Work

Cell-type-resolved RNP topologies reveal dynamic structural mechanisms of splicing and therapeutic targets

Year: 2026

Type: preprint

Abstract: Resolving RNA conformations in native ribonucleoprotein (RNP) complexes remains a fundamental challenge. Here, we introduce spatial hydroxyl acylation reversible crosslinking with immunoprecipitation (SHARCLIP) to simultaneously capture RNA-RNA, RNA-protein and protein-protein contacts in cells. SHARCLIP profiling of HNRNPC-associated RNA conformations established a global phased map of ribonucleosomes, resolving a decades-old debate on heterogenous nuclear (hn)RNP assembly. We built a dynamic structural atlas across seven cell lineages for >10,000 RNAs, generating ~200 million contacts, and identifying millions of dynamic loops, steric blockers and conformational switches that control splicing outcome. Deciphering the structural logic of mutually exclusive exons (MXEs) enabled rational design of structure-breaking and stabilizing antisense oligonucleotides (ASOs). We demonstrate effective isoform swapping in 12 genes linked to genetic disorders. SHARCLIP provides a comprehensive roadmap for cellular RNA structural biology and structure-guided RNA therapeutics.

Source: bioRxiv (Cold Spring Harbor Laboratory)

DOI: 10.64898/2026.05.17.725762

Authors: Jianhui Bai, Kongpan Li, Wei Zhang, Minjie Zhang, Grant Shoffner, Willem A. Velema, Jianfu Chen, Feng Guo, Zhipeng Lu

Institutions: University of Southern California, USC Norris Comprehensive Cancer Center, University of California, Los Angeles, Radboud University Nijmegen

Language: English

Topic: RNA Research and Splicing

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

Funders: U.S. Department of Defense, National Human Genome Research Institute, National Institute of General Medical Sciences, National Institute of Allergy and Infectious Diseases

Awards: G1212220100, Decoding the RNA Structurome: Method Development and Function Analysis., DEVELOP 3D-BRIDGE ANTISENSE OLIGONUCLEOTIDES AND STEM CELL-TARGETING MODALITY FOR SKIPPING EXONS OF DUCHENNE MUSCULAR DYSTROPHY, Decoding global RNP topologies in splicing regulation, High Throughput Determination of RNA 3D Structures and Dynamics in Vivo

OpenAlex ID: W7161574489

Cites: 109

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Related to: 10