Related Experiment Video
Updated: Aug 7, 2026
10:59
Visualizing and Quantifying Endonuclease-Based Site-Specific DNA Damage
Published on: August 21, 2021
Methods for studying chromatin assembly coupled to DNA repair
Annabelle Gérard1, Sophie E Polo, Danièle Roche
1Laboratory of Nuclear Dynamics and Genome Plasticity, Institut Curie, UMR 218, CNRS, Paris, France.
Methods in Enzymology
|June 24, 2006
Summary
Researchers developed new methods to study how cells rebuild DNA and chromatin structure after DNA repair. These techniques allow simultaneous analysis of DNA repair and nucleosome assembly in vitro and in vivo.
Area of Science:
- Molecular Biology
- Genetics
- Cell Biology
Background:
- DNA repair in eukaryotic nuclei occurs on chromatin-embedded DNA.
- A key model suggests transient chromatin disruption for DNA repair access.
- Restoring proper chromatin structure post-repair is crucial but less understood.
Purpose of the Study:
- To develop and present methods for simultaneously analyzing chromatin assembly and DNA repair.
- To investigate the restoration of chromatin organization following DNA damage repair.
Main Methods:
- Development of cell-free systems for in vitro DNA repair and nucleosome assembly analysis.
- Utilizing complementary assays: circular DNA for repair synthesis and supercoiling, and immobilized DNA for protein interactions and histone deposition.
- Designing in vivo assays to monitor chromatin assembly factors at global and local levels at DNA damage sites.
Main Results:
- Established cell-free systems capable of reproducing both DNA repair and nucleosome assembly.
- Demonstrated complementary in vitro assays for monitoring repair synthesis, supercoiling, protein interactions, and histone deposition.
- Developed in vivo assays for assessing chromatin assembly factor recruitment to damaged chromatin.
Conclusions:
- The described methods provide powerful tools for studying chromatin restoration after DNA repair.
- Simultaneous analysis of DNA repair and chromatin assembly offers insights into the underlying mechanisms.
- These approaches facilitate a deeper understanding of how chromatin organization is re-established post-lesion repair.
Related Concept Videos
02:05Duplication of Chromatin Structure
The process of chromosome duplication during cell division requires genome-wide disruption and re-assembly of chromatin. The chromatin structure must be accurately inherited, reassembled, and maintained in the daughter cells to ensure lineage propagation.
The basic unit of the chromatin is the nucleosome, consisting of DNA wrapped around octameric histone proteins and short stretches of linker DNA separating individual nucleosomes. The histone proteins within the nucleosome have their...
The basic unit of the chromatin is the nucleosome, consisting of DNA wrapped around octameric histone proteins and short stretches of linker DNA separating individual nucleosomes. The histone proteins within the nucleosome have their...
02:31Homologous Recombination
The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
02:54Nucleosome Remodeling
Nucleosomes are the basic units of chromatin compaction. Each nucleosome consists of the DNA bound tightly around a histone core, which makes the DNA inaccessible to DNA binding proteins such as DNA polymerase and RNA polymerase. Hence, the fundamental problem is to ensure access to DNA when appropriate, despite the compact and protective chromatin structure.
Nucleosome remodeling complex
Eukaryotic cells have specialized enzymes called ATP-dependent nucleosome remodeling enzymes. These enzymes...
Nucleosome remodeling complex
Eukaryotic cells have specialized enzymes called ATP-dependent nucleosome remodeling enzymes. These enzymes...
02:36Chromatin Immunoprecipitation- ChIP
Chromatin immunoprecipitation, or ChIP, is an antibody-based technique used to identify sites on DNA that bind to transcription factors of interest or histone proteins. It also helps determine the type of histone modifications such as acetylation, phosphorylation, or methylation.
Types of ChIP
ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...
Types of ChIP
ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...