Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays

Localized accessibility of critical DNA sequences to the regulatory machinery is a key requirement for regulation of human genes. Here we describe a high-resolution, genome-scale approach for quantifying chromatin accessibility by measuring DNase I sensitivity as a continuous function of genome position using tiling DNA microarrays (DNase-array). We demonstrate this approach across 1% (∼30 Mb) of the human genome, wherein we localized 2,690 classical DNase I hypersensitive sites with high sensitivity and specificity, and also mapped larger-scale patterns of chromatin architecture. DNase I hypersensitive sites exhibit marked aggregation around transcriptional start sites (TSSs), though the majority mark nonpromoter functional elements. We also developed a computational approach for visualizing higher-order features of chromatin structure. This revealed that human chromatin organization is dominated by large (100–500 kb) 'superclusters' of DNase I hypersensitive sites, which encompass both gene-rich and gene-poor regions. DNase-array is a powerful and straightforward approach for systematic exposition of the cis-regulatory architecture of complex genomes.

[1]  M. Groudine,et al.  Chromosomal subunits in active genes have an altered conformation. , 1976, Science.

[2]  Carl Wu.  The 5′ ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I , 1980, Nature.

[3]  J. D. Engel,et al.  A 200 base pair region at the 5′ end of the chicken adult β-globin gene is accessible to nuclease digestion , 1981, Cell.

[4]  S. Elgin,et al.  DNase I hypersensitive sites in Drosophila chromatin occur at the 5' ends of regions of transcription. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[5]  D. S. Gross,et al.  Nuclease hypersensitive sites in chromatin. , 1988, Annual review of biochemistry.

[6]  S. Elgin,et al.  The formation and function of DNase I hypersensitive sites in the process of gene activation. , 1988, The Journal of biological chemistry.

[7]  G. Felsenfeld,et al.  Chromatin as an essential part of the transcriptional mechanim , 1992, Nature.

[8]  C. Disteche,et al.  Down syndrome phenotypes: the consequences of chromosomal imbalance. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[9]  John J. Wyrick,et al.  Genome-wide location and function of DNA binding proteins. , 2000, Science.

[10]  W. Miller,et al.  Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. , 2000, Science.

[11]  G. Stamatoyannopoulos,et al.  Quantification of DNaseI-sensitivity by real-time PCR: quantitative analysis of DNaseI-hypersensitivity of the mouse beta-globin LCR. , 2001, Journal of molecular biology.

[12]  Todd R. Ogden,et al.  Wavelet Methods for Time Series Analysis , 2002 .

[13]  M. Groudine,et al.  Controlling the double helix , 2003, Nature.

[14]  J. T. Kadonaga,et al.  The RNA polymerase II core promoter. , 2003, Annual review of biochemistry.

[15]  Xiangdong Fang,et al.  Locus control regions. , 2002, Blood.

[16]  Erez Y. Levanon,et al.  Widespread occurrence of antisense transcription in the human genome , 2003, Nature Biotechnology.

[17]  R. Flavell,et al.  Regulation of the Th2 cytokine locus by a locus control region. , 2003, Immunity.

[18]  S. Cawley,et al.  Unbiased Mapping of Transcription Factor Binding Sites along Human Chromosomes 21 and 22 Points to Widespread Regulation of Noncoding RNAs , 2004, Cell.

[19]  J. Stamatoyannopoulos,et al.  High-throughput localization of functional elements by quantitative chromatin profiling , 2004, Nature Methods.

[20]  F. Alt,et al.  Deletion of a conserved Il4 silencer impairs T helper type 1–mediated immunity , 2004, Nature Immunology.

[21]  Paul T. Groth,et al.  The ENCODE (ENCyclopedia Of DNA Elements) Project , 2004, Science.

[22]  J. Stamatoyannopoulos,et al.  Genome-wide identification of DNaseI hypersensitive sites using active chromatin sequence libraries. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[23]  R. Ghirlando,et al.  Chromatin boundaries and chromatin domains. , 2004, Cold Spring Harbor symposia on quantitative biology.

[24]  J. Stamatoyannopoulos,et al.  Discovery of functional noncoding elements by digital analysis of chromatin structure. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[25]  R. Flavell,et al.  Hypersensitive site 7 of the TH2 locus control region is essential for expressing TH2 cytokine genes and for long-range intrachromosomal interactions , 2005, Nature Immunology.

[26]  Peter Fraser,et al.  Remote control of gene transcription. , 2005, Human molecular genetics.

[27]  S. Batalov,et al.  Antisense Transcription in the Mammalian Transcriptome , 2005, Science.

[28]  Nick Gilbert,et al.  The role of chromatin structure in regulating the expression of clustered genes , 2005, Nature Reviews Genetics.

[29]  Terrence S. Furey,et al.  The UCSC Genome Browser Database: update 2006 , 2005, Nucleic Acids Res..

[30]  David Haussler,et al.  The UCSC genome browser database: update 2007 , 2006, Nucleic Acids Res..