Chemical decoding strategies for detecting RNA modifications, dynamics and structures

Abstract

RNA modifications, along with dynamics and structures, constitute critical regulatory layers that collectively influence diverse biological processes by regulating gene expression. Recent advances in chemical decoding strategies have enabled the transformation of specific RNA sites into detectable sequencing signals, such as mutations, terminations and deletions. These strategies have emerged as powerful approaches to precisely map, quantify, and interpret RNA modifications, dynamic transitions, and structural conformations at single-nucleotide resolution. In this review, we summarize recent progress in nucleotide-targeted chemical reactions that facilitate the detection of RNA modifications, monitoring of RNA dynamics, and characterization of RNA structures through sequencing-based decoding approaches. These reactions achieve site-specific decoding by switching or blocking hydrogen bonds of ribonucleotide bases, or disrupting local ribonucleotide structures. We further highlight how these innovative chemical tools facilitate comprehensive decoding of complex RNA landscapes through sequencing and imaging, offering powerful strategies for elucidating RNA-related biological functions.