RNAalong

RNAalong is an emerging concept in transcriptomics that describes a method to map regulatory features along the entire length of RNA molecules in a single assay. The approach aims to integrate information about RNA–protein interactions, RNA modifications, and secondary structure across full-length transcripts by combining crosslinking-based capture with long-read sequencing.

Conceptually, RNAalong begins with stabilization of RNA–protein contacts by UV or chemical crosslinking, followed by preparation of RNA suitable for sequencing in a way that preserves transcript-length information. Long-read sequencing platforms, such as nanopore-based or single-molecule technologies, are used to read full-length cDNA or native RNA, enabling localization of binding events and structural signals along each transcript.

The resulting data can yield base-resolution maps of occupancy by RNA-binding proteins, regions of structured RNA, and signatures of chemical modifications along the entire transcript. Retaining isoform-specific transcript length allows analysis of alternative splicing in concert with regulatory features across the 5' untranslated region, coding sequence, and 3' untranslated region.

Applications include investigations of post-transcriptional regulation, viral RNA biology, and complex eukaryotic transcriptomes. Compared with fragmentary approaches such as CLIP-seq or short-fragment structure probing, RNAalong emphasizes continuous along-transcript profiles, but it requires high-quality RNA, careful bias control, and substantial computational resources.

Status and outlook: as an emerging concept, RNAalong remains under development, with ongoing work to optimize crosslinking chemistries and data-analysis pipelines capable of interpreting long-read, transcript-length information.