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Related Concept Videos

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Nucleosome Remodeling

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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.
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Related Experiment Video

Updated: Feb 17, 2026

Methyl-binding DNA capture Sequencing for Patient Tissues
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Nucleosome Occupancy and Methylome Sequencing (NOMe-seq).

Fides D Lay1,2,3, Theresa K Kelly4, Peter A Jones5,6

  • 1Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.

Methods in Molecular Biology (Clifton, N.J.)
|December 11, 2017
PubMed
Summary

Nucleosome Occupancy and Methylome sequencing (NOMe-seq) directly measures DNA methylation and chromatin accessibility. This method provides insights into how these epigenetic factors interact to regulate cellular transcription programs.

Keywords:
Bisulfite sequencingChromatin accessibilityDNA methylationGenome-wideM.CviPINucleosome occupancy

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Area of Science:

  • Epigenetics
  • Molecular Biology
  • Genomics

Background:

  • Understanding epigenetic mechanisms like DNA methylation and nucleosome occupancy is crucial for deciphering gene regulation.
  • Interactions between epigenetic components are key to comprehending cellular transcription programs in health and disease.

Purpose of the Study:

  • To introduce and detail the Nucleosome Occupancy and Methylome sequencing (NOMe-seq) assay.
  • To highlight NOMe-seq's capability in directly measuring the interplay between DNA methylation and nucleosome occupancy.

Main Methods:

  • NOMe-seq utilizes the methyltransferase M.CviPI to footprint accessible DNA regions.
  • The assay generates dual DNA methylation and nucleosome occupancy data at single-DNA resolution.
  • Data can be analyzed via DNA sequencing of cloned PCR products or integrated with next-generation sequencing for genome-wide analysis.

Main Results:

  • NOMe-seq provides direct measurement of DNA methylation and nucleosome occupancy.
  • The assay requires minimal cell input (200,000 cells) and has a short reaction time (15 minutes).
  • Enables locus-specific or genome-wide correlation analysis of epigenetic components.

Conclusions:

  • NOMe-seq is an effective method for studying the relationship between DNA methylation and nucleosome occupancy.
  • This assay facilitates a comprehensive understanding of how these epigenetic marks jointly regulate transcription.
  • NOMe-seq offers a versatile approach for epigenetic research in both normal and disease states.