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RNA-seq

RNA-seq

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...

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Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

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Detecting haplotype-specific transcript variation in long reads with FLAIR2.

Alison D Tang¹, Colette Felton¹, Eva Hrabeta-Robinson¹

¹Department of Biomolecular Engineering, University of California, Santa Cruz, USA.

|July 3, 2024

Summary

This summary is machine-generated.

Long-read sequencing enables simultaneous analysis of RNA variants and splicing changes. This approach clarifies the role of adenosine-to-inosine editing enzyme ADAR in lung cancer progression.

Keywords:

A-to-I editing ADAR FLAIR Long-read RNA-seq

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Last Updated: Jun 22, 2025

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Published on: June 23, 2012

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Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

RNA sequencing (RNA-seq) reveals RNA processing aberrations linked to diseases.
Aberrant splicing and RNA single nucleotide variants (SNVs) affect transcript stability, localization, and function.
ADAR enzyme upregulation is linked to lung adenocarcinoma invasiveness and splicing regulation.

Purpose of the Study:

To overcome short-read RNA-seq limitations in interrogating RNA variants and splicing simultaneously.
To elucidate the cis-effects of variants on splicing changes at a single molecule level using long-read sequencing.
To clarify the role of ADAR in tumorigenesis by identifying inosine isoform associations.

Main Methods:

Utilized long-read sequencing to obtain full-length transcript sequences.
Developed a computational workflow augmenting FLAIR to integrate RNA variant calls with isoforms.
Generated Nanopore sequencing data from lung adenocarcinoma cells with and without ADAR knockdown.

Main Results:

Successfully integrated RNA variant calls with associated isoforms from long-read data.
Identified key inosine isoform associations relevant to ADAR's role in tumorigenesis.
Demonstrated the capability of the developed workflow in analyzing complex RNA variations.

Conclusions:

Long-read sequencing provides valuable insights into RNA variant and splicing pattern relationships.
The developed computational workflow enhances the analysis of RNA variations.
This approach aids in understanding the functional importance of RNA editing and splicing in diseases.