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Updated: May 28, 2026

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Published on: February 24, 2015

Epigenome characterization at single base-pair resolution.

Jorja G Henikoff¹, Jason A Belsky, Kristina Krassovsky

¹Basic Sciences Division, The Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.

Proceedings of the National Academy of Sciences of the United States of America

|October 26, 2011

Summary

This summary is machine-generated.

This study maps nucleosomes and DNA-binding proteins in yeast using a novel sequencing method. The technique reveals dynamic chromatin structures and precisely defines transcription factor binding sites.

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Last Updated: May 28, 2026

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Published on: February 24, 2015

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The ChIP-exo Method: Identifying Protein-DNA Interactions with Near Base Pair Precision

The ChIP-exo Method: Identifying Protein-DNA Interactions with Near Base Pair Precision

Published on: December 23, 2016

Area of Science:

Molecular Biology
Genomics
Epigenetics

Background:

Nucleosomes and subnucleosome-sized particles play crucial roles in genome regulation.
Understanding their precise location and dynamics is essential for deciphering gene expression.
Current methods have limitations in single-base-pair resolution and dynamic profiling.

Purpose of the Study:

To develop a high-resolution method for mapping nucleosomes and subnucleosome particles.
To characterize the DNA-binding features and genomic organization of transcription factors.
To provide a general strategy for epigenome characterization.

Main Methods:

Combined micrococcal nuclease (MNase) digestion with modified paired-end DNA sequencing library construction.
Analyzed fragment length versus genomic position to define protected regions.
Varied MNase digestion time to observe dynamic changes in chromatin structure.

Main Results:

Achieved single base-pair resolution mapping of nucleosomes and subnucleosome particles across the yeast genome.
Observed co-occurrence of partially unwrapped nucleosomes and subnucleosome particles, indicating dynamic behavior.
Precisely mapped transcription factor binding sites and flanking nucleosome phasing.

Conclusions:

The developed protocol enables detailed epigenome characterization from a single sample.
Provides insights into nucleosome dynamics, phasing, and transcription factor interactions.
Offers a powerful tool for studying chromatin remodeling and gene regulation.