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Cis-regulatory Sequences02:02

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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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Disubstituted Cyclohexanes: cis-trans Isomerism02:37

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Depending upon the different spatial orientation of the substituents, the disubstituted cycloalkanes exhibit two types of stereoisomers. The cis isomers have the substituents on the same side of the ring, whereas the trans isomers have the substituents on the opposite sides. These stereoisomers exhibit different physical properties and cannot be interconverted without breaking the carbon-carbon bonds.
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Reduction of Alkynes to cis-Alkenes: Catalytic Hydrogenation02:24

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Related Experiment Video

Updated: Jan 26, 2026

Quantifying the Activity of cis-Regulatory Elements in the Mouse Retina by Explant Electroporation
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Multiplex cis-regulatory analysis.

Jongmin Nam1

  • 1Department of Biology and Center for Computational & Integrative Biology, Rutgers, The State University of New Jersey, Camden, NJ, United States.

Methods in Cell Biology
|April 6, 2019
PubMed
Summary
This summary is machine-generated.

This study provides guidelines for using barcode reporters in sea urchin embryos to speed up cis-regulatory analysis. These methods enhance the identification of enhancers and promoters for gene regulatory network models.

Keywords:
EmbryoHigh-throughputMultiplexReporter assaycis-Regulatory analysis

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Area of Science:

  • Developmental Biology
  • Genomics
  • Molecular Biology

Background:

  • Multiplex cis-regulatory analysis accelerates the identification of enhancers and promoters.
  • Cis-regulatory information is crucial for building accurate gene regulatory network models.
  • Barcode reporter assays are essential tools in developmental biology research.

Purpose of the Study:

  • To provide practical guidelines for utilizing barcode reporters in sea urchin embryos.
  • To facilitate the adoption of high-throughput cis-regulatory analysis in sea urchin research.
  • To offer methods applicable to other invertebrate model organisms.

Main Methods:

  • Development of barcode reporters for quantitative PCR (qPCR): 13-tags and 129-tags.
  • Development of barcode reporters for NanoString technology: 130 Nanotags.
  • Development of barcode reporters for next-generation sequencing (NGS): 100 million N25-tags.

Main Results:

  • Established multiplex reporter assays for sea urchin embryos.
  • Detailed protocols for qPCR and NGS compatible barcode reporters.
  • Demonstrated efficiency in identifying cis-regulatory elements.

Conclusions:

  • Guidelines facilitate high-throughput cis-regulatory analysis in sea urchin embryos.
  • Barcode reporter systems are versatile for different analysis platforms (qPCR, NanoString, NGS).
  • The presented methods are potentially applicable to other invertebrate model systems.