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Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis
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Profiling Nucleosome Occupancy by MNase-seq: Experimental Protocol and Computational Analysis.

Alice Pajoro1, Jose M Muiño2, Gerco C Angenent3,4

  • 1Laboratory of Molecular Biology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands. alice.pajoro@gmail.com.

Methods in Molecular Biology (Clifton, N.J.)
|October 21, 2017
PubMed
Summary
This summary is machine-generated.

Profiling in vivo nucleosome locations is crucial for understanding gene regulation. Micrococcal nuclease sequencing (MNase-seq) precisely maps genome-wide nucleosome occupancy by sequencing DNA protected from MNase digestion.

Keywords:
ChromatinMNase digestionMNase-seqNext-generation sequencingNucleosome occupancy

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Area of Science:

  • Molecular Biology
  • Genomics
  • Epigenetics

Background:

  • Nucleosomes are fundamental units of eukaryotic chromatin, essential for DNA packaging.
  • Nucleosome positioning significantly influences gene expression and chromatin accessibility.
  • Accurate mapping of nucleosome locations in vivo is vital for functional genomics studies.

Purpose of the Study:

  • To present a method for genome-wide profiling of nucleosome occupancy.
  • To demonstrate the utility of micrococcal nuclease sequencing (MNase-seq) for precise nucleosome localization.

Main Methods:

  • Utilizing micrococcal nuclease (MNase) digestion to selectively digest DNA.
  • Employing high-throughput Illumina sequencing to analyze protected DNA fragments.
  • Combining MNase digestion with sequencing for genome-wide nucleosome mapping (MNase-seq).

Main Results:

  • Nucleosome-associated DNA exhibits resistance to MNase digestion.
  • Mild MNase treatment allows for purification of nucleosome-protected DNA.
  • Sequencing these protected fragments enables precise, genome-wide localization of in vivo nucleosomes.

Conclusions:

  • MNase-seq is an effective technique for high-resolution mapping of nucleosome positions.
  • This method provides insights into chromatin structure and its role in gene regulation.
  • Genome-wide nucleosome occupancy profiling is essential for understanding eukaryotic gene expression.