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Related Concept Videos

Reporter Genes02:11

Reporter Genes

Reporter genes are a type of protein-coding gene that are often tagged to a gene of interest. Once inside a target cell, reporter genes usually produce visually identifiable characteristics like fluorescence and luminescence when expressed along with the gene of interest. Thus, reporter genes “report” the presence or absence of genes of interest in an organism, determine the gene expression pattern, or track the physical location of a DNA segment or protein in the cell.
Commonly used reporter...
Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form dimers that...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

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...
DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

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Related Experiment Video

Updated: May 22, 2026

Genetic Barcoding with Fluorescent Proteins for Multiplexed Applications
13:14

Genetic Barcoding with Fluorescent Proteins for Multiplexed Applications

Published on: April 14, 2015

Barcoded DNA-tag reporters for multiplex cis-regulatory analysis.

Jongmin Nam1, Eric H Davidson

  • 1Division of Biology, California Institute of Technology, Pasadena, California, United States of America. jn322@camden.rutgers.edu

Plos One
|May 8, 2012
PubMed
Summary

Researchers developed Nanotags, a novel barcoded DNA reporter system, enabling simultaneous quantitative analysis of numerous cis-regulatory modules (CRMs). This breakthrough simplifies studying gene expression control systems in complex biological processes.

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Area of Science:

  • Molecular Biology
  • Developmental Biology
  • Genomics

Background:

  • Cis-regulatory DNA sequences control gene expression but are difficult to study experimentally.
  • Existing methods lack the capacity for simultaneous, high-throughput analysis of multiple regulatory elements.

Purpose of the Study:

  • To develop a novel reporter system for efficient, simultaneous quantitative analysis of multiple cis-regulatory modules (CRMs).
  • To demonstrate the utility of this new method in studying gene regulation during embryonic development and in response to genetic perturbations.

Main Methods:

  • Development of "Nanotags," barcoded DNA reporters designed for multiplexed analysis.
  • Utilizing NanoString RNA counting and other quantitative methods to measure Nanotag activity.
  • Application in studying temporal gene expression patterns in developing sea urchin embryos.

Main Results:

  • Simultaneous quantitative analysis of up to 130 distinct CRMs is achievable.
  • Successfully measured hourly temporal activities of 126 CRMs from 46 genes in sea urchin embryos.
  • Demonstrated Nanotags' utility in gene perturbation experiments to assess CRM responses.

Conclusions:

  • Nanotag methodology offers an efficient solution for analyzing complex cis-regulatory networks.
  • This technique significantly advances the study of gene regulatory networks, functional genomics, and evolutionary genomics.
  • Nanotags enable previously challenging experiments, such as high-resolution temporal profiling of numerous CRMs.