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The Nucleosome

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Human DNA is almost two meters long. However, it is compressed inside a tiny nucleus measuring only a few microns in diameter. To make this degree of compaction possible, DNA is organized into several sequential levels so that it can fit into such a tiny space. The most compact form of DNA is a chromosome that can be seen under a microscope in a dividing cell.
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Related Experiment Video

Updated: Apr 11, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

Protein-DNA binding in high-resolution.

Shaun Mahony¹, B Franklin Pugh¹

¹a Department of Biochemistry & Molecular Biology , Center for Eukaryotic Gene Regulation, The Pennsylvania State University , University Park , PA , USA.

Critical Reviews in Biochemistry and Molecular Biology

|June 4, 2015

Summary

This summary is machine-generated.

New methods allow ultra-high resolution genome-wide mapping of protein-DNA interactions. These techniques precisely identify nucleotide-level binding events for transcription factors and other regulatory proteins, advancing genomic research.

Keywords:

ChIP-exo ChIP-seq DNase-seq high-resolution protein–DNA binding transcription factor binding

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Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Experimental and computational advances enable genome-wide protein-DNA binding profiling.
Techniques like ChIP-exo, DNase-seq, and ATAC-seq offer high resolution.
Understanding protein-DNA interactions is crucial for regulatory biology.

Purpose of the Study:

To review experimental assays for high-resolution protein-DNA binding profiling.
To explain computational analysis methods for these profiles.
To discuss challenges and opportunities in the field.

Main Methods:

Chromatin immunoprecipitation (ChIP) combined with exonuclease digestion (ChIP-exo).
Deeply sequenced chromatin accessibility assays (DNase-seq, ATAC-seq) for footprint detection.
Integration of diverse experimental and computational approaches.

Main Results:

High-resolution genome-wide maps of protein-DNA binding events are achievable.
Individual nucleotide interactions with regulatory proteins can be characterized.
These methods provide precise insights into gene regulation.

Conclusions:

Ultra-high resolution profiling of protein-DNA interactions is a rapidly advancing area.
These techniques offer unprecedented detail into the mechanisms of gene regulation.
Further development holds significant potential for biological discovery.