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Related Concept Videos

Transcription Factors02:16

Transcription Factors

83.1K
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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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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Cis-regulatory Sequences02:02

Cis-regulatory Sequences

12.0K
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...
12.0K
Co-activators and Co-repressors02:04

Co-activators and Co-repressors

8.7K
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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General Transcription Factors01:30

General Transcription Factors

7.3K
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...
7.3K

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Related Experiment Video

Updated: Feb 27, 2026

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy
06:38

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

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Quantifying the Impact of Non-coding Variants on Transcription Factor-DNA Binding.

Jingkang Zhao1,2, Dongshunyi Li3, Jungkyun Seo2

  • 1Center for Genomic and Computational Biology, Duke University, Durham NC 27708, USA.

Research in Computational Molecular Biology : ... Annual International Conference, RECOMB ... : Proceedings. RECOMB (Conference : 2005- )
|July 11, 2017
PubMed
Summary

Genetic variants in non-coding DNA can disrupt gene regulation. This study introduces a method to predict how these mutations impact transcription factor (TF) binding, revealing a significant regulatory role in disease.

Keywords:
TF-DNA bindingnon-coding variantsregression models

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Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis
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Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA
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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Genetic variants in non-coding DNA are increasingly linked to complex diseases.
  • These variants can alter regulatory interactions between transcription factors (TFs) and DNA.
  • Assessing the functional impact of non-coding mutations is crucial for understanding disease mechanisms.

Purpose of the Study:

  • To develop and validate a computational method for predicting the impact of non-coding mutations on TF-DNA binding.
  • To assess the significance of TF binding alterations caused by pathogenic non-coding variants.

Main Methods:

  • Regression models of DNA-binding specificity were trained using high-throughput in vitro data.
  • Ordinary Least Squares (OLS) was used to estimate TF binding model parameters.
  • Z-scores and P-values were computed to quantify confidence in predicted TF binding changes.

Main Results:

  • Predicted changes in TF binding due to mutations showed good correlation with measured gene expression changes.
  • Pathogenic non-coding variants demonstrated significant allele-specific differences in TF binding compared to common variants.
  • The developed method effectively identifies regulatory impacts of non-coding mutations.

Conclusions:

  • Non-coding mutations can significantly alter TF binding, contributing to disease pathogenesis.
  • A strong regulatory component underlies many identified pathogenic non-coding variants.
  • The computational approach provides a reliable way to assess the functional consequences of non-coding genetic variations.