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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 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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Cis-regulatory Sequences02:02

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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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Elements and Compounds01:27

Elements and Compounds

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Pure substances consist of only one type of matter. A pure substance can be an element or a compound. An element consists of only one type of atom, while a compound consists of two or more types of atoms held together by a chemical bond.
Elements
Elements are classified as atomic or molecular based on the nature of their basic units. They are unique forms of matter with specific chemical and physical properties that cannot break down into smaller substances by ordinary chemical reactions. There...
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Cell Specific Gene Expression01:58

Cell Specific Gene Expression

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Multicellular organisms contain a variety of structurally and functionally distinct cell types, but the DNA in all the cells originated from the same parent cells. The differences in the cells can be attributed to the differential gene expression. Liver cells, whose functions include detoxification of blood, production of bile to metabolize fats, and synthesis of proteins essential for metabolism, must express a specific set of genes to perform their functions. Gene expression also varies with...
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Elements: Chemical Symbols and Isotopes02:31

Elements: Chemical Symbols and Isotopes

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A chemical symbol is an abbreviation used to indicate an element or an atom of an element. For example, the symbol for mercury is Hg. The same symbol is used to indicate one atom of mercury (microscopic domain) or to label a container of many atoms of the element mercury (macroscopic domain).
Some symbols are derived from the common English name of the element; others are abbreviations of the name in another language — Latin, Greek or German. For example, the symbol for aluminum (common name)...
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Updated: Jan 31, 2026

Site Specific Lysine Acetylation of Histones for Nucleosome Reconstitution using Genetic Code Expansion in Escherichia coli
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Reveal cell type-specific regulatory elements and their characterized histone code classes via a hidden Markov model.

Can Wang1,2, Shihua Zhang3,4,5

  • 1Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China.

BMC Genomics
|January 2, 2019
PubMed
Summary

We developed CsreHMM, a new method to identify cell type-specific regulatory elements (CSREs) and their associated histone codes from epigenomic data. This aids in understanding cell identity and gene regulation mechanisms.

Keywords:
Cell type-specific regulatory elementsEpigenomicsHidden Markov modelHistone modification

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Area of Science:

  • Genomics
  • Epigenetics
  • Computational Biology

Background:

  • Vast amounts of epigenomic data are available due to advances in next-generation sequencing.
  • These data offer opportunities to explore complex biological questions.

Purpose of the Study:

  • To develop an integrative and comparative method for identifying cell type-specific regulatory elements (CSREs).
  • To simultaneously recognize the histone codes that characterize these CSREs.
  • To reveal subclasses of CSREs, including those shared across cell types.

Main Methods:

  • Developed CsreHMM, a hidden Markov model-based approach.
  • Applied the method to analyze epigenomic data from 9 cell types and 9 chromatin marks.

Main Results:

  • Successfully identified CSREs genome-wide and their characteristic histone codes.
  • Revealed CSRE subclasses, including cell type-specific and shared elements.
  • Found significant associations between CSREs and functional regulatory regions with cell type-specific gene expression.

Conclusions:

  • CsreHMM effectively identifies cell type-specific regulatory elements and their associated histone codes.
  • The method provides insights into cell identity and diverse gene regulatory mechanisms.