Global survey of chromatin accessibility using DNA microarrays

M. Ryan Weil, Piotr Widlak, John D. Minna, Harold R. Garner

Research output: Contribution to journalArticle

24 Citations (Scopus)

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 1 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.

Original languageEnglish (US)
Pages (from-to)1374-1381
Number of pages8
JournalGenome Research
Volume14
Issue number7
DOIs
StatePublished - Jul 2004

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Oligonucleotide Array Sequence Analysis
Chromatin
Comparative Genomic Hybridization
Chromatin Assembly and Disassembly
Deoxyribonucleases
Gene Expression Regulation
Tumor Cell Line
Solubility
Digestion
Buffers
Surveys and Questionnaires
Genome
Breast Neoplasms
DNA
Population
Genes

ASJC Scopus subject areas

  • Genetics

Cite this

Global survey of chromatin accessibility using DNA microarrays. / Weil, M. Ryan; Widlak, Piotr; Minna, John D.; Garner, Harold R.

In: Genome Research, Vol. 14, No. 7, 07.2004, p. 1374-1381.

Research output: Contribution to journalArticle

Weil, M. Ryan ; Widlak, Piotr ; Minna, John D. ; Garner, Harold R. / Global survey of chromatin accessibility using DNA microarrays. In: Genome Research. 2004 ; Vol. 14, No. 7. pp. 1374-1381.
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