Dynamic characterization and interpretation for protein-RNA interactions across diverse cellular conditions using HDRNet

Haoran Zhu, Yuning Yang, Yunhe Wang, Fuzhou Wang, Yujian Huang, Yi Chang, Ka-chun Wong () and Xiangtao Li ()
Additional contact information
Haoran Zhu: Jilin University
Yuning Yang: University of Toronto
Yunhe Wang: Hebei University of Technology
Fuzhou Wang: City University of Hong Kong
Yujian Huang: Chengdu University of Technology
Yi Chang: Jilin University
Ka-chun Wong: City University of Hong Kong
Xiangtao Li: Jilin University

Nature Communications, 2023, vol. 14, issue 1, 1-22

Abstract: Abstract RNA-binding proteins play crucial roles in the regulation of gene expression, and understanding the interactions between RNAs and RBPs in distinct cellular conditions forms the basis for comprehending the underlying RNA function. However, current computational methods pose challenges to the cross-prediction of RNA-protein binding events across diverse cell lines and tissue contexts. Here, we develop HDRNet, an end-to-end deep learning-based framework to precisely predict dynamic RBP binding events under diverse cellular conditions. Our results demonstrate that HDRNet can accurately and efficiently identify binding sites, particularly for dynamic prediction, outperforming other state-of-the-art models on 261 linear RNA datasets from both eCLIP and CLIP-seq, supplemented with additional tissue data. Moreover, we conduct motif and interpretation analyses to provide fresh insights into the pathological mechanisms underlying RNA-RBP interactions from various perspectives. Our functional genomic analysis further explores the gene-human disease associations, uncovering previously uncharacterized observations for a broad range of genetic disorders.

Date: 2023
References: View references in EconPapers View complete reference list from CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41467-023-42547-1 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-42547-1

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-023-42547-1

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().