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Recombinant DNA

Recombinant DNA

Spreading of Chromatin Modifications

Spreading of Chromatin Modifications

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.
Writers
The writer...

Overview of Transposition and Recombination

Overview of Transposition and Recombination

Transposons make up a significant part of genomes of various organisms. Therefore, it is believed that transposition played a major evolutionary role in speciation by changing genome sizes and modifying gene expression patterns. For example, in bacteria, transposition can lead to conferring antibiotic resistance. Movement of transposable elements within the genetic pool of pathogenic bacteria can aid in transfer of antibiotic-resistant genetic elements. In eukaryotes, transposons can carry out...

Chromatin Packaging

Chromatin Packaging

Each human somatic cell contains 6 billion base-pairs of DNA. Each base-pair is 0.34 nm long, which means that each diploid cell contains a staggering 2 meters of DNA. How is such a long DNA strand packed inside a nucleus measuring only 10 - 20 microns in diameter?
The chromatin
In combination with specialized DNA binding protein called Histones, the DNA double helix forms a compact DNA: protein complex called chromatin. The chromatin itself is further compacted into higher-order...

Inheritance of Chromatin Structures

Inheritance of Chromatin Structures

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...

Chromatin Position Affects Gene Expression

Chromatin Position Affects Gene Expression

Chromatin is the massive complex of DNA and proteins packaged inside the nucleus. The complexity of chromatin folding and how it is packaged inside the nucleus greatly influences access to genetic information. Generally, the nucleus' periphery is considered transcriptionally repressive, while the cell's interior is considered a transcriptionally active area.
Topologically Associated Domains (TADs)
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Related Experiment Video

Updated: Jan 23, 2026

Sequential Salt Extractions for the Analysis of Bulk Chromatin Binding Properties of Chromatin Modifying Complexes

Sequential Salt Extractions for the Analysis of Bulk Chromatin Binding Properties of Chromatin Modifying Complexes

Published on: October 2, 2017

Chromatin Modifiers Alter Recombination Between Divergent DNA Sequences.

Ujani Chakraborty¹, Beata Mackenroth¹, David Shalloway¹

¹Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703.

|June 22, 2019

Summary

This summary is machine-generated.

Epigenetic factors and chromatin structure influence DNA repair decisions. Nucleosomes stabilize recombination intermediates, preventing mismatch repair (MMR) and promoting heteroduplex rejection in yeast.

Keywords:

chromatin modifiers heteroduplex rejection histone chaperones homologous recombination mismatch repair

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Area of Science:

Molecular Biology
Genetics
Epigenetics

Background:

Recombination between divergent DNA sequences is normally prevented by heteroduplex rejection mechanisms.
In baker's yeast, mismatch recognition by MutS homolog (MSH) proteins initiates antirecombination.
Histone chaperone machinery interacts with mismatch repair (MMR) factors.

Purpose of the Study:

To investigate the role of epigenetic factors and chromatin conformation in regulating the decision to reject or repair recombination between divergent DNA substrates.
To explore how histone chaperones and deacetylases influence heteroduplex rejection.

Main Methods:

Utilized an inverted repeat recombination assay in baker's yeast.
Assessed the impact of mutations in histone chaperones (CAF-1, Rtt106) and deacetylases (Sir2, Rpd3, Hst3, Hst4) on recombination outcomes.
Performed double-mutant analysis.

Main Results:

Histone chaperones CAF-1, Rtt106, and deacetylase Sir2 suppressed heteroduplex rejection.
Deacetylases Rpd3, Hst3, and Hst4 promoted heteroduplex rejection.
Nucleosomes at DNA lesions stabilize recombination intermediates, competing with MMR factors.

Conclusions:

Epigenetic factors and chromatin structure play a critical role in regulating DNA repair pathway choice.
Nucleosome positioning and histone modifications influence the balance between heteroduplex rejection and repair.
A model is proposed where nucleosomes stabilize recombination intermediates, thereby influencing the competition with MMR factors for heteroduplex processing.