Ribo-DT: An automated pipeline for inferring codon dwell times from ribosome profiling data

Exploring the potential of large language model-based chatbots in challenges of ribosome profiling data analysis: a review

Ribosome profiling (Ribo-seq) provides transcriptome-wide insights into protein synthesis dynamics, yet its analysis poses challenges, particularly for nonbioinformatics researchers. Large language model-based chatbots offer promising solutions by leveraging natural language processing. This review explores their convergence, highlighting opportunities for synergy. We discuss challenges in Ribo-seq analysis and how chatbots mitigate them, facilitating scientific discovery. Through case studies, we illustrate chatbots' potential contributions, including data analysis and result interpretation. Despite the absence of applied examples, existing software underscores the value of chatbots and the large language model. We anticipate their pivotal role in future Ribo-seq analysis, overcoming limitations. Challenges such as model bias and data privacy require attention, but emerging trends offer promise. The integration of large language models and Ribo-seq analysis holds immense potential for advancing translational regulation and gene expression understanding.

ROS-induced ribosome impairment underlies ZAKα-mediated metabolic decline in obesity and aging

The ribotoxic stress response (RSR) is a signaling pathway in which the p38- and c-Jun N-terminal kinase (JNK)-activating mitogen-activated protein kinase kinase kinase (MAP3K) ZAKα senses stalling and/or collision of ribosomes. Here, we show that reactive oxygen species (ROS)-generating agents trigger ribosomal impairment and ZAKα activation. Conversely, zebrafish larvae deficient for ZAKα are protected from ROS-induced pathology. Livers of mice fed a ROS-generating diet exhibit ZAKα-activating changes in ribosomal elongation dynamics. Highlighting a role for the RSR in metabolic regulation, ZAK-knockout mice are protected from developing high-fat high-sugar (HFHS) diet-induced blood glucose intolerance and liver steatosis. Finally, ZAK ablation slows animals from developing the hallmarks of metabolic aging. Our work highlights ROS-induced ribosomal impairment as a physiological activation signal for ZAKα that underlies metabolic adaptation in obesity and aging.