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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

Histone Modification

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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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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.
Nucleosomes, paradoxically, perform two opposite functions simultaneously. On the one hand, their primary aim is to protect the delicate DNA strands from physical damage and help achieve a higher compaction ratio. On the other hand, they must allow polymerase enzymes to access histone-bound DNA during...
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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
Nucleosomes, paradoxically, perform two opposite functions simultaneously. On the one hand, their main responsibility is to protect the delicate DNA strands from physical damage and help achieve a higher compaction ratio. While on the other hand, they must allow polymerase enzymes to access DNA...
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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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Updated: Mar 28, 2026

Assays for Validating Histone Acetyltransferase Inhibitors
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Assays for Validating Histone Acetyltransferase Inhibitors

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Multicomplex Integrative Structural Modeling of a Human Histone Deacetylase Interactome.

Jules Nde1,2, Kartik Majila3,2, Rosalyn C Zimmermann1

  • 1Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, USA.

Biorxiv : the Preprint Server for Biology
|March 27, 2026
PubMed
Summary
This summary is machine-generated.

Histone Deacetylase (HDAC) 1 and 2 protein complexes were structurally modeled using crosslinking mass spectrometry. The study reveals intrinsically disordered regions of HDAC1 fold into alpha helices within these complexes.

Keywords:
CoRESTCrosslinking Mass SpectrometryEndogenous Complex StructuresHDAC1HDAC2Integrative Structural ModelingIntrinsically Disordered RegionsNuRDSIN3A

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Simultaneous Measurement of HDAC1 and HDAC6 Activity in HeLa Cells Using UHPLC-MS
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Area of Science:

  • Biochemistry
  • Structural Biology
  • Molecular Biology

Background:

  • Histone Deacetylase (HDAC) 1 and 2 are crucial enzymes in chromatin remodeling complexes like NuRD, SIN3, and CoREST.
  • HDAC1/2 possess intrinsically disordered regions (IDRs) in their C-terminal domains (CTDs), whose structures and assembly roles are unclear.

Purpose of the Study:

  • To elucidate the structural assembly of HDAC1/2 within chromatin remodeling complexes.
  • To investigate the structural behavior of the CTD IDR in HDAC1/2.

Main Methods:

  • Utilized crosslinking mass spectrometry (XL-MS) and the Integrative Modeling Platform to map protein interaction networks and build complex models.
  • Employed an AlphaFold-enabled XL-MS constrained modeling approach to determine HDAC1 assembly.
  • Developed integrative structural models for NuRD, SIN3A, and CoREST complexes, including a detailed NuRD subcomplex model.

Main Results:

  • Successfully modeled the structures of NuRD, SIN3A, and CoREST complexes.
  • Demonstrated that the CTD IDR of HDAC1 folds into alpha helices upon complex assembly.
  • Generated a comprehensive structural model of a NuRD subcomplex comprising six IDRs.

Conclusions:

  • The study provides novel structural insights into HDAC1/2 complex assembly and the role of IDRs.
  • The integrative modeling approaches are broadly applicable for studying complex protein interactions and IDRs.