High-throughput mapping of the chromatin structure of human promoters

Nat Biotechnol. 2007 Feb;25(2):244-8. doi: 10.1038/nbt1279. Epub 2007 Jan 14.


Our understanding of how chromatin structure influences cellular processes such as transcription and replication has been limited by a lack of nucleosome-positioning data in human cells. We describe a high-resolution microarray approach combined with an analysis algorithm to examine nucleosome positioning in 3,692 promoters within seven human cell lines. Unlike unexpressed genes without transcription-preinitiation complexes at their promoters, expressed genes or genes containing preinitiation complexes exhibit characteristic nucleosome-free regions at their transcription start sites. The combination of these nucleosome data with chromatin immunoprecipitation-chip analyses reveals that the melanocyte master regulator microphthalmia-associated transcription factor (MITF) predominantly binds nucleosome-free regions, supporting the model that nucleosomes limit sequence accessibility. This study presents a global view of human nucleosome positioning and provides a high-throughput tool for analyzing chromatin structure in development and disease.

Publication types

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

MeSH terms

  • Algorithms*
  • Base Sequence
  • Chromosome Mapping / methods*
  • Genome, Human / genetics*
  • Humans
  • Molecular Sequence Data
  • Nucleosomes / genetics*
  • Oligonucleotide Array Sequence Analysis / methods*
  • Promoter Regions, Genetic / genetics*
  • Sequence Analysis, DNA / methods*


  • Nucleosomes

Associated data

  • GEO/GSE6385