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Related Concept Videos

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...

Cooperative Binding of Transcription Regulators

Cooperative Binding of Transcription Regulators

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...

Co-activators and Co-repressors

Co-activators and Co-repressors

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Related Experiment Video

Updated: Apr 8, 2026

Quantitative Comparison of cis-Regulatory Element CRE Activities in Transgenic Drosophila melanogaster

Quantitative Comparison of cis-Regulatory Element CRE Activities in Transgenic Drosophila melanogaster

Published on: December 19, 2011

Deciphering cis-regulatory elements using REgulamentary.

Simone G Riva^1,2, Edward Sanders^1,2, Emily Georgiades^1,2

¹MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, United Kingdom.

Bioinformatics Advances

|April 7, 2026

Summary

This summary is machine-generated.

A new rule-based framework, REgulamentary, enables precise, cell-type-specific identification of cis-regulatory elements. This advances the functional interpretation of genetic variants linked to complex diseases.

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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

Published on: October 5, 2018

Related Experiment Videos

Last Updated: Apr 8, 2026

Quantitative Comparison of cis-Regulatory Element CRE Activities in Transgenic Drosophila melanogaster

Quantitative Comparison of cis-Regulatory Element CRE Activities in Transgenic Drosophila melanogaster

Published on: December 19, 2011

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes

Published on: May 31, 2011

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

Published on: October 5, 2018

Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Genome-wide association studies (GWAS) identify disease-associated variants, often in non-coding regions.
Accurate classification of cis-regulatory elements is crucial for understanding variant function.
Current methods like Hidden Markov Models (HMMs) yield abstract states requiring manual interpretation.

Purpose of the Study:

Introduce REgulamentary, a novel rule-based framework for de novo, genome-wide annotation of cis-regulatory elements.
Compare REgulamentary with existing count-based and segmentation-based approaches.
Demonstrate REgulamentary's utility in prioritizing causal variants in complex disease loci.

Main Methods:

REgulamentary employs a rule-based framework for cis-regulatory element annotation.
The study compares REgulamentary's classification strategy against count-based and segmentation-based methods.
REgulamentary was applied to published genetic association data.

Main Results:

REgulamentary provides a de novo, cell type-specific annotation of cis-regulatory elements.
The rule-based approach offers advantages in interpretability compared to HMM-based methods.
Application to disease loci successfully prioritized likely causal variants.

Conclusions:

REgulamentary enhances the functional interpretation of non-coding genetic variants.
The framework facilitates cell type-specific regulatory element annotation.
This tool aids in prioritizing variants from GWAS for complex disease research.