SERIPH: A Two-Step Extraction Protocol for Selective Enrichment of Semi-Extractable RNAs

Conventional RNA extraction with acid guanidinium thiocyanate–phenol–chloroform (AGPC) reagents incompletely recovers a subset of transcripts, termed semi-extractable RNAs (seRNAs). This underrepresented RNA population includes architectural RNAs (arcRNAs), which scaffold membraneless organelles, as well as stress-induced downstream-of-gene readthrough transcripts (DoGs). Although our previously developed “improved” AGPC protocol incorporating physical disruption enhances seRNA recovery, it also co-extracts abundant, readily extractable RNAs, yielding mixed populations that hinder precise characterization of seRNAs. Here, we present SERIPH (Semi-Extractable RNA Isolation from the InterPHase), a simple two-step protocol that selectively enriches seRNAs by separating them from readily extractable RNA species. By depleting abundant extractable RNAs, SERIPH increases detection sensitivity, enabling the capture of weakly semi-extractable transcripts, including those of low abundance, that were overlooked by previous approaches. This increased sensitivity expands the detectable seRNA repertoire and reveals a broader genomic extent of DoG transcription than previously appreciated. Together, SERIPH provides a robust framework for high-resolution analysis of seRNA populations, advancing studies of RNA processing, transcriptional regulation, and RNA-mediated nuclear organization in stress responses and disease