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Related Experiment Video

Updated: Jun 6, 2026

Determining Genetic Expression Profiles in C. elegans Using Microarray and Real-time PCR
10:27

Determining Genetic Expression Profiles in C. elegans Using Microarray and Real-time PCR

Published on: July 30, 2011

Identifying novel genes in C. elegans using SAGE tags.

Matthew J Nesbitt1, Donald G Moerman, Nansheng Chen

  • 1Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada.

BMC Molecular Biology
|December 15, 2010
PubMed
Summary

A new method called sequence tag-based amplification of cDNA ends (STACE) reconstructs full-length gene sequences from short expressed tags. This approach effectively identifies genes missed by current prediction methods, aiding in comprehensive genome annotation.

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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Existing gene prediction methods struggle with accuracy in eukaryote genomes due to incomplete understanding of gene features.
  • Low or rare expression levels of many genes and their isoforms hinder the acquisition of full-length cDNA sequences.
  • Novel approaches are essential for obtaining complete protein-coding gene sequences.

Purpose of the Study:

  • To develop a method for reconstructing full-length cDNA sequences from short expressed sequence tags.
  • To address limitations in current gene prediction and cDNA sequencing approaches.

Main Methods:

  • Developed sequence tag-based amplification of cDNA ends (STACE).
  • Utilized expressed tags as anchors for two-round PCR amplification to retrieve full-length transcripts.

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Automated Analysis of C. elegans Fluorescence Images using SegElegans
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Last Updated: Jun 6, 2026

Determining Genetic Expression Profiles in C. elegans Using Microarray and Real-time PCR
10:27

Determining Genetic Expression Profiles in C. elegans Using Microarray and Real-time PCR

Published on: July 30, 2011

Automated Analysis of C. elegans Fluorescence Images using SegElegans
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Automated Analysis of C. elegans Fluorescence Images using SegElegans

Published on: October 10, 2025

  • Applied STACE to C. elegans cDNA libraries using serial analysis of gene expression (SAGE) data.

    • Main Results:

    • Successfully applied STACE to recover sequence information for 12 genes.
    • Identified isoforms for two of the recovered genes.
    • Successfully recovered full-length cDNA sequences for seven genes using STACE.

    Conclusions:

    • STACE effectively reconstructs full-length cDNA sequences for under-represented genes.
    • The method identifies genes missed by existing prediction tools but suggested by short sequence tags like SAGE tags.
    • STACE enhances the completeness of gene annotation in genomic studies.