Castelo-Szekely et al. 2017 (PRJNA321185)

General Details

Title Translational contributions to tissue-specificity in rhythmic and constitutive gene expression
Organism
Number of Samples 45
Release Date 2016/05/10 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP074765
ENA SRP074765
GEO
BioProject PRJNA321185

Publication

Title
Authors Castelo-Szekely V,Arpat AB,Janich P,Gatfield D
Journal Genome biology
Publication Date 2017 Jun 16
Abstract The daily gene expression oscillations that underlie mammalian circadian rhythms show striking differences between tissues and involve post-transcriptional regulation. Both aspects remain poorly understood. We have used ribosome profiling to explore the contribution of translation efficiency to temporal gene expression in kidney and contrasted our findings with liver data available from the same mice. Rhythmic translation of constantly abundant messenger RNAs (mRNAs) affects largely non-overlapping transcript sets with distinct phase clustering in the two organs. Moreover, tissue differences in translation efficiency modulate the timing and amount of protein biosynthesis from rhythmic mRNAs, consistent with organ specificity in clock output gene repertoires and rhythmicity parameters. Our comprehensive datasets provided insights into translational control beyond temporal regulation. Between tissues, many transcripts show differences in translation efficiency, which are, however, of markedly smaller scale than mRNA abundance differences. Tissue-specific changes in translation efficiency are associated with specific transcript features and, intriguingly, globally counteracted and compensated transcript abundance variations, leading to higher similarity at the level of protein biosynthesis between both tissues. We show that tissue specificity in rhythmic gene expression extends to the translatome and contributes to define the identities, the phases and the expression levels of rhythmic protein biosynthesis. Moreover, translational compensation of transcript abundance divergence leads to overall higher similarity at the level of protein production across organs. The unique resources provided through our study will serve to address fundamental questions of post-transcriptional control and differential gene expression in vivo.
PMC PMC5473967
PMID 28622766
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR3494961 PRJNA321185 Mus musculus Ribo-Seq
SRR3494962 PRJNA321185 Mus musculus Ribo-Seq
SRR3494963 PRJNA321185 Mus musculus Ribo-Seq
SRR3494964 PRJNA321185 Mus musculus Ribo-Seq
SRR3494965 PRJNA321185 Mus musculus Ribo-Seq
SRR3494966 PRJNA321185 Mus musculus Ribo-Seq
SRR3494967 PRJNA321185 Mus musculus Ribo-Seq
SRR3494968 PRJNA321185 Mus musculus Ribo-Seq
SRR3494969 PRJNA321185 Mus musculus Ribo-Seq
SRR3494970 PRJNA321185 Mus musculus Ribo-Seq
SRR3494971 PRJNA321185 Mus musculus Ribo-Seq
SRR3494972 PRJNA321185 Mus musculus Ribo-Seq
SRR3494973 PRJNA321185 Mus musculus Ribo-Seq
SRR3494974 PRJNA321185 Mus musculus Ribo-Seq
SRR3494975 PRJNA321185 Mus musculus Ribo-Seq
SRR3494976 PRJNA321185 Mus musculus Ribo-Seq
SRR3494977 PRJNA321185 Mus musculus Ribo-Seq
SRR3494978 PRJNA321185 Mus musculus Ribo-Seq
SRR3494979 PRJNA321185 Mus musculus Ribo-Seq
SRR3494980 PRJNA321185 Mus musculus Ribo-Seq
SRR3494981 PRJNA321185 Mus musculus Ribo-Seq
SRR3494982 PRJNA321185 Mus musculus Ribo-Seq
SRR3494983 PRJNA321185 Mus musculus Ribo-Seq
SRR3494984 PRJNA321185 Mus musculus Ribo-Seq
SRR3494985 PRJNA321185 Mus musculus Ribo-Seq
SRR3494986 PRJNA321185 Mus musculus Ribo-Seq
SRR3494987 PRJNA321185 Mus musculus Ribo-Seq
SRR3494988 PRJNA321185 Mus musculus Ribo-Seq
SRR3494989 PRJNA321185 Mus musculus Ribo-Seq
SRR3494990 PRJNA321185 Mus musculus Ribo-Seq
SRR3494991 PRJNA321185 Mus musculus Ribo-Seq
SRR3494992 PRJNA321185 Mus musculus Ribo-Seq
SRR3494993 PRJNA321185 Mus musculus Ribo-Seq
SRR3494994 PRJNA321185 Mus musculus Ribo-Seq
SRR3494995 PRJNA321185 Mus musculus Ribo-Seq
SRR3494996 PRJNA321185 Mus musculus Ribo-Seq
SRR3494997 PRJNA321185 Mus musculus Ribo-Seq
SRR3494998 PRJNA321185 Mus musculus Ribo-Seq
SRR3494999 PRJNA321185 Mus musculus Ribo-Seq
SRR3495000 PRJNA321185 Mus musculus Ribo-Seq
SRR3495001 PRJNA321185 Mus musculus Ribo-Seq
SRR3495002 PRJNA321185 Mus musculus Ribo-Seq
SRR3495003 PRJNA321185 Mus musculus Ribo-Seq
SRR3495004 PRJNA321185 Mus musculus Ribo-Seq
SRR3495005 PRJNA321185 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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