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Updated: Jun 16, 2026

Profiling DNA Replication Timing Using Zebrafish as an In Vivo Model System

Profiling DNA Replication Timing Using Zebrafish as an In Vivo Model System

Published on: April 30, 2018

A parallel reporter assay for zebrafish.

Gloria D Ligunas¹, Stefan C Materna²

¹Department of Molecular and Cell Biology, University of California Merced, Merced, CA, 95343, USA; Quantitative and Systems Biology Graduate Program, University of California Merced, Merced, CA, 95343, USA.

Developmental Biology

|June 13, 2026

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TAEL 2.0: An Improved Optogenetic Expression System for Zebrafish.

Zebrafish·2021

We developed a new zebrafish assay to test multiple gene regulatory elements (CRMs) simultaneously in vivo. This method efficiently validates candidate CRMs, overcoming a key bottleneck in gene regulation research.

Area of Science:

Developmental Biology
Genetics
Molecular Biology

Background:

* Cis-regulatory modules (CRMs) are crucial for gene regulation.
* In vivo validation of candidate CRMs is a significant challenge.

Purpose of the Study:

* To introduce a novel parallel reporter assay for zebrafish to authenticate candidate CRMs.
* To enable simultaneous, quantitative analysis of multiple transcriptional reporters in vivo.

Main Methods:

* Utilized standard Tol2-mediated transgenesis in zebrafish.
* Employed molecular barcodes to distinguish and quantify individual reporters.
* Analyzed reporter activity in whole embryos and after pre-enrichment.

Main Results:

Keywords:

Cis-Regulatory module Enhancer activity Gene regulation Quantitative reporter analysis Tol2 transgenesis Zebrafish

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Last Updated: Jun 16, 2026

Profiling DNA Replication Timing Using Zebrafish as an In Vivo Model System

Profiling DNA Replication Timing Using Zebrafish as an In Vivo Model System

Published on: April 30, 2018

An Assay for Lateral Line Regeneration in Adult Zebrafish

An Assay for Lateral Line Regeneration in Adult Zebrafish

Published on: April 8, 2014

Sample Preparation and Analysis of RNASeq-based Gene Expression Data from Zebrafish

Sample Preparation and Analysis of RNASeq-based Gene Expression Data from Zebrafish

Published on: October 27, 2017

* Demonstrated independent function of barcoded reporters.
* Showed mitigation of variability from mosaicism and genomic position effects.
* Achieved robust detection of CRM activity across different spatial domains and levels.
* Confirmed enhanced sensitivity with pre-enrichment for cell type-specific comparisons.

Conclusions:

* Established zebrafish transgenesis as a reliable platform for multiplexed reporter analysis.
* Provided a practical framework for high-throughput in vivo authentication of candidate CRMs.
* Complemented existing methods for detailed spatial characterization of gene regulation.