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Related Concept Videos

Transcription Factors02:16

Transcription Factors

82.2K
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...
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Eukaryotic Transcription Inhibitors01:52

Eukaryotic Transcription Inhibitors

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Certain biochemical processes, such as embryonic development and cell growth regulation, depend on the repression of specific genes. DNA binding proteins known as eukaryotic transcription inhibitors regulate the repression of gene expression in eukaryotes. The presence of these inhibitors at the required location and time in the cell is triggered by the presence of hormones and additional signals from other cells.
Eukaryotic transcription inhibitors usually contain two distinct domains, a...
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Co-activators and Co-repressors02:04

Co-activators and Co-repressors

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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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Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

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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...
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Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

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Conserved Binding Sites01:49

Conserved Binding Sites

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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
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Related Experiment Video

Updated: Jan 14, 2026

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy
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High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy

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baal-nf identifies motif-disrupting variants that decrease transcription factor binding affinity.

Breeshey Roskams-Hieter1,2, Øyvind Almelid3, Chris P Ponting4

  • 1Institute of Genetics and Cancer, MRC Human Genetics Unit, Western General Hospital, University of Edinburgh, Edinburgh, EH4 2XU, UK. b.j.roskams-hieter@sms.ed.ac.uk.

Genome Biology
|January 12, 2026
PubMed
Summary
This summary is machine-generated.

Researchers identified 1,935 genetic variants that may alter human traits by changing transcription factor binding. This discovery aids in understanding the genetic basis of human variation.

Keywords:
Allele-specific bindingAllelic imbalanceChIP-sequencingMotifsTranscription factors

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Area of Science:

  • Genetics
  • Genomics
  • Molecular Biology

Background:

  • Human traits exhibit genetic variation, partly due to changes in transcription factor binding affinity within gene regulatory regions.
  • Identifying specific trait-causal variants and their mechanisms remains a challenge in genetics.

Purpose of the Study:

  • To identify and propose candidate variants causally altering human traits.
  • To develop a method for investigating trait variation linked to altered transcription factor binding.

Main Methods:

  • Utilized baal-nf, a computational tool, to analyze chromatin immunoprecipitation-sequencing data.
  • Identified allele-specific binding sites at heterozygous loci within transcription factor and co-factor binding motifs.
  • Focused on affinity-concordant positions to pinpoint functional variants.

Main Results:

  • Proposed 1,935 variants as strong candidates for causally altering human traits.
  • Demonstrated that these identified allele-specific binding sites are evolutionarily conserved.
  • Showed enrichment of these sites for associations with human traits and gene expression.

Conclusions:

  • The baal-nf method effectively identifies high-quality allele-specific binding sites.
  • These findings provide a valuable resource for studying the genetic underpinnings of human trait variation.
  • Altered transcription factor binding is a significant mechanism contributing to human trait diversity.