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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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In order to be passed through generations, genomic DNA must be undamaged and error-free. However, every day, DNA in a cell undergoes several thousand to a million damaging events by natural causes and external factors. Ionizing radiation such as UV rays, free radicals produced during cellular respiration, and hydrolytic damage from metabolic reactions can alter the structure of DNA. Damages caused include single-base alteration, base dimerization, chain breaks, and cross-linkage.
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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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The double-stranded structure of DNA has two major advantages. First, it serves as a safe repository of genetic information where one strand serves as the back-up in case the other strand is damaged. Second, the double-helical structure can be wrapped around proteins called histones to form nucleosomes, which can then be tightly wound to form chromosomes. This way, DNA chains up to 2 inches long can be contained within microscopic structures in a cell. A double-stranded break not only damages...
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Related Experiment Video

Updated: Apr 18, 2026

Author Spotlight: Quantitative Detection of DNA Protein Crosslinks and Their Post-Translational Modifications
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Protein-Protein Cross-Linking by a DNA Damage-Derived Histone Modification.

Zehui Zhou1, Hanrui Yu1, Marc M Greenberg1

  • 1Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland 21218, United States.

Journal of the American Chemical Society
|April 17, 2026
PubMed
Summary
This summary is machine-generated.

A novel molecule forms a specific nonenzymatic covalent modification (NECM), known as KMP, on histones within nucleosome core particles. This modification can lead to protein-protein cross-links, impacting cellular functions.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Epigenetics

Background:

  • Nonenzymatic covalent modification (NECM) of lysine residues, particularly the 5-methylene pyrrolone NECM (KMP) formed from oxidized abasic sites (C4-AP), can have significant physiological consequences.
  • KMP formation on histones within nucleosome core particles (NCPs) is linked to DNA damage and has been observed in human cells.

Purpose of the Study:

  • To investigate the formation and consequences of KMP on histones within NCPs using a synthetic molecule.
  • To identify proteins that form cross-links with KMP-modified histones and understand the functional implications.

Main Methods:

  • Synthesis of a molecule (1a) that directly induces KMP formation on histone lysines in NCPs.
  • Incubation of KMP-containing NCPs with nuclear lysates, followed by enrichment and identification of protein-protein cross-links (PPCs) using LC-MS/MS.
  • Analysis of PPCs formed by KMP generated directly on DNA via C4-AP.

Main Results:

  • KMP modification occurs on all four core histones, with a preference for H3.
  • NCP-protein and protein-protein cross-links were identified, indicating KMP's reactivity within the NCP environment.
  • Enriched proteins were functionally biased towards DNA binding, histone binding, histone modifications, and transcription regulation.
  • KMP-induced PPC formation is influenced by the NCP context and the location of C4-AP.

Conclusions:

  • The synthetic molecule effectively generates KMP on histones within NCPs, enabling the study of its cross-linking potential.
  • KMP-mediated protein-protein cross-linking within NCPs is specific and functionally relevant.
  • Further investigation into the in vivo impact of KMP-induced cross-linking on cellular processes is warranted.