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Related Experiment Video

Updated: Jul 12, 2025

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis

Published on: December 12, 2017

SEM: sized-based expectation maximization for characterizing nucleosome positions and subtypes.

Jianyu Yang¹, Kuangyu Yen^2,3, Shaun Mahony¹

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

Biorxiv : the Preprint Server for Biology

|October 31, 2023

Summary

This summary is machine-generated.

A new tool, Size-based Expectation Maximization (SEM), identifies diverse nucleosome types from MNase-seq data. SEM reveals short-fragment nucleosomes in regulatory regions, aiding the study of atypical nucleosomes and their functions.

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Last Updated: Jul 12, 2025

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis

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Area of Science:

* Molecular Biology
* Genomics
* Epigenetics

Background:

* Nucleosome profiling commonly uses MNase-seq, assuming uniform 147bp DNA protection.
* Existing analysis tools overlook shorter DNA fragments, potentially missing regulatory roles of atypical nucleosomes.
* Variation in nucleosome DNA protection length is linked to histone composition and chemical modifications.

Approach:

* Introduced Size-based Expectation Maximization (SEM), a novel package for nucleosome analysis.
* SEM utilizes a hierarchical Gaussian mixture model to identify nucleosome positions and subtypes.
* Nucleosome subtypes are automatically classified based on protected DNA fragment length distributions.

Key Points:

* SEM achieves comparable accuracy to existing packages while uniquely identifying nucleosome subtypes.
* Analysis of mouse embryonic stem cell data revealed three nucleosome types: short-fragment, canonical, and di-nucleosomes.
* Short-fragment nucleosomes in accessible regions, termed 'fragile nucleosomes', associate with regulatory elements and chromatin remodelers.

Conclusions:

* SEM effectively distinguishes diverse nucleosome subtypes from MNase-seq data.
* This capability enables deeper investigation into the functional roles of non-standard nucleosomes.
* The findings highlight the importance of considering nucleosome heterogeneity in genomic studies.