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Updated: Feb 12, 2026

A Method to Study de novo Formation of Chromatin Domains

A Method to Study de novo Formation of Chromatin Domains

Published on: August 23, 2019

Versatile and efficient chromatin pull-down methodology based on DNA triple helix formation.

Asako Isogawa^1,2,3,4, Robert P Fuchs^5,6,7,8,9, Shingo Fujii^10,11,12,13

¹DNA Damage Tolerance CNRS, UMR7258, Marseille, F-13009, France.

Scientific Reports

|April 14, 2018

Summary

This summary is machine-generated.

This study introduces a DNA-based method for isolating protein complexes bound to DNA. The technique uses triple helix formation to specifically capture and study DNA-associated proteins and chromatin structures.

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Area of Science:

Molecular Biology
Biochemistry
Genomics

Background:

Studying protein-DNA interactions is crucial for understanding gene regulation and cellular processes.
Existing methods for isolating DNA-bound proteins can be limited in specificity and scope.

Purpose of the Study:

To develop a reliable and versatile DNA-based method for isolating protein complexes bound to DNA (Isolation of DNA Associated Proteins: IDAP).
To enable the capture of specific DNA sequences and their associated proteins for further analysis.

Main Methods:

Utilizes a triple helix formation strategy between a DNA sequence tag and a complementary triple helix forming oligonucleotide (TFO).
The TFO is coupled to a desthiobiotin residue for efficient pull-down of target DNA-protein complexes.
Procedure optimized for in vitro recovery of native plasmids and applied to bacterial and human cellular extracts.

Main Results:

Successfully isolated proteins associated with plasmids in E. coli.
Recovered nucleosomes in vitro, enabling study of histone post-translational modifications.
Captured a specific transcription factor (NF-κB) bound to a model promoter in human nuclear extracts.
Achieved isolation of a specific locus from human genomic chromatin (Chromatin-of-Interest Fragment Isolation: CoIFI).

Conclusions:

The IDAP methodology provides a robust and versatile approach for capturing proteins that specifically bind to any sequence-of-interest.
This technique is applicable to DNA adducts or secondary structures, provided a nearby sequence tag for triple helix formation.
Opens new avenues for studying protein-DNA interactions, chromatin structure, and epigenetic modifications in various biological contexts.