Dynamic Regulation of Nucleosome Positioning in the Human Genome

Dustin E. Schones, Kairong Cui, Suresh Cuddapah, Tae Young Roh, Artem Barski, Zhibin Wang, Gang Wei, Keji Zhao

Research output: Contribution to journalArticlepeer-review

1067 Scopus citations


The positioning of nucleosomes with respect to DNA plays an important role in regulating transcription. However, nucleosome mapping has been performed for only limited genomic regions in humans. We have generated genome-wide maps of nucleosome positions in both resting and activated human CD4+ T cells by direct sequencing of nucleosome ends using the Solexa high-throughput sequencing technique. We find that nucleosome phasing relative to the transcription start sites is directly correlated to RNA polymerase II (Pol II) binding. Furthermore, the first nucleosome downstream of a start site exhibits differential positioning in active and silent genes. TCR signaling induces extensive nucleosome reorganization in promoters and enhancers to allow transcriptional activation or repression. Our results suggest that H2A.Z-containing and modified nucleosomes are preferentially lost from the -1 nucleosome position. Our data provide a comprehensive view of the nucleosome landscape and its dynamic regulation in the human genome.

Original languageEnglish
Pages (from-to)887-898
Number of pages12
Issue number5
StatePublished - 7 Mar 2008


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