CBC Seminar, Dr. Aya Narunsky - Illuminating molecular evolution through computational discovery of protein and RNA motifs

Chemistry & Biochemistry Seminar

Dr. Aya Narunsky, Yale University

Illuminating molecular evolution through computational discovery of protein and RNA motifs

Motifs in biological sequences are molecular signatures of evolution: conserved elements that trace back to a common ancestor and often carry out similar functions. Identifying these motifs in proteins and RNA not only deepens our understanding of their evolution but also uncovers novel molecular functions and guides biomolecular design. In this talk, I will explore computational strategies for identifying these motifs and highlight the discoveries they have made possible.

Structured noncoding RNAs (ncRNAs) are central to essential cellular processes, including chemical catalysis, gene regulation, and other functions. I will present a computational pipeline designed for the identification of structured ncRNAs in bacteria, applied to 50 bacterial genomes spanning diverse phylogeny. This analysis uncovered hundreds of novel ncRNA candidates, including over 40 riboswitches candidates, cis-regulatory elements that control gene expression by sensing small molecules. Riboswitch discoveries have often preceded our understanding of their ligands’ physiological roles in bacteria, as seen in the case of guanidine. Inspired by these insights, I will introduce a novel search approach applied to mammalian genomes and discuss its potential to uncover previously unrecognized biochemical signaling pathways that play a crucial role in human physiology.

Finally, I will explore how AI-driven approaches can transform RNA motif discovery. By leveraging these powerful methods to uncover protein and RNA interaction partners and analyze the protein motifs involved in binding, we can retrace the evolutionary journey of protein-RNA complexes. This deeper understanding not only sheds light on how these molecular interactions have shaped biological functions over time but also opens new avenues for exploring the fundamental principles of molecular evolution.