Protocol

Chromatin Remodeling

Volume 833 of the series Methods in Molecular Biology pp 413-419

Date:

Genome-Wide Approaches to Determining Nucleosome Occupancy in Metazoans Using MNase-Seq

  • Kairong CuiAffiliated withLaboratory of Molecular Immunology, National Heart, Lung and Blood Institute, National Institutes of Health
  • , Keji ZhaoAffiliated withLaboratory of Molecular Immunology, National Heart, Lung and Blood Institute, National Institutes of Health Email author 

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Abstract

The precise location of nucleosomes in functional regulatory regions in chromatin is critical to the regulation of transcription. The nucleosome structure protects DNA from microccocal nuclease (MNase) digestion and leaves a footprint on DNA that indicates the position of nucleosomes. Short sequence reads (25–36 bp) from ends of mononucleosome-sized DNA generated from MNase digestion of chromatin can be determined using next-generation sequencing techniques. Mapping of these short reads to the genome provides a powerful genome-wide approach to precisely define the nucleosome positions in any genome with known genomic sequence. This chapter outlines the reagents and experimental procedures of MNase-Seq for mapping nucleosome positions in the human genome.

Key words

Nucleosome mapping MNase-Seq Chromatin structure