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SERIPH: A Two-Step Extraction Protocol for Selective Enrichment of Semi-Extractable RNAs
Naoko Fujiwara1, Junichi Iwakiri2, Chao Zeng3
1Osaka Daigaku.
RNA (New York, N.Y.)
|June 25, 2026
Summary
SERIPH (Semi-Extractable RNA Isolation from the InterPHase) selectively enriches semi-extractable RNAs (seRNAs), like architectural RNAs and stress-induced transcripts. This method improves RNA analysis by separating these crucial molecules from abundant RNAs.
Area of Science:
- Molecular Biology
- Genomics
- Biochemistry
Background:
- Conventional RNA extraction methods incompletely recover semi-extractable RNAs (seRNAs), including architectural RNAs (arcRNAs) and downstream-of-gene readthrough transcripts (DoGs).
- Previously improved protocols enhance seRNA recovery but co-extract abundant RNAs, complicating analysis.
Purpose of the Study:
- To develop a method for selectively enriching seRNAs.
- To enable high-resolution analysis of seRNA populations.
Main Methods:
- SERIPH (Semi-Extractable RNA Isolation from the InterPHase) is a two-step protocol.
- It involves initial removal of readily extractable RNAs followed by improved extraction of the interphase.
Main Results:
- SERIPH robustly enriches seRNAs (arcRNAs, DoGs) and depletes abundant mRNAs.
- The method increases detectable DoG loci and sensitivity for weakly semi-extractable transcripts.
- SERIPH reveals enrichment of intron-retaining transcripts within the seRNA fraction.
Conclusions:
- SERIPH provides a practical framework for focused, high-resolution seRNA analysis.
- This method facilitates comprehensive characterization of seRNAs, advancing studies in RNA processing, transcriptional regulation, and nuclear organization.
- SERIPH is valuable for research in stress responses and disease.
