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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

Regulation of Expression at Multiple Steps

Regulation of Expression at Multiple Steps

The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the...

Regulation of Expression Occurs at Multiple Steps

Regulation of Expression Occurs at Multiple Steps

Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...

Regulation of Expression Occurs at Multiple Steps

Regulation of Expression Occurs at Multiple Steps

Genome Annotation and Assembly

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

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Related Experiment Video

Updated: Mar 18, 2026

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA

Published on: August 21, 2016

Establishing and validating regulatory regions for variant annotation and expression analysis.

Alexander Kaplun¹, Mathias Krull², Karthick Lakshman²

¹QIAGEN Bioinformatics, 35 Gatehouse Drive, Waltham, MA, 02451, USA. kapluns@gmail.com.

|July 1, 2016

Summary

Regulatory mutations in gene promoters are increasingly linked to disease. This study validates a method for identifying gene promoters and establishes a workflow to analyze disease-associated genetic variants within transcription factor binding sites (TFBS).

Keywords:

Annotation Promoter Regulatory variants TRANSFAC Transcription factor binding Transcription start site

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Published on: January 16, 2019

Related Experiment Videos

Last Updated: Mar 18, 2026

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA

Published on: August 21, 2016

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation

Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation

Published on: January 16, 2019

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Genetic variants in regulatory regions, not just coding areas, significantly contribute to disease.
Thousands of regulatory mutations are documented in databases like HGMD and ClinVar.
Accurate annotation of variants in transcription factor binding sites (TFBS) is crucial for understanding their functional impact.

Purpose of the Study:

To validate TRANSFAC's virtual transcription start site (vTSS) method for defining optimal gene promoters.
To develop and implement a systematic workflow for analyzing disease-associated variants within TFBS.
To assess the impact of genetic variants on transcription factor binding.

Main Methods:

Comparison of best-supported and secondary promoters using vTSS calculation in hg19 and hg38 genomes.
Integration of Genome Trax and TRANSFAC databases for variant analysis.
Mapping of experimentally verified and predicted TFBSs to mutation sites from HGMD and ClinVar.

Main Results:

Validation of TRANSFAC's promoter definition approach.
Systematic mapping of thousands of TFBSs to disease-associated mutations.
Identification of potential regulatory effects of variants on transcription factor binding.

Conclusions:

TRANSFAC's method for defining gene promoters is validated.
A robust workflow for annotating regulatory genetic variants in TFBS has been established.