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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.
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Spreading of Chromatin Modifications02:25

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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.
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Covalently Linked Protein Regulators02:04

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Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
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Histone Variants at the Centromere02:30

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Histone variants are the histone proteins with structural and sequence variations. These variants may be regarded as “mutant” forms that replace their canonical histone counterparts in the nucleosomes. Specific post-translational modifications on the histone variants enable further chromatin complexity and regulate tissue-specific gene expression. The most common histone variants are from histone H2A, H2B, and linker histone H1 families. However, several variants of histone H3...
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Chromatin Modification in iPS Cells01:32

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Chromatin modification alters gene expression; therefore, scientists can add histone-modifying enzymes, histone variants, and chromatin remodeling complexes to somatic cells to aid reprogramming into pluripotent stem (iPS) cells.
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Nucleosome Remodeling02:54

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Nucleosomes are the basic units of chromatin compaction. Each nucleosome consists of the DNA bound tightly around a histone core, which makes the DNA inaccessible to DNA binding proteins such as DNA polymerase and RNA polymerase. Hence, the fundamental problem is to ensure access to DNA when appropriate, despite the compact and protective chromatin structure.
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Related Experiment Video

Updated: May 12, 2025

Isolation and Cultivation of Neural Progenitors Followed by Chromatin-Immunoprecipitation of Histone 3 Lysine 79 Dimethylation Mark
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Why do histone monomethylation and dimethylation cause a significant difference in binding to LEDGF?

Hinako X Suzuki1,2, Hisashi Okumura2,3,4, Satoru G Itoh2,3,4

  • 1Faculty of Science, Shinshu University, Matsumoto, Japan.

The Journal of Chemical Physics
|May 8, 2025
PubMed
Summary

Lens epithelium-derived growth factor (LEDGF) protein binding to histone H3 is crucial for gene transcription. Methylation of histone H3 at K36 stabilizes this interaction, impacting cancer and AIDS.

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Isolation and Cultivation of Neural Progenitors Followed by Chromatin-Immunoprecipitation of Histone 3 Lysine 79 Dimethylation Mark
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Area of Science:

  • Molecular Biology
  • Biochemistry
  • Structural Biology

Background:

  • Lens epithelium-derived growth factor (LEDGF) is a chromatin-binding protein involved in gene transcription.
  • LEDGF is implicated in diseases such as acquired immunodeficiency syndrome (AIDS) and various cancers.
  • The PWWP domain of LEDGF specifically interacts with histone H3 at lysine 36 (H3K36).

Purpose of the Study:

  • To investigate the dependency of LEDGF PWWP domain binding affinity on the methylation state of H3K36.
  • To elucidate the molecular mechanisms underlying the interaction between LEDGF PWWP and methylated H3K36.

Main Methods:

  • Molecular dynamics simulations were employed.
  • Simulations involved the LEDGF PWWP domain and histone H3 fragments with varying H3K36 methylation states (nonmethylated, monomethylated, dimethylated, trimethylated).

Main Results:

  • Both hydrophobic and electrostatic interactions are critical for LEDGF PWWP domain binding to H3K36.
  • Binding is unstable with nonmethylated and monomethylated H3K36 due to hydrogen bonding with water molecules.
  • Dimethylated and trimethylated H3K36 exhibit stable binding as they do not form these water-mediated hydrogen bonds.

Conclusions:

  • The methylation state of H3K36 significantly influences the stability of LEDGF PWWP domain binding.
  • Specific methylation patterns (di- and trimethylation) stabilize the interaction, suggesting a role in regulating gene transcription in health and disease contexts.