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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
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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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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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Inheritance of Chromatin Structures03:17

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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...
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The Nucleosome Core Particle01:12

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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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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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Inferring direction of associations between histone modifications using a neural processes-based framework.

Ananthakrishnan Ganesan1,2,3, Denis Dermadi1,3, Laurynas Kalesinskas1,3

  • 1Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA.

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|January 9, 2023
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Summary

We developed a new computational framework to predict interactions between histone post-translational modifications (HPTMs). This method accurately identifies HPTM associations, revealing insights into immune responses after influenza vaccination.

Keywords:
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Area of Science:

  • Epigenetics
  • Systems Biology
  • Immunology

Background:

  • Predicting interactions between histone post-translational modifications (HPTMs) at a system-level is currently not feasible.
  • Histone post-translational modifications play crucial roles in regulating gene expression and cellular processes.

Purpose of the Study:

  • To develop and validate a computational framework for predicting directed associations between HPTMs at a single-cell resolution.
  • To apply this framework to identify HPTM interactions in healthy individuals and in response to influenza vaccination.

Main Methods:

  • Developed an imputation-followed-by-inference computational framework.
  • Utilized EpiTOF, a mass cytometry platform, for single-cell profiling of multiple HPTMs.
  • Applied the framework to >55 million peripheral mononuclear blood cells from 158 healthy subjects and an influenza vaccine cohort.

Main Results:

  • Neural processes (NP) demonstrated superior accuracy in imputing HPTM abundance compared to linear regression and k-nearest neighbors.
  • The framework successfully recapitulated known HPTM associations and identified novel ones in healthy individuals.
  • Identified changes in 6 HPTM pairs 30 days post-influenza vaccination, with several linked to innate memory.

Conclusions:

  • The developed computational framework enables system-level prediction of directed HPTM interactions.
  • This approach provides novel insights into HPTM dynamics in healthy states and in response to vaccination.
  • The findings highlight the potential of this framework for understanding epigenetic regulation in complex biological systems.