A Genetic Circuit Formed by Ribosomes

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PROJECT SUMMARY Following transcription, mRNAs transmit the genetic information that dictates protein production. In eukaryotes, transcription and translation occur at different timings and in distinct subcellular compartments. It is commonly believed that these two fundamental processes are uncoupled and have little “cross-talk”. Recent evidence suggests that translation of aberrant mRNAs leads to genetic compensation, a transcriptional response to rapidly upregulate genes with similar functions. However, the molecular mechanisms by which cytoplasmic translation communicates with nuclear transcription remain elusive. During the course of studying translational control in response to amino acid starvation, we observed transcriptional upregulation of genes undergoing stress-induced ribosome pausing. Relying on a newly developed sequencing method, Ezra-seq, we discovered the existence of endogenous ribosome footprints. We hypothesize that these mRNA fragments serve as novel chromatin modulators by influencing gene expression in a sequence-dependent manner. The goal of this proposal is to characterize the genetic circuit coupling cytoplasmic translation and nuclear transcription. By identifying and mapping chromatin-associated ribosome footprints, we will elucidate the novel type of RNA- mediated epigenetic regulation of gene expression. We propose that the genetic circuit formed by ribosomes contributes to genetic robustness and is a common mechanism for stress adaptation. We will also explore the potential of designing artificial ribosome footprints to achieve controllable gene expression, revealing new routes toward novel therapeutics. The conceptual establishment of ribosome-mediated genetic circuit is transformative in our understanding of the central dogma in molecular biology and opens a new research avenue towards genetic reprogramming.