Genome-wide Mapping of the Nucleosome Landscape by Micrococcal Nuclease and Chemical Mapping

Lilien N. Voong, Liqun Xi, Jiping Wang*, Xiaozhong Wang

*Corresponding author for this work

Research output: Contribution to journalReview article

8 Scopus citations

Abstract

Nucleosomes regulate the transcription output of the genome by occluding the underlying DNA sequences from DNA-binding proteins that must act on it. Knowledge of the precise locations of nucleosomes in the genome is thus essential towards understanding how transcription is regulated. Current nucleosome-mapping strategies involve digesting chromatin with nucleases or chemical cleavage followed by high-throughput sequencing. In this review, we compare the traditional micrococcal nuclease (MNase)-based approach with a chemical cleavage strategy, with discussion on the important insights each has uncovered about the role of nucleosomes in shaping transcriptional processes. Genome-wide nucleosome positioning maps provide deep insight into the regulatory role of nucleosomes in transcriptional processes. Micrococcal nuclease (MNase) digests linker DNA in between nucleosomes while nucleosome-protected DNA remains intact. Sequencing the protected DNA allows for the determination of nucleosome positions genome-wide. The chemical mapping method relies on site-directed hydroxyl radical cleavage of nucleosomes carrying modified histones to determine the positions of nucleosomes in the genome. MNase-defined NDRs of cis regulatory elements are nucleosome enriched in the chemical map of mouse ES cells. Emerging evidence shows that such regions are occupied by ‘fragile nucleosomes’, which are lost due to overdigestion by MNase. Results in mouse ES cells illustrate that fragile nucleosomes exist in the mouse genome and chemical mapping is capable of detecting them.

Original languageEnglish (US)
Pages (from-to)495-507
Number of pages13
JournalTrends in Genetics
Volume33
Issue number8
DOIs
StatePublished - Aug 1 2017

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Keywords

  • MNase
  • chemical mapping
  • chromatin
  • nucleosomes
  • transcriptional regulation

ASJC Scopus subject areas

  • Genetics

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