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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

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 analyses the...
DNA as a Genetic Template02:05

DNA as a Genetic Template

Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...
Histone Modification02:32

Histone Modification

The histone proteins have a flexible N-terminal tail extending out from the nucleosome. These histone tails are often subjected to post-translational modifications such as acetylation, methylation, phosphorylation, and ubiquitination. Particular combinations of these modifications form “histone codes” that influence the chromatin folding and tissue-specific gene expression.
Acetylation
The enzyme histone acetyltransferase adds acetyl group to the histones. Another enzyme, histone deacetylase,...
Heterochromatin02:38

Heterochromatin

The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions that take up more dye are called heterochromatin. Heterochromatin is further classified into two forms – constitutive heterochromatin and facultative heterochromatin.
Constitutive heterochromatin: It is a highly compact region of chromatin that is mostly concentrated in the centromere and telomere. Unlike euchromatin, the amino acid at 9th...
DNA as a Genetic Template02:05

DNA as a Genetic Template

Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...
Histone Modification02:32

Histone Modification

The histone proteins have a flexible N-terminal tail extending out from the nucleosome. These histone tails are often subjected to post-translational modifications such as acetylation, methylation, phosphorylation, and ubiquitination. Particular combinations of these modifications form “histone codes” that influence the chromatin folding and tissue-specific gene expression.
Acetylation
The enzyme histone acetyltransferase adds acetyl group to the histones. Another enzyme, histone deacetylase,...

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Related Experiment Video

Updated: May 11, 2026

DamID-seq: Genome-wide Mapping of Protein-DNA Interactions by High Throughput Sequencing of Adenine-methylated DNA Fragments
09:14

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A lexicon for homeodomain-DNA recognition.

Markus Affolter1, Matthew Slattery, Richard S Mann

  • 1Growth and Development, Biozentrum der Universität Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland. markus.affolter@unibas.ch

Cell
|July 1, 2008
PubMed
Summary

Researchers mapped the DNA-binding specificities for most Drosophila and mouse homeodomains. This work reveals the intricate nature of identifying transcription factor targets within living organisms.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Understanding eukaryotic genome regulation necessitates comprehensive knowledge of transcription factor (TF) DNA-binding specificities.
  • Homeodomains are crucial DNA-binding domains found in many TFs, playing vital roles in gene regulation.

Discussion:

  • Recent studies by Berger et al. (2008) and Noyes et al. (2008) have systematically determined the DNA-binding specificities for a large proportion of Drosophila and mouse homeodomains.
  • These datasets provide valuable resources for researchers investigating gene regulation in these model organisms.

Key Insights:

  • The data highlight the significant complexity involved in accurately predicting or determining TF target specificities in a physiological context (in vivo).
  • Individual homeodomain specificities are not always sufficient to predict in vivo binding due to various regulatory factors.

Outlook:

  • Further research is needed to integrate these specificity data with other regulatory information (e.g., chromatin accessibility, TF expression) for a more complete understanding of cis-regulatory logic.
  • These findings pave the way for more accurate computational modeling of gene regulatory networks and prediction of TF function.