Jungfleisch et al. 2016 (GSE87892)

General Details

Title	Ribosome profiling of dhh1∆ yeast
Organism	Saccharomyces cerevisiae
Number of Samples	3
Release Date	00/11/2016
Sequencing Types
Protocol Details	Overall-Design: Cells were grown in rich medium and sequencing was performed on ribosome-protected footprints and matched samples of randomly fragmented polyA-enriched RNA. Dataset contains three biological replicates. Treatment-Protocol: YPD medium; cycloheximide (1 min) Growth-Protocol: Cells were grown from OD600 of 0.02 to OD600 Extract-Protocol: Frozen cells were pulverized under cryogenic conditions in 20 mM Tris-HCl (pH; Footprints were dephosphorylated and ligated to a preadenylated 3' linker. Following reverse transcription, cDNA was cirularized and amplified by PCR.; Frozen cells were were resuspended in 50 mM NaOAc (pH; Fragmented poly(A) RNA was dephosphorylated and ligated to a preadenylated 3' linker. Following reverse transcription, cDNA was cirularized and amplified by PCR. Data-Processing: Library strategy: Ribo-seq; Basecalls were performed with Illumina Casava 1.8.; 3' adapter sequences were removed with FastX-toolkit; Reads were aligned to rRNA genes with Bowtie 1.0.0. Non-rRNA reads were mapped with Bowtie to reference sets consisting of CDS sequences containing 18 nt of genomic flanking regions. Only reads with unique matches to the sense strand were retained for further analysis.; Raw read counts were determined using custom scripts. Yeast footprint reads mapping within the first 15 codons of coding sequences were omitted to avoid effects of growth conditions and translation inhibitor treatement on ribosome density in the beginning of ORFs.; Genome_build: sacCer3; Supplementary_files_format_and_content: Tab-delimited text files containing gene annotations and raw read count data.

Repository Details

SRA	SRP091454
ENA	SRP091454
GEO	GSE87892
BioProject

Publication

Title
Authors	Jungfleisch J,Nedialkova DD,Dotu I,Sloan KE,Martinez-Bosch N,Brüning L,Raineri E,Navarro P,Bohnsack MT,Leidel SA,Díez J
Journal	Genome research
Publication Date	2017 Jan
Abstract	The impact of RNA structures in coding sequences (CDS) within mRNAs is poorly understood. Here, we identify a novel and highly conserved mechanism of translational control involving RNA structures within coding sequences and the DEAD-box helicase Dhh1. Using yeast genetics and genome-wide ribosome profiling analyses, we show that this mechanism, initially derived from studies of the Brome Mosaic virus RNA genome, extends to yeast and human mRNAs highly enriched in membrane and secreted proteins. All Dhh1-dependent mRNAs, viral and cellular, share key common features. First, they contain long and highly structured CDSs, including a region located around nucleotide 70 after the translation initiation site; second, they are directly bound by Dhh1 with a specific binding distribution; and third, complementary experimental approaches suggest that they are activated by Dhh1 at the translation initiation step. Our results show that ribosome translocation is not the only unwinding force of CDS and uncover a novel layer of translational control that involves RNA helicases and RNA folding within CDS providing novel opportunities for regulation of membrane and secretome proteins. © 2017 Jungfleisch et al.; Published by Cold Spring Harbor Laboratory Press.
PMC	PMC5204348
PMID	27821408
DOI

	Run Accession	Study Accession	Scientific Name	Description	Cell Line	Library Type	Treatment	Trips-Viz	GWIPS-viz	RiboCrypt
	SRR4418656	GSE87892	Saccharomyces cerevisiae	Whole cells	nan	RFP	chx	Trips-Viz	GWIPS-viz	RiboCrypt
	SRR4418657	GSE87892	Saccharomyces cerevisiae	Whole cells	nan	RFP	chx	Trips-Viz	GWIPS-viz	RiboCrypt
	SRR4418658	GSE87892	Saccharomyces cerevisiae	Whole cells	nan	RFP	chx	Trips-Viz	GWIPS-viz	RiboCrypt
	Run Accession	Study Accession	Scientific Name	Description	Cell Line	Library Type	Treatment	Trips-Viz	GWIPS-viz	RiboCrypt