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Spreading of Chromatin Modifications02:25

Spreading of Chromatin Modifications

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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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Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
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Epigenetic changes alter the physical structure of the DNA without changing the genetic sequence and often regulate whether genes are turned on or off. This regulation ensures that each cell produces only proteins necessary for its function. For example, proteins that promote bone growth are not produced in muscle cells. Epigenetic mechanisms play an essential role in healthy development. Conversely, precisely regulated epigenetic mechanisms are disrupted in diseases like cancer.
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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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Related Experiment Video

Updated: Apr 27, 2026

Deacetylation Assays to Unravel the Interplay between Sirtuins SIRT2 and Specific Protein-substrates
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Studying SIRT6 regulation using H3K56 based substrate and small molecules.

Piia Kokkonen1, Minna Rahnasto-Rilla1, Paolo Mellini2

  • 1School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland.

European Journal of Pharmaceutical Sciences : Official Journal of the European Federation for Pharmaceutical Sciences
|July 9, 2014
PubMed
Summary

Researchers identified specific small molecules that inhibit SIRT6, a key protein in healthy aging. These findings offer potential therapeutic targets for age-related diseases by modulating SIRT6 activity at the H3K56 deacetylation site.

Keywords:
Fluorometric assayHistone deacetylaseNicotinamideSIRT6Sirtuins

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Aging Research

Background:

  • Sirtuin 6 (SIRT6) is a chromatin-modulating protein crucial for healthy aging.
  • Developing specific SIRT6 modulators is essential for therapeutic interventions.
  • Understanding SIRT6 activity requires diverse investigation methods.

Purpose of the Study:

  • To identify and characterize specific small molecule inhibitors of SIRT6.
  • To evaluate SIRT6 deacetylation activity using novel fluorogenic substrates.
  • To discover modulators targeting the H3K56 deacetylation site.

Main Methods:

  • Screening of five fluorogenic substrates based on p53 and histone H3 sequences.
  • Optimization of a substrate targeting the H3K56 deacetylation site for SIRT6 activity assays.
  • Testing known sirtuin inhibitors (nicotinamide) and 15 additional small molecules for SIRT6 inhibition.

Main Results:

  • A substrate based on the H3K56 deacetylation site demonstrated optimal signal-to-background ratio.
  • Nicotinamide showed lower potency as a SIRT6 inhibitor compared to SIRT1.
  • EX-527, quercetin, and three pseudopeptidic compounds emerged as potent SIRT6 inhibitors, achieving >50% inhibition.

Conclusions:

  • The study presents the first identified modulators of SIRT6 activity specifically at the H3K56 deacetylation site.
  • These findings pave the way for developing targeted therapies for age-related conditions by modulating SIRT6.
  • The developed H3K56-based substrate is a valuable tool for future SIRT6 research.