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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.
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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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Translesion (TLS) polymerases rescue stalled DNA polymerases at sites of damaged bases by replacing the replicative polymerase and installing a nucleotide across the damaged site. Doing so, TLS allows additional time for the cell to repair the damage before resuming regular DNA replication.
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Behavioral approaches have often been criticized for ignoring mental processes and focusing solely on observable behavior. However, these approaches provide an optimistic perspective for individuals seeking to change their behaviors. Rather than concentrating on intrinsic personality traits, behavioral approaches suggest that even longstanding habits can be modified by changing the reward contingencies that maintain them.
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Modification of secretory and transmembrane proteins entering the rough ER begins in the ER lumen. These modifications aid in protein folding and stabilize the acquired tertiary structure. Protein modifications in the rough ER co-occur at different stages of protein folding.
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Immunostaining for DNA Modifications: Computational Analysis of Confocal Images
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DNAmod: the DNA modification database.

Ankur Jai Sood1,2, Coby Viner2,3, Michael M Hoffman4,5,6,7

  • 1Department of Medical Biophysics, University of Toronto, Princess Margaret Cancer Research Tower 15-701, 101 College Street, Toronto, ON, M5G 1L7, Canada.

Journal of Cheminformatics
|April 25, 2019
PubMed
Summary
This summary is machine-generated.

DNAmod is a new open-source database cataloging DNA modifications, crucial for epigenetic regulation. It provides a centralized resource for researchers to explore properties, occurrence, and nomenclature of modified DNA bases.

Keywords:
DNA modificationsEpigenomicsNucleobases

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Area of Science:

  • Epigenetics
  • Molecular Biology
  • Bioinformatics

Background:

  • Covalent DNA modifications like 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) are vital epigenetic marks in eukaryotes.
  • Diverse DNA modifications exist across bacteria, archaea, and viruses.
  • Existing databases primarily focus on RNA and histone modifications, neglecting DNA modifications.

Purpose of the Study:

  • To address the lack of a centralized resource for DNA modifications.
  • To develop DNAmod, an open-source database cataloging DNA modifications.
  • To provide researchers with a comprehensive source for DNA modification information.

Main Methods:

  • Development of an open-source database, DNAmod.
  • Creation of a web interface for browsing and searching modifications.
  • Manual curation and annotation of chemical properties, structures, occurrence, and nomenclature.

Main Results:

  • DNAmod catalogues curated modified DNA bases and candidate entities.
  • The database includes annotations on sequencing methods and natural occurrence.
  • A nomenclature system for modified DNA bases is provided.

Conclusions:

  • DNAmod serves as a single-source repository for DNA modification data.
  • The database facilitates research by enabling easy access to information on modified DNA bases.
  • DNAmod supports researchers in reviewing literature, selecting methods, and tracking developments in the field.