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Updated: Jul 1, 2026
11:42
Sample Preparation and Analysis of RNASeq-based Gene Expression Data from Zebrafish
Published on: October 27, 2017
Advancing Functional Transcriptomics in Zebrafish with High-accuracy Full-length RNA Sequencing
Monika Kwiatkowska1, Tomasz Mądry1, Marta Blangiewicz1
1Department of Computational Biology of Non-coding RNA, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland.
Genomics, Proteomics & Bioinformatics
|June 30, 2026
Summary
CapTrap-seq enhances zebrafish transcriptomics by capturing full-length RNA, improving gene discovery and isoform resolution. This method offers a robust framework for studying complex transcriptomes in under-annotated species.
Area of Science:
- * Genomics
- * Molecular Biology
- * Developmental Biology
Background:
- * Zebrafish (Danio rerio) is a key vertebrate model organism with human genetic and physiological similarities.
- * Current transcriptomic research in zebrafish is limited by incomplete gene annotations and inefficient methods.
- * Need for high-resolution transcript-level analysis in zebrafish for functional genomics.
Purpose of the Study:
- * To apply CapTrap-seq, a long-read RNA sequencing method, to zebrafish developmental stages and adult tissues.
- * To improve the capture of full-length transcripts and enhance transcriptomic resolution.
- * To benchmark CapTrap-seq against existing methods like template-switching oligo (TSO) and assess its performance in a non-mammalian system.
Main Methods:
- * Utilized CapTrap-seq, a platform-agnostic approach combining cap-trapping with oligo(dT) priming for selective capture of 5'-capped, full-length transcripts.
- * Incorporated a size-selection step to improve recovery of longer RNA molecules.
- * Applied the method to zebrafish developmental stages and adult tissues, comparing results with existing long-read catalogues.
Main Results:
- * CapTrap-seq enabled accurate and reproducible transcript reconstruction in zebrafish without external ribodepletion or validation.
- * Detected a greater number of biologically relevant genes, including oxidative phosphorylation, cardiac, and OMIM disease genes.
- * Revealed extensive novel isoform diversity and resolved complex splicing landscapes in lncRNA loci, uncovering new full-length isoforms.
Conclusions:
- * CapTrap-seq provides a robust, genome-agnostic framework for high-quality transcriptome characterization in zebrafish.
- * The method overcomes limitations of incomplete annotations and improves transcript-level resolution.
- * Offers significant implications for functional genomics and translational research in zebrafish and other under-annotated species.
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