Nucleosome positioning in human HOX gene clusters

  1. Peter V. Kharchenko1,2,4,
  2. Caroline J. Woo3,4,
  3. Michael Y. Tolstorukov1,
  4. Robert E. Kingston3,5, and
  5. Peter J. Park1,2,5
  1. 1 Harvard Partners Center for Genetics and Genomics, Boston, Massachusetts 02115, USA;
  2. 2 Children’s Hospital Informatics Program, Boston, Massachusetts 02115, USA;
  3. 3 Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
  1. 4 These authors contributed equally to this work.

Abstract

The distribution of nucleosomes along the genome is a significant aspect of chromatin structure and is thought to influence gene regulation through modulation of DNA accessibility. However, properties of nucleosome organization remain poorly understood, particularly in mammalian genomes. Toward this goal we used tiled microarrays to identify stable nucleosome positions along the HOX gene clusters in human cell lines. We show that nucleosome positions exhibit sequence properties and long-range organization that are different from those characterized in other organisms. Despite overall variability of internucleosome distances, specific loci contain regular nucleosomal arrays with 195-bp periodicity. Moreover, such arrays tend to occur preferentially toward the 3′ ends of genes. Through comparison of different cell lines, we find that active transcription is correlated with increased positioning of nucleosomes, suggesting an unexpected role for transcription in the establishment of well-positioned nucleosomes.

Footnotes

  • 5 Corresponding authors.

    5 E-mail peter_park{at}harvard.edu; fax (617) 525-4488.

    5 E-mail kingston{at}molbio.mgh.harvard.edu; fax (617) 643-2119.

  • [Supplemental material is available online at www.genome.org. The sequence data from this study have been submitted to GEO under accession no. GSE10042.]

  • Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.075952.107.

    • Received December 29, 2007.
    • Accepted June 24, 2008.
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