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766434 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766435 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766436 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766437 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766438 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766439 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766440 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766441 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766442 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766443 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766444 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766445 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766446 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766447 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766448 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766449 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766450 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766451 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766452 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766453 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766454 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766455 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766456 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766457 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766458 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766459 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766460 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766461 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766462 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766463 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766464 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766465 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766466 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766467 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766468 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766469 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766470 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766471 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766472 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766473 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766474 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766475 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766476 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766477 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766478 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766479 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766480 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766481 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766482 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766483 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766484 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766485 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766486 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766487 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766488 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766489 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766490 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766491 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766492 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766493 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766494 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766495 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766496 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766497 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766498 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766499 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766500 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766501 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766502 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766503 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766504 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766505 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766506 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766507 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766508 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Cycloheximide
SRR5766576 PRJNA392312 Saccharomyces cerevisiae 0.0 RiboMeth Cycloheximide
SRR5766577 PRJNA392312 Saccharomyces cerevisiae 0.0 RiboMeth Cycloheximide
SRR5766578 PRJNA392312 Saccharomyces cerevisiae 0.0 RiboMeth Cycloheximide
SRR5766579 PRJNA392312 Saccharomyces cerevisiae 0.0 RiboMeth Cycloheximide
SRR5766580 PRJNA392312 Saccharomyces cerevisiae 0.0 RiboMeth Cycloheximide
SRR5766581 PRJNA392312 Saccharomyces cerevisiae 0.0 RiboMeth Cycloheximide
SRR5766582 PRJNA392312 Saccharomyces cerevisiae 0.0 RiboMeth Cycloheximide
SRR5766583 PRJNA392312 Saccharomyces cerevisiae 0.0 RiboMeth Cycloheximide
SRR5766584 PRJNA392312 Saccharomyces cerevisiae 0.0 RiboMeth Cycloheximide
SRR5766585 PRJNA392312 Saccharomyces cerevisiae 0.0 RiboMeth Cycloheximide
SRR5766586 PRJNA392312 Saccharomyces cerevisiae 0.0 RiboMeth Cycloheximide
SRR5766587 PRJNA392312 Saccharomyces cerevisiae 0.0 RiboMeth Cycloheximide
SRR5766588 PRJNA392312 Saccharomyces cerevisiae 0.0 RiboMeth Cycloheximide
SRR5766589 PRJNA392312 Saccharomyces cerevisiae 0.0 RiboMeth Cycloheximide
SRR5766590 PRJNA392312 Saccharomyces cerevisiae 0.0 RiboMeth Cycloheximide
SRR5766591 PRJNA392312 Saccharomyces cerevisiae 0.0 RiboMeth Cycloheximide
SRR5766592 PRJNA392312 Saccharomyces cerevisiae 0.0 RiboMeth Cycloheximide
SRR5766593 PRJNA392312 Saccharomyces cerevisiae 0.0 RiboMeth Cycloheximide
SRR5766594 PRJNA392312 Saccharomyces cerevisiae 0.0 RiboMeth Cycloheximide
SRR5766595 PRJNA392312 Saccharomyces cerevisiae 0.0 RiboMeth Cycloheximide
SRR5766596 PRJNA392312 Saccharomyces cerevisiae 0.0 RiboMeth Cycloheximide
SRR5766597 PRJNA392312 Saccharomyces cerevisiae 0.0 RiboMeth Cycloheximide
SRR5766598 PRJNA392312 Saccharomyces cerevisiae 0.0 RiboMeth Cycloheximide
SRR5766599 PRJNA392312 Saccharomyces cerevisiae 0.0 RiboMeth Cycloheximide
SRR5766600 PRJNA392312 Saccharomyces cerevisiae 0.0 RiboMeth Cycloheximide
SRR5766601 PRJNA392312 Saccharomyces cerevisiae 0.0 RiboMeth Cycloheximide
SRR5766602 PRJNA392312 Saccharomyces cerevisiae 0.0 RiboMeth Cycloheximide
SRR5766603 PRJNA392312 Saccharomyces cerevisiae 0.0 RiboMeth Cycloheximide
SRR5766604 PRJNA392312 Saccharomyces cerevisiae 0.0 RiboMeth Cycloheximide
SRR5766605 PRJNA392312 Saccharomyces cerevisiae 0.0 RiboMeth Cycloheximide
SRR5766606 PRJNA392312 Saccharomyces cerevisiae 0.0 RiboMeth Cycloheximide
SRR5766607 PRJNA392312 Saccharomyces cerevisiae 0.0 RiboMeth Cycloheximide
SRR6075747 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Frozen
SRR6075748 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Frozen
SRR6075749 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Frozen
SRR6075750 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Frozen
SRR6075751 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Frozen
SRR6075752 PRJNA392312 Saccharomyces cerevisiae BY4741 Ribo-Seq Frozen
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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