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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...

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 dimers that...

The Eukaryotic Promoter Region

The Eukaryotic Promoter Region

The eukaryotic promoter region is a segment of DNA located upstream of a gene. It contains an RNA polymerase binding site, a transcription start site, and several cis-regulatory sequences. The proximal promoter region is located in the vicinity of the gene and has cis-regulatory sequences and the core promoter. The core promoter is the binding site for RNA polymerase and is usually located between -35 and +35 nucleotides from the transcription start site. The distal promoter regions are...

General Transcription Factors

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Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...

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...

The Eukaryotic Promoter Region

The Eukaryotic Promoter Region

The eukaryotic promoter region is a segment of DNA located upstream of a gene. It contains an RNA polymerase binding site, a transcription start site, and several cis-regulatory sequences. The proximal promoter region is located in the vicinity of the gene and has cis-regulatory sequences and the core promoter. The core promoter is the binding site for RNA polymerase and is usually located between -35 and +35 nucleotides from the transcription start site. The distal promoter regions are...

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Related Experiment Video

Updated: Jun 27, 2026

Genome-wide Snapshot of Chromatin Regulators and States in Xenopus Embryos by ChIP-Seq

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Published on: February 26, 2015

Beyond the "recognition code": structures of two Cys2His2 zinc finger/TATA box complexes.

S A Wolfe¹, R A Grant, M Elrod-Erickson

¹Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

Structure (London, England : 1993)

|October 6, 2001

Summary

Structural studies of novel Cys2His2 zinc finger proteins reveal complex DNA interactions. These findings challenge the concept of a simple "recognition code" for protein-DNA binding.

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Last Updated: Jun 27, 2026

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Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C

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Published on: October 14, 2022

Area of Science:

Structural Biology
Molecular Biology
Genetics

Background:

Cys2His2 zinc finger proteins are engineered to bind specific DNA sequences, with potential applications in research and gene therapy.
Despite advances in protein design, the fundamental principles of DNA recognition remain unclear.
A proposed

Purpose of the Study:

To investigate the structural basis of DNA recognition by engineered Cys2His2 zinc finger proteins.
To assess the validity of a simple

Main Methods:

High-resolution cocrystal structures of two selected zinc finger proteins bound to a eukaryotic TATA box DNA sequence.
Comparison of these structures with the known Zif268-DNA complex.

Main Results:

The overall protein-DNA docking arrangement was similar to Zif268.
Significant differences in side chain-base interactions were observed between Zif268 and the selected variants.
Side chain-side chain interactions within and between fingers were identified as crucial for stabilizing the protein-DNA interface and recognition.

Conclusions:

The determined structures reveal unexpected complexity in zinc finger-DNA interactions.
The diversity of interactions, even among proteins derived from Zif268, challenges established concepts of zinc finger-DNA recognition.
Developing a predictive recognition code for these proteins is significantly more difficult than previously assumed.