Janich et al. 2015 (PRJNA279465)

General Details

Title Ribosome profiling reveals the rhythmic liver translatome and circadian clock regulation by upstream open reading frames
Organism
Number of Samples 36
Release Date 2015/03/26 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP056576
ENA SRP056576
GEO
BioProject PRJNA279465

Publication

Title
Authors Janich P,Arpat AB,Castelo-Szekely V,Lopes M,Gatfield D
Journal Genome research
Publication Date 2015 Dec
Abstract Mammalian gene expression displays widespread circadian oscillations. Rhythmic transcription underlies the core clock mechanism, but it cannot explain numerous observations made at the level of protein rhythmicity. We have used ribosome profiling in mouse liver to measure the translation of mRNAs into protein around the clock and at high temporal and nucleotide resolution. We discovered, transcriptome-wide, extensive rhythms in ribosome occupancy and identified a core set of approximately 150 mRNAs subject to particularly robust daily changes in translation efficiency. Cycling proteins produced from nonoscillating transcripts revealed thus-far-unknown rhythmic regulation associated with specific pathways (notably in iron metabolism, through the rhythmic translation of transcripts containing iron responsive elements), and indicated feedback to the rhythmic transcriptome through novel rhythmic transcription factors. Moreover, estimates of relative levels of core clock protein biosynthesis that we deduced from the data explained known features of the circadian clock better than did mRNA expression alone. Finally, we identified uORF translation as a novel regulatory mechanism within the clock circuitry. Consistent with the occurrence of translated uORFs in several core clock transcripts, loss-of-function of Denr, a known regulator of reinitiation after uORF usage and of ribosome recycling, led to circadian period shortening in cells. In summary, our data offer a framework for understanding the dynamics of translational regulation, circadian gene expression, and metabolic control in a solid mammalian organ. © 2015 Janich et al.; Published by Cold Spring Harbor Laboratory Press.
PMC PMC4665006
PMID 26486724
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR1930188 PRJNA279465 Mus musculus Ribo-Seq
SRR1930189 PRJNA279465 Mus musculus Ribo-Seq
SRR1930190 PRJNA279465 Mus musculus Ribo-Seq
SRR1930191 PRJNA279465 Mus musculus Ribo-Seq
SRR1930192 PRJNA279465 Mus musculus Ribo-Seq
SRR1930193 PRJNA279465 Mus musculus Ribo-Seq
SRR1930194 PRJNA279465 Mus musculus Ribo-Seq
SRR1930195 PRJNA279465 Mus musculus Ribo-Seq
SRR1930196 PRJNA279465 Mus musculus Ribo-Seq
SRR1930197 PRJNA279465 Mus musculus Ribo-Seq
SRR1930198 PRJNA279465 Mus musculus Ribo-Seq
SRR1930199 PRJNA279465 Mus musculus Ribo-Seq
SRR1930200 PRJNA279465 Mus musculus Ribo-Seq
SRR1930201 PRJNA279465 Mus musculus Ribo-Seq
SRR1930202 PRJNA279465 Mus musculus Ribo-Seq
SRR1930203 PRJNA279465 Mus musculus Ribo-Seq
SRR1930204 PRJNA279465 Mus musculus Ribo-Seq
SRR1930205 PRJNA279465 Mus musculus Ribo-Seq
SRR1930206 PRJNA279465 Mus musculus Ribo-Seq
SRR1930207 PRJNA279465 Mus musculus Ribo-Seq
SRR1930208 PRJNA279465 Mus musculus Ribo-Seq
SRR1930209 PRJNA279465 Mus musculus Ribo-Seq
SRR1930210 PRJNA279465 Mus musculus Ribo-Seq
SRR1930211 PRJNA279465 Mus musculus Ribo-Seq
SRR1930212 PRJNA279465 Mus musculus RNA-Seq
SRR1930213 PRJNA279465 Mus musculus RNA-Seq
SRR1930214 PRJNA279465 Mus musculus RNA-Seq
SRR1930215 PRJNA279465 Mus musculus RNA-Seq
SRR1930236 PRJNA279465 Mus musculus Ribo-Seq
SRR1930237 PRJNA279465 Mus musculus Ribo-Seq
SRR1930238 PRJNA279465 Mus musculus Ribo-Seq
SRR1930239 PRJNA279465 Mus musculus Ribo-Seq
SRR1930240 PRJNA279465 Mus musculus Ribo-Seq
SRR1930241 PRJNA279465 Mus musculus Ribo-Seq
SRR1930242 PRJNA279465 Mus musculus Ribo-Seq
SRR1930243 PRJNA279465 Mus musculus 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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