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Histone Modification02:32

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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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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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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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Complete Workflow for Analysis of Histone Post-translational Modifications Using Bottom-up Mass Spectrometry: From Histone Extraction to Data Analysis
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iHMS: a database integrating human histone modification data across developmental stages and tissues.

Yanglan Gan1, Han Tao2, Jihong Guan3

  • 1School of Computer Science and Technology, Donghua University, Shanghai, China.

BMC Bioinformatics
|February 12, 2017
PubMed
Summary

We developed iHMS, a human histone modification database, to explore how changes in chromatin states influence cell development. This resource aids in understanding epigenetic dynamics across human tissues and developmental stages.

Keywords:
Data integrationDatabaseDevelopmental stagesHuman histone modification

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Area of Science:

  • Epigenetics
  • Genomics
  • Developmental Biology

Background:

  • Chromatin states are crucial for diverse cell states.
  • Genome-wide histone modification maps for human development and tissues are increasingly available.

Purpose of the Study:

  • To create an integrated database for investigating epigenetic dynamics.
  • To facilitate research on regulatory mechanisms in cellular differentiation.

Main Methods:

  • Developed iHMS, an integrated human histone modification database.
  • Incorporated massive histone modification maps, genome-wide expression data, gene annotations, GC content, and CpG island information.
  • Provided an intuitive query interface for comprehensive analysis and an efficient browser for visualization and comparison.

Main Results:

  • iHMS integrates diverse histone modification and expression data across human development and tissues.
  • The database enables comparative analysis based on genes, genomic regions, histone marks, and cell types.
  • Users can visualize and compare multiple genome-wide maps and expression profiles.

Conclusions:

  • iHMS is a valuable resource for understanding histone modification transitions and their impact on cellular phenotypes.
  • The database supports epigenetic and developmental studies by cataloging histone modification states across human development.