Translational Profiling of Clock Cells Reveals Circadianly Synchronized Protein Synthesis

Huang, Yanmei; Ainsley, Joshua A.; Reijmers, Leon G.; Jackson, F. Rob

doi:10.1371/journal.pbio.1001703

Cited by 69 publications

(96 citation statements)

References 65 publications

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“…To our knowledge, this is the first study to use ribosome profiling to conduct a survey of global circadian translational control in mammalian cells. We found that rhythmic RNA accumulation and translation is consolidated into two distinct peaks per day, which parallels recent findings using other methods in clock cells obtained from whole head extracts of Drosophila melanogaster (Huang et al 2013) and in the mammalian circadian system (Zhang et al 2014). These peaks occur at ∼5 and 17 h after the start of collection (Supplemental Fig.…”

Section: Discussionsupporting

confidence: 89%

Ribosome profiling reveals an important role for translational control in circadian gene expression

et al. 2015

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Physiological and behavioral circadian rhythms are driven by a conserved transcriptional/translational negative feedback loop in mammals. Although most core clock factors are transcription factors, post-transcriptional control introduces delays that are critical for circadian oscillations. Little work has been done on circadian regulation of translation, so to address this deficit we conducted ribosome profiling experiments in a human cell model for an autonomous clock. We found that most rhythmic gene expression occurs with little delay between transcription and translation, suggesting that the lag in the accumulation of some clock proteins relative to their mRNAs does not arise from regulated translation. Nevertheless, we found that translation occurs in a circadian fashion for many genes, sometimes imposing an additional level of control on rhythmically expressed mRNAs and, in other cases, conferring rhythms on noncycling mRNAs. Most cyclically transcribed RNAs are translated at one of two major times in a 24-h day, while rhythmic translation of most noncyclic RNAs is phased to a single time of day. Unexpectedly, we found that the clock also regulates the formation of cytoplasmic processing (P) bodies, which control the fate of mRNAs, suggesting circadian coordination of mRNA metabolism and translation.

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Section: Discussionsupporting

confidence: 89%

Ribosome profiling reveals an important role for translational control in circadian gene expression

et al. 2015

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“…5D, RPFseq error bars) is remarkable for genetically identical animals and could point to a behavioral component contributing to the regulatory mechanism. Interestingly, and reminiscent of the timing in the liver, increased ribosome association of mRNAs in Drosophila occurs at phases of relative behavioral quiescence, just prior to locomotor activity bouts (Huang et al 2013). It remains to be explored whether this similarity is indicative of mechanistic parallels.…”

Section: Discussionmentioning

confidence: 99%

Ribosome profiling reveals the rhythmic liver translatome and circadian clock regulation by upstream open reading frames

et al. 2015

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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.

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“…We utilized methods identical to our published studies (Huang et al, 2013, 2014, 2015) to isolate ribosomes and translating RNAs from adult fly astrocytes; the protocols are outlined in detail in a recent review (Jackson et al, 2015). The current study utilized a Gal4 driver ( alrm-Gal4 ) that expresses in fly astrocytes but not in CNS neurons or other glial cell types (Doherty et al, 2009) to drive expression of a characterized UAS-EGFP-L10a transgene (Huang et al, 2013; encoding an EGFP-tagged L10a ribosomal subunit).…”

Section: Methodsmentioning

confidence: 99%

“…In the present report, we describe experiments employing Translating Ribosome Affinity Purification (TRAP) procedures, which we adapted to the Drosophila model (Huang et al, 2013), to define the genome-wide expression profile of adult fly astrocytes. With that dataset as a starting point, we have performed RNA interference (RNAi)-based genetic screens to identify proteins participating in glia-neuron signaling that is relevant for behavioral regulation.…”

Section: Introductionmentioning

confidence: 99%

TRAP-seq Profiling and RNAi-Based Genetic Screens Identify Conserved Glial Genes Required for Adult Drosophila Behavior

Sengupta

Huang

et al. 2016

Front. Mol. Neurosci.

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Although, glial cells have well characterized functions in the developing and mature brain, it is only in the past decade that roles for these cells in behavior and plasticity have been delineated. Glial astrocytes and glia-neuron signaling, for example, are now known to have important modulatory functions in sleep, circadian behavior, memory and plasticity. To better understand mechanisms of glia-neuron signaling in the context of behavior, we have conducted cell-specific, genome-wide expression profiling of adult Drosophila astrocyte-like brain cells and performed RNA interference (RNAi)-based genetic screens to identify glial factors that regulate behavior. Importantly, our studies demonstrate that adult fly astrocyte-like cells and mouse astrocytes have similar molecular signatures; in contrast, fly astrocytes and surface glia—different classes of glial cells—have distinct expression profiles. Glial-specific expression of 653 RNAi constructs targeting 318 genes identified multiple factors associated with altered locomotor activity, circadian rhythmicity and/or responses to mechanical stress (bang sensitivity). Of interest, 1 of the relevant genes encodes a vesicle recycling factor, 4 encode secreted proteins and 3 encode membrane transporters. These results strongly support the idea that glia-neuron communication is vital for adult behavior.

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Translational Profiling of Clock Cells Reveals Circadianly Synchronized Protein Synthesis

Cited by 69 publications

References 65 publications

Ribosome profiling reveals an important role for translational control in circadian gene expression

Ribosome profiling reveals an important role for translational control in circadian gene expression

Ribosome profiling reveals the rhythmic liver translatome and circadian clock regulation by upstream open reading frames

TRAP-seq Profiling and RNAi-Based Genetic Screens Identify Conserved Glial Genes Required for Adult Drosophila Behavior

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