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Related Concept Videos

Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
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...
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.
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Structure of Cadherins01:25

Structure of Cadherins

The cadherins were one of the first cell adhesion molecules discovered; the term “cadherins”   is based on their calcium-dependent adhering properties. The first cadherins discovered on the epithelial, neuronal, and placental cells were named E-cadherin, P-cadherin, and N-cadherin, respectively. These classical cadherins share sequence and structural similarities. Other cadherins, including those involved in cell signaling, are grouped into non-classical cadherins. This diversity of cadherins...
Polytene Chromosomes02:04

Polytene Chromosomes

Polytene chromosomes are giant interphase chromosomes with several DNA strands placed side by side. They were discovered in the year 1881 by Balbiani in salivary glands, intestine, muscles, malpighian tubules, and hypoderm of larvae Chironomus plumosus. Hence, these are also called "Salivary gland chromosomes." These are found in insects of the order Diptera and Collembola; in certain organs of mammals; and synergids, antipodes of flowering plants. Polytene chromosomes are also regularly...
Inheritance of Chromatin Structures03:17

Inheritance of Chromatin Structures

Epigenetics is the study of inherited changes in a cell's phenotype without changing the DNA sequences. It provides a form of memory for the differential gene expression pattern to maintain cell lineage, position-effect variegation, dosage compensation, and maintenance of chromatin structures such as telomeres and centromeres. For example, the structure and location of the centromere on chromosomes are epigenetically inherited. Its functionality is not dictated or ensured by the underlying DNA...

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Related Experiment Video

Updated: Jul 18, 2026

A Method to Study de novo Formation of Chromatin Domains
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Published on: August 23, 2019

Structural polymorphism of chromodomains in Chd1.

Masahiko Okuda1, Masami Horikoshi, Yoshifumi Nishimura

  • 1Graduate School of Supramolecular Biology, Yokohama City University, Tsurumi-ku, Yokohama 230-0045, Japan.

Journal of Molecular Biology
|November 14, 2006
PubMed
Summary

Yeast Chd1 chromodomains do not bind histone peptides, unlike human CHD1. Structural analysis reveals key differences in the peptide-binding site, explaining the lack of binding affinity for methylated histone H3 peptides.

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Deciphering Molecular Mechanism of Histone Assembly by DNA Curtain Technique
06:32

Deciphering Molecular Mechanism of Histone Assembly by DNA Curtain Technique

Published on: March 9, 2022

Area of Science:

  • Chromatin biology
  • Molecular structural biology
  • Epigenetics

Background:

  • Chromodomains are known histone H3 tail-binding modules.
  • Human CHD1, an ATP-dependent chromatin remodeler, has two chromodomains essential for binding H3 MeK4 peptides.
  • Previous studies suggested yeast Chd1's second chromodomain binds H3 MeK4 peptides.

Purpose of the Study:

  • To investigate the binding activity of yeast Chd1 chromodomains to methylated histone peptides.
  • To determine the structural basis for any observed binding differences between yeast Chd1 and human CHD1.

Main Methods:

  • Biochemical assays to test binding of yeast Chd1 chromodomains to various methylated histone peptides.
  • Nuclear Magnetic Resonance (NMR) spectroscopy to analyze the structure of yeast Chd1 chromodomains.
  • Structural comparison between yeast Chd1 and human CHD1 chromodomains.

Main Results:

  • Neither the second chromodomain nor tandem chromodomains of yeast Chd1 bound to any examined lysine- or arginine-methylated histone peptides.
  • NMR analysis revealed conserved secondary structures in yeast Chd1 chromodomains, similar to human CHD1.
  • Key structural differences, particularly in the peptide-binding site helix, were identified between yeast Chd1 and human CHD1 chromodomains.
  • Sequence alignment indicated yeast Chd1 lacks crucial residues for methylated lysine binding.

Conclusions:

  • Yeast Chd1 likely lacks binding affinity for H3 MeK peptides, contrary to previous suggestions.
  • Structural divergence in the chromodomains explains the differential binding activities between yeast Chd1 and human CHD1.
  • This study refines our understanding of chromodomain-mediated histone recognition in chromatin remodeling.