RNA accessibility sequencing reveals transcriptome-wide RBP binding and RNA structure
- 1Univ. Chicago
Abstract
We introduce RAD-seq (RNA Accessibility via Deamination sequencing), a simple and scalable method that quantifies RNA accessibility by protein binding in vivo. RAD-seq uses TadA8.20-mediated adenosine deamination to report the local exposure of each adenosine to its molecular environment, integrating the combined effects of base pairing, RNA folding, and RNA-binding protein (RBP) occupancy in a single experiment. RAD-seq profiles recapitulate known structural signatures, reveal high-resolution RBP footprints, report on the influence of RNA modifications, and capture dynamic remodeling of RNA accessibility during oxidative and heat-shock stress. By integrating RAD-seq with RNA Bind-n-Seq motifs, we detected local enrichment of the RNA N6-methyladenosine (m6A) methyltransferase recruiter TRA2A following knockdown of the exon junction anchor protein EIF4A3, revealing a potential mechanism that links RNA accessibility to enhanced TRA2A recruitment and m6A deposition. Extending this framework, we introduce an unsupervised statistical model that combines RAD-seq with motif priors to infer binding landscapes for multiple RBPs, reproducing the information from numerous CLIP-seq datasets from a single RAD-seq experiment. These results indicate RAD-seq as a generalizable approach for joint profiling of RNA structure and protein occupancy, defining enzymatic RNA accessibility as a new dimension to investigate regulatory elements on RNA.
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BibTeX
@misc{li2026accessibility,
title = {{RNA accessibility sequencing reveals transcriptome-wide RBP binding and RNA structure}},
author = {Y. Li and C. Ye and R. Ge and C.-W. Ju and Y. Xiao and W. Tang and M. Chen and C. He},
howpublished = {bioRxiv},
year = {2026},
month = nov,
doi = {10.64898/2026.11.02.763788},
url = {https://www.biorxiv.org/content/10.64898/2026.11.02.763788v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - RNA accessibility sequencing reveals transcriptome-wide RBP binding and RNA structure
AU - Y. Li
AU - C. Ye
AU - R. Ge
AU - C.-W. Ju
AU - Y. Xiao
AU - W. Tang
AU - M. Chen
AU - C. He
PY - 2026
DA - 2026/11/02
PB - bioRxiv
DO - 10.64898/2026.11.02.763788
UR - https://www.biorxiv.org/content/10.64898/2026.11.02.763788v1
AB - We introduce RAD-seq (RNA Accessibility via Deamination sequencing), a simple and scalable method that quantifies RNA accessibility by protein binding in vivo. RAD-seq uses TadA8.20-mediated adenosine deamination to report the local exposure of each adenosine to its molecular environment, integrating the combined effects of base pairing, RNA folding, and RNA-binding protein (RBP) occupancy in a single experiment. RAD-seq profiles recapitulate known structural signatures, reveal high-resolution RBP footprints, report on the influence of RNA modifications, and capture dynamic remodeling of RNA accessibility during oxidative and heat-shock stress. By integrating RAD-seq with RNA Bind-n-Seq motifs, we detected local enrichment of the RNA N6-methyladenosine (m6A) methyltransferase recruiter TRA2A following knockdown of the exon junction anchor protein EIF4A3, revealing a potential mechanism that links RNA accessibility to enhanced TRA2A recruitment and m6A deposition. Extending this framework, we introduce an unsupervised statistical model that combines RAD-seq with motif priors to infer binding landscapes for multiple RBPs, reproducing the information from numerous CLIP-seq datasets from a single RAD-seq experiment. These results indicate RAD-seq as a generalizable approach for joint profiling of RNA structure and protein occupancy, defining enzymatic RNA accessibility as a new dimension to investigate regulatory elements on RNA.
ER -