Authors: Ahmed Mohammed Almutairi , Abdulrahman Saleh Alshakrh , Khaliel Rafee Almutairi , Abdullah Ayad Alaujan , Amal Mohammed Almutiry

Abstract

RNA-binding proteins are essential regulators of post-transcriptional gene expression, controlling RNA splicing, transport, localization, stability, and translation within the nervous system. Dysregulation of RNA–protein interaction networks has emerged as a critical mechanism underlying multiple neurogenetic and neurodegenerative disorders. Crosslinking and Immunoprecipitation technologies, including High-Throughput Sequencing Crosslinking and Immunoprecipitation, Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation, Individual-Nucleotide Resolution Crosslinking and Immunoprecipitation, and Enhanced Crosslinking and Immunoprecipitation, have significantly advanced the ability to identify transcriptome-wide RNA-binding protein interaction sites with high specificity and resolution. These methodologies have enabled detailed characterization of RNA regulatory networks involved in neuronal homeostasis, synaptic plasticity, neurodegeneration, and tumor progression. This narrative review summarizes the principles and major variants of Crosslinking and Immunoprecipitation technologies and discusses their applications in neurogenetic disorders, including amyotrophic lateral sclerosis, Fragile X syndrome, Alzheimer’s disease, and neuroblastoma. Furthermore, the review highlights current technical limitations, analytical challenges, and future perspectives involving single-cell transcriptomics, multi-omics integration, artificial intelligence, and RNA-targeted therapeutic development. Collectively, Crosslinking and Immunoprecipitation-based methodologies represent powerful tools for elucidating disease-associated RNA regulatory mechanisms and may contribute to the identification of novel biomarkers and therapeutic targets in neurological and neuro-oncological diseases.

Keywords: CLIP, RNA-binding proteins, RNA–protein interactions, neurological disorders, neurodegenerative diseases, neuro-oncology, HITS-CLIP, PAR-CLIP, iCLIP, eCLIP, irCLIP, uvCLAP.