High-throughput mapping of the chromatin structure of human promoters.
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.
Ozsolak
Fatih
F
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.
Song
Jun S
JS
Liu
X Shirley
XS
Fisher
David E
DE
D000465:Algorithms; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D009707:Nucleosomes / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011401:Promoter Regions, Genetic / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*
D009707:Nucleosomes