High-Resolution Mapping and Characterization of Open Chromatin across the Genome.

@article{boyle08dnaseI, abstract = {Mapping DNase I hypersensitive (HS) sites is an accurate method of identifying the location of genetic regulatory elements, including promoters, enhancers, silencers, insulators, and locus control regions. We employed high-throughput sequencing and whole-genome tiled array strategies to identify DNase I HS sites within human primary CD4(+) T cells. Combining these two technologies, we have created a comprehensive and accurate genome-wide open chromatin map. Surprisingly, only 16\%-21\% of the identified 94,925 DNase I HS sites are found in promoters or first exons of known genes, but nearly half of the most open sites are in these regions. In conjunction with expression, motif, and chromatin immunoprecipitation data, we find evidence of cell-type-specific characteristics, including the ability to identify transcription start sites and locations of different chromatin marks utilized in these cells. In addition, and unexpectedly, our analyses have uncovered detailed features of nucleosome structure.}, address = {Institute for Genome Sciences \& Policy, Duke University, Durham, NC 27708, USA.}, author = {Boyle, A. P. and Davis, S. and Shulha, H. P. and Meltzer, P. and Margulies, E. H. and Weng, Z. and Furey, T. S. and Crawford, G. E. }, citeulike-article-id = {2343584}, doi = {http://dx.doi.org/10.1016/j.cell.2007.12.014}, issn = {0092-8674}, journal = {Cell}, keywords = {chromatin, epigenetics, human\_genome}, month = {January}, number = {2}, pages = {311--322}, posted-at = {2008-05-10 14:23:20}, priority = {2}, title = {High-Resolution Mapping and Characterization of Open Chromatin across the Genome.}, url = {http://dx.doi.org/10.1016/j.cell.2007.12.014}, volume = {132}, year = {2008} }

TY - JOUR ID - boyle08dnaseI L3 - citeulike-article-id:2343584 N2 - Mapping DNase I hypersensitive (HS) sites is an accurate method of identifying the location of genetic regulatory elements, including promoters, enhancers, silencers, insulators, and locus control regions. We employed high-throughput sequencing and whole-genome tiled array strategies to identify DNase I HS sites within human primary CD4(+) T cells. Combining these two technologies, we have created a comprehensive and accurate genome-wide open chromatin map. Surprisingly, only 16%-21% of the identified 94,925 DNase I HS sites are found in promoters or first exons of known genes, but nearly half of the most open sites are in these regions. In conjunction with expression, motif, and chromatin immunoprecipitation data, we find evidence of cell-type-specific characteristics, including the ability to identify transcription start sites and locations of different chromatin marks utilized in these cells. In addition, and unexpectedly, our analyses have uncovered detailed features of nucleosome structure. IS - 2 JF - Cell SN - 0092-8674 AD - Institute for Genome Sciences & Policy, Duke University, Durham, NC 27708, USA. EP - 322 TI - High-Resolution Mapping and Characterization of Open Chromatin across the Genome. VL - 132 SP - 311 KW - chromatin KW - epigenetics KW - human_genome AU - Boyle, AP AU - Davis, S AU - Shulha, HP AU - Meltzer, P AU - Margulies, EH AU - Weng, Z AU - Furey, TS AU - Crawford, GE PY - 2008/January/25/ UR - http://dx.doi.org/10.1016/j.cell.2007.12.014 ER -