Physiological mapping and prediction reveal stress-responsive translation initiation landscapes

Translation initiation plays a crucial role in determining protein output from the transcriptome, but its physiological dynamics in cells and tissues have not been thoroughly explored. Researchers have now developed TISCA2, an innovative method that captures ribosomes associated with eIF5B, the protein responsible for translation initiation, allowing for a genome-wide map of translation initiation sites.

Unlike previous methods that inferred translation from elongating ribosome periodicity, TISCA2 directly identifies start sites, leading to more accurate detection of short and overlapping translons.

The TISCA2 method was validated by identifying start sites of translons that were subsequently confirmed through N-terminal proteomics and HLA-I immunopeptidomics. Furthermore, the researchers found that arsenite-induced integrated stress response leads to a redistribution of start-site usage, shifting the focus from upstream initiation to downstream initiation.

TISCA2 also provides valuable insights into tissue-specific initiation landscapes in living organisms. The method revealed an increased detection of downstream candidate start sites in the testis, highlighting the importance of understanding tissue-specific translation initiation patterns. To complement their experimental findings, the team developed IncepTIS, a sequence-based deep learning model capable of predicting position-resolved and condition-dependent initiation landscapes.

IncepTIS guided the researchers in optimizing the generation of de novo mRNA 5' leaders with stress-responsive initiation patterns. By combining TISCA2 and IncepTIS, the researchers have created a comprehensive experimental and computational framework for mapping, predicting, and engineering translation initiation in mammalian cells and tissues. This breakthrough offers new avenues for understanding and manipulating protein synthesis in response to various physiological and environmental conditions.