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Novel RNA-Binding Proteins Isolation by the RaPID Methodology

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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

This summary is machine-generated.

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...

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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:

Keywords:

architectural RNAs membraneless organelles readthrough transcripts semi-extractable RNAs stress responses

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Novel RNA-Binding Proteins Isolation by the RaPID Methodology

Novel RNA-Binding Proteins Isolation by the RaPID Methodology

Published on: September 30, 2016

3' End Sequencing Library Preparation with A-seq2

3' End Sequencing Library Preparation with A-seq2

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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.