Global Survey of Chromatin Accessibility Using DNA Microarrays (original) (raw)

  1. M. Ryan Weil1,4,5,6,9,
  2. Piotr Widlak2,8,
  3. John D. Minna3,5,7, and
  4. Harold R. Garner1,4,5,6
  5. 1 Program in Molecular Biophysics, Division of Cell and Molecular Biology, Southwestern Graduate School of Biomedical Science, UT Southwestern Medical Center, Dallas, Texas 75390, USA
  6. 2 Department of Molecular Biology, UT Southwestern Medical Center, Dallas, Texas 75390, USA
  7. 3 Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, Texas 75390, USA
  8. 4 Center for Biomedical Inventions, UT Southwestern Medical Center, Dallas, Texas 75390, USA
  9. 5 Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas 75390, USA
  10. 6 Eugene McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, Texas 75390, USA
  11. 7 Department of Pharmacology, UT Southwestern Medical Center, Dallas, Texas 75390, USA
  12. 8 Department of Experimental and Clinical Radiobiology, Center of Oncology, Gliwice, 44-100, Poland

Abstract

An increasing number of studies indicate a central role for chromatin remodeling in the regulation of gene expression. Current methods for high-resolution studies of the relationship between chromatin accessibility and transcription are low throughput, making a genome-wide study impractical. To enable the simultaneous measurement of the global chromatin accessibility state at the resolution of single genes, we developed the Chromatin Array technique, in which chromatin is separated by its condensation state using either the solubility differences of mono- and oligonucleosomes in specific buffers or controlled DNase I digestion and selection of the large refractory (condensed) DNA fragments. By probing with a comparative genomic hybridization style microarray, we can determine the condensation state of thousands of individual loci and correlate this with transcriptional activity. Applying this technique to the breast tumor model cell line, MCF7, we found that when the condensation is homogeneous in the population of cells, expression is inversely proportional to the level of accessibility and the two methods of accessibility-based target selection correlate well. Using functional annotation and comparative genomic hybridization data, we have begun to decipher the possible biological implications of the relationship between chromatin accessibility and expression.

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