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Genome Biology

, 18:116

First Online: 16 June 2017Received: 07 February 2017Accepted: 26 April 2017DOI: 10.1186-s13059-017-1222-2

Cite this article as: Castelo-Szekely, V., Arpat, A.B., Janich, P. et al. Genome Biol 2017 18: 116. doi:10.1186-s13059-017-1222-2


BackgroundThe 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.

ResultsRhythmic 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.

ConclusionsWe 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.

KeywordsCircadian clocks Translation Ribosome profiling Kidney Liver Electronic supplementary materialThe online version of this article doi:10.1186-s13059-017-1222-2 contains supplementary material, which is available to authorized users.

Autor: Violeta Castelo-Szekely - Alaaddin Bulak Arpat - Peggy Janich - David Gatfield


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