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Related Concept Videos

Histone Modification02:32

Histone Modification

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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...
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Histone Modification02:32

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Spreading of Chromatin Modifications02:25

Spreading of Chromatin Modifications

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The histone proteins in the nucleosomes are post-translationally modified (PTM) to increase or decrease access to DNA. The commonly observed PTMs are methylation, acetylation, phosphorylation, and ubiquitination of lysine amino acids in the histone H3 tail region. These histone modifications have specific meaning for the cell. Hence, they are called "histone code". The protein complex involved in histone modification is termed as "reader-writer" complex.
Writers
The writer...
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The Nucleosome Core Particle01:12

The Nucleosome Core Particle

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Nucleosomes are the DNA-histone complex, where the DNA strand is wound around the histone core. The histone core is an octamer containing two copies of H2A, H2B, H3, and H4 histone proteins.
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The Nucleosome Core Particle02:10

The Nucleosome Core Particle

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Nucleosomes are the DNA-histone complex, where the DNA strand is wound around the histone core. The histone core is an octamer containing two copies of H2A, H2B, H3, and H4 histone proteins.
The paradox
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Heterochromatin02:38

Heterochromatin

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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...
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Analysis of Histone Antibody Specificity with Peptide Microarrays
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Structure-function relationships in KDM7 histone demethylases.

Shobhit S Chaturvedi1, Rajeev Ramanan1, Sodiq O Waheed1

  • 1Department of Chemistry, Michigan Technological University, Houghton, MI, United States.

Advances in Protein Chemistry and Structural Biology
|October 1, 2019
PubMed
Summary

Histone demethylases (KDMs) regulate gene expression. This chapter details structural, biochemical, and computational studies of the KDM7 subfamily, crucial for understanding epigenetic regulation in diseases like cancer.

Keywords:
Histone lysine demethylasesKDM7Molecular dynamicsQM/MM

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Area of Science:

  • Epigenetics
  • Molecular Biology
  • Enzymology

Background:

  • Histone demethylases (KDMs) are key epigenetic regulators.
  • The Jumonji C (JmjC) domain-containing enzymes, including the KDM7 subfamily, are crucial for demethylation.
  • KDM7 enzymes are Fe(II) and 2-Oxoglutarate (2OG)-dependent dioxygenases.

Purpose of the Study:

  • To review the current understanding of KDM7 subfamily enzymes.
  • To highlight structural, biochemical, and computational findings for KDM7A and KDM7B.
  • To underscore the role of KDM7 enzymes in cellular processes and disease.

Main Methods:

  • Structural biology techniques (e.g., X-ray crystallography).
  • Biochemical assays to study enzyme kinetics and substrate specificity.
  • Computational methods including molecular dynamics and docking.

Main Results:

  • KDM7 enzymes (PHF8/KDM7B and KIAA1718/KDM7A) demethylate specific histone lysine residues (H3K27me2/1, H3K9me2/1, H4K20me1).
  • Detailed structural insights into the JmjC domain and cofactor binding.
  • Biochemical characterization reveals substrate preferences and catalytic mechanisms.
  • Computational studies provide dynamic views of enzyme-substrate interactions.

Conclusions:

  • KDM7 enzymes are vital human Nε-methyl lysine demethylases.
  • Dysregulation of KDM7 activity is implicated in pathologies such as cancers and mental retardation.
  • Further research into KDM7 structure-function relationships can inform therapeutic strategies.