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Transcription Factors02:16

Transcription Factors

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 Sequences02:02

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 Regulators02:13

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...
Cooperative Binding of Transcription Regulators02:13

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...
Position-effect Variegation02:32

Position-effect Variegation

In 1928, a German botanist Emil Heitz observed the moss nuclei with a DNA binding dye. He observed that while some chromatin regions decondense and spread out in the interphase nucleus, others do not. He termed them euchromatin and heterochromatin, respectively. He proposed that the heterochromatin regions reflect a functionally inactive state of the genome. It was later confirmed that heterochromatin is transcriptionally repressed, and euchromatin is transcriptionally active chromatin.
RNA Polymerase II Accessory Proteins02:36

RNA Polymerase II Accessory Proteins

Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in...

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Related Experiment Video

Updated: May 7, 2026

Dissection and Immunostaining of Imaginal Discs from Drosophila melanogaster
10:10

Dissection and Immunostaining of Imaginal Discs from Drosophila melanogaster

Published on: September 20, 2014

Flanking sequence context-dependent transcription factor binding in early Drosophila development.

Jessica L Stringham1, Adam S Brown, Robert A Drewell

  • 1Mathematics Department, Harvey Mudd College, 301 Platt Boulevard, Claremont, CA 91711, USA. jdresch@amherst.edu.

BMC Bioinformatics
|October 8, 2013
PubMed
Summary

Researchers found conserved sequences flanking transcription factor binding sites in Drosophila embryos. Including this sequence context improves the prediction of cis-regulatory modules, aiding in gene regulation studies.

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Last Updated: May 7, 2026

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Published on: September 20, 2014

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Area of Science:

  • Developmental Biology
  • Genomics
  • Molecular Biology

Background:

  • Gene expression in Drosophila embryos relies on transcription factors (TFs) and cis-regulatory modules (CRMs).
  • Position weight matrices (PWMs) represent TF binding sites but have limitations in predicting their genomic locations.
  • Understanding TF-DNA interactions is crucial for deciphering gene regulatory networks.

Purpose of the Study:

  • To investigate the role of flanking sequences in TF binding site specificity.
  • To assess the impact of sequence context on the functional identification of CRMs.
  • To enhance the predictive power of PWMs for TF binding sites.

Main Methods:

  • Analysis of 127 CRMs in Drosophila embryos.
  • Focus on four TFs regulating anteroposterior axis development.
  • Examination of conserved sequences adjacent to predicted TF binding regions.

Main Results:

  • Conserved flanking sequences were identified beyond predicted TF binding regions for all four TFs studied.
  • These flanking sequences appear to enhance TF binding specificity.
  • The abundance of flanking sequences decreased when considering only high-affinity binding sites.

Conclusions:

  • Incorporating sequence context-dependence into PWMs increases their information content.
  • This expansion facilitates more efficient functional identification and dissection of CRMs.
  • The findings suggest a refined approach for predicting TF binding and CRM function.