Letter abstract


Nature Biotechnology 25, 244 - 248 (2007)
Published online: 14 January 2007 | doi:10.1038/nbt1279

High-throughput mapping of the chromatin structure of human promoters

Fatih Ozsolak1,4, Jun S Song2,3,4, X Shirley Liu2,3 & David E Fisher1

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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.

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  1. Melanoma Program in Medical Oncology, and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Children's Hospital Boston, Harvard Medical School, 44 Binney Street, Boston, Massachusetts 02115, USA.
  2. Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, Massachusetts 02115, USA.
  3. Harvard School of Public Health, 677 Huntington Avenue, Boston, Massachusetts 02115, USA.
  4. These authors contributed equally to this work.

Correspondence to: David E Fisher1 e-mail: david_fisher@dfci.harvard.edu

Correspondence to: X Shirley Liu2,3 e-mail: xsliu@jimmy.harvard.edu

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