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Cis-regulatory Sequences

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...

Cis-regulatory Sequences

Cis-regulatory Sequences

Cooperative Binding of Transcription Regulators

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...

Co-activators and Co-repressors

Co-activators and Co-repressors

Gene transcription is regulated by the synergistic action of several proteins that form a complex at a gene regulatory site. This is observed in eukaryotes, where the regulation of gene expression is a complex process. Regulatory proteins in eukaryotes can broadly be classified into two types – regulators that bind directly to specific DNA sequences and co-regulators that associate with regulatory proteins but cannot directly bind to the DNA. These co-regulators are further divided into...

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Related Experiment Video

Updated: Oct 24, 2025

Author Spotlight: An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations

Author Spotlight: An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations

Published on: April 21, 2023

Single-cell analysis of cis-regulatory elements.

Alexandre P Marand¹, Robert J Schmitz¹

¹Department of Genetics, University of Georgia, Athens, GA 30602, USA.

Current Opinion in Plant Biology

|August 14, 2021

Summary

This summary is machine-generated.

Single-cell profiling reveals how cis-regulatory elements control plant cell identity and function. This technology helps understand cell differentiation and specialization by analyzing transcriptional and regulatory states in individual plant cells.

Keywords:

ATAC-seq Cell fate Chromatin Development Differentiation Single cell cis-regulatory elements

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Published on: April 21, 2023

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Area of Science:

Plant biology
Genomics
Cellular and molecular biology

Background:

Plant tissues comprise diverse cell types, all sharing the same genome.
Cell-type variation is linked to differential accessibility of cis-regulatory elements controlling gene expression.
Technical limitations have hindered exploration of cis-regulatory elements' roles in plant cell identity and function.

Purpose of the Study:

To review advanced single-cell profiling techniques for plant systems.
To establish the connection between cellular phenotypic variation and cis-regulatory mechanisms in plants.
To overcome past obstacles in studying cis-regulatory elements in plants.

Main Methods:

Review of state-of-the-art single-cell profiling approaches.
Analysis of analytical frameworks for single-cell data.
Focus on cis-regulatory element accessibility and transcriptional states.

Main Results:

Single-cell profiling enables unbiased charting of transcriptional states.
This technology allows analysis at the resolution of individual plant cells.
It facilitates linking cis-regulatory mechanisms to cell identity and function.

Conclusions:

Single-cell profiling is crucial for understanding plant cell-type variation.
It provides insights into cis-regulatory element function in cell identity, differentiation, and specialization.
This approach opens new avenues for exploring plant developmental biology.