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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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Types of Genetic Transfer Between Organisms02:18

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Genetic transfer occurs when genetic information is passed from one organism to another. It occurs via two mechanisms: vertical gene transfer and horizontal gene transfer. Vertical gene transfer occurs when genetic information is transferred from one generation to the next, which happens much more frequently than horizontal gene transfer. Both sexual and asexual reproduction are forms of vertical gene transfer, where one or more organisms pass some or all of their genome onto their progeny.
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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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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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Chromatin Immunoprecipitation ChIP to Assay Dynamic Histone Modification in Activated Gene Expression in Human Cells
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Genetic Contexts Characterize Dynamic Histone Modification Patterns Among Cell Types.

Yanmei Lin1, Yan Li1, Xingyong Zhu1

  • 1College of Chemistry, Sichuan University, Chengdu, 610064, China.

Interdisciplinary Sciences, Computational Life Sciences
|June 6, 2019
PubMed
Summary
This summary is machine-generated.

Histone modifications are crucial for mammalian development. This study quantifies histone modification changes across cell types, revealing links to DNA sequence and identifying lineage-specific epigenetic regulators.

Keywords:
ConservationDNA primary sequenceGC-contentHistone modification

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Area of Science:

  • Epigenetics and Genomics
  • Developmental Biology
  • Molecular Biology

Background:

  • Histone modifications regulate chromatin structure and gene expression, impacting mammalian development.
  • Quantitative measurement of histone modification alterations across cell types and genetic contexts is limited.
  • The relationship between histone modifications and primary DNA sequence is not well understood.

Purpose of the Study:

  • To quantitatively measure histone modification alterations across different cell types.
  • To investigate the correlation between histone modifications and primary DNA sequence.
  • To identify lineage-specific histone modification genes and their genomic characteristics.

Main Methods:

  • Employed an entropy-based method to measure histone modification alterations.
  • Analyzed six genomic regions across five distinct cell types.
  • Developed a predictive model using k-mer sequence composition to link DNA sequence to histone modification patterns.

Main Results:

  • Histone modification alterations were found to enrich in 5'-UTR exons, 3'-UTR exons, and downstream regions.
  • K-mer sequence frequencies effectively predicted histone modification patterns, indicating DNA sequence correlation.
  • Lineage-specific histone modification genes exhibited higher conservation and lower GC content.

Conclusions:

  • Histone modification alterations are quantitatively measurable and vary across cell types.
  • Primary DNA sequence composition is a significant predictor of histone modification patterns.
  • Identified genomic region-specific epigenetic and genetic regulatory elements influencing histone modification patterns.