MPE-seq, a new method for the genome-wide analysis of chromatin structure

Proc Natl Acad Sci U S A. 2015 Jul 7;112(27):E3457-65. doi: 10.1073/pnas.1424804112. Epub 2015 Jun 15.


The analysis of chromatin structure is essential for the understanding of transcriptional regulation in eukaryotes. Here we describe methidiumpropyl-EDTA sequencing (MPE-seq), a method for the genome-wide characterization of chromatin that involves the digestion of nuclei withMPE-Fe(II) followed by massively parallel sequencing. Like micrococcal nuclease (MNase), MPE-Fe(II) preferentially cleaves the linker DNA between nucleosomes. However, there are differences in the cleavage of nuclear chromatin by MPE-Fe(II) relative to MNase. Most notably, immediately upstream of the transcription start site of active promoters, we frequently observed nucleosome-sized (141-190 bp) and subnucleosome-sized (such as 101-140 bp) peaks of digested chromatin fragments with MPE-seq but not with MNase-seq. These peaks also correlate with the presence of core histones and could thus be due, at least in part, to noncanonical chromatin structures such as labile nucleosome-like particles that have been observed in other contexts. The subnucleosome-sized MPE-seq peaks exhibit a particularly distinct association with active promoters. In addition, unlike MNase, MPE-Fe(II) cleaves nuclear DNA with little sequence bias. In this regard, we found that DNA sequences at RNA splice sites are hypersensitive to digestion by MNase but not by MPE-Fe(II). This phenomenon may have affected the analysis of nucleosome occupancy over exons. These findings collectively indicate that MPE-seq provides a unique and straightforward means for the genome-wide analysis of chromatin structure with minimal DNA sequence bias. In particular, the combined use of MPE-seq and MNase-seq enables the identification of noncanonical chromatin structures that are likely to be important for the regulation of gene expression.

Keywords: MPE-Fe(II); chromatin; genome-wide analysis; micrococcal nuclease; promoter.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Sequence
  • Cell Nucleus / genetics
  • Cell Nucleus / metabolism
  • Cells, Cultured
  • Chromatin / genetics*
  • Chromatin / metabolism
  • DNA / chemistry
  • DNA / genetics
  • DNA / metabolism
  • Edetic Acid / analogs & derivatives*
  • Edetic Acid / metabolism
  • Electrophoresis, Agar Gel
  • Embryonic Stem Cells / metabolism
  • Exons / genetics
  • Genome / genetics*
  • Introns / genetics
  • Mice
  • Nucleosomes / genetics
  • Nucleosomes / metabolism
  • Promoter Regions, Genetic / genetics
  • Reproducibility of Results
  • Sequence Analysis, DNA / methods*


  • Chromatin
  • Nucleosomes
  • methidiumpropyl-EDTA-iron(II)
  • DNA
  • Edetic Acid

Associated data

  • GEO/GSE69098