Identifying gene regulatory elements by genomic microarray mapping of DNaseI hypersensitive sites.

@article{citeulike:878424, abstract = {The identification of cis-regulatory elements is central to understanding gene transcription. Hypersensitivity of cis-regulatory elements to digestion with DNaseI remains the gold-standard approach to locating such elements. Traditional methods used to identify DNaseI hypersensitive sites are cumbersome and can only be applied to short stretches of DNA at defined locations. Here we report the development of a novel genomic array-based approach to DNaseI hypersensitive site mapping (ADHM) that permits precise, large-scale identification of such sites from as few as 5 million cells. Using ADHM we identified all previously recognized hematopoietic regulatory elements across 200 kb of the mouse T-cell acute lymphocytic leukemia-1 (Tal1) locus, and, in addition, identified two novel elements within the locus, which show transcriptional regulatory activity. We further validated the ADHM protocol by mapping the DNaseI hypersensitive sites across 250 kb of the human TAL1 locus in CD34(+) primary stem/progenitor cells and K562 cells and by mapping the previously known DNaseI hypersensitive sites across 240 kb of the human alpha-globin locus in K562 cells. ADHM provides a powerful approach to identifying DNaseI hypersensitive sites across large genomic regions.}, address = {Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 2XY, United Kingdom;}, author = {Follows, George A A. and Dhami, Pawan and G\"{o}ttgens, Berthold and Bruce, Alexander W W. and Campbell, Peter J J. and Dillon, Shane C C. and Smith, Aileen M M. and Koch, Christoph and Donaldson, Ian J J. and Scott, Mike A A. and Dunham, Ian and Janes, Mary E E. and Vetrie, David and Green, Anthony R R. }, citeulike-article-id = {878424}, doi = {10.1101/gr.5373606}, issn = {1088-9051}, journal = {Genome Res}, keywords = {array, dnasei, hypersensitive, prediction}, month = {September}, posted-at = {2006-09-30 00:26:22}, priority = {2}, title = {Identifying gene regulatory elements by genomic microarray mapping of DNaseI hypersensitive sites.}, url = {http://dx.doi.org/10.1101/gr.5373606}, year = {2006} }

TY - JOUR ID - citeulike:878424 L3 - citeulike-article-id:878424 TI - Identifying gene regulatory elements by genomic microarray mapping of DNaseI hypersensitive sites. JF - Genome Res AD - Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 2XY, United Kingdom; SN - 1088-9051 N2 - The identification of cis-regulatory elements is central to understanding gene transcription. Hypersensitivity of cis-regulatory elements to digestion with DNaseI remains the gold-standard approach to locating such elements. Traditional methods used to identify DNaseI hypersensitive sites are cumbersome and can only be applied to short stretches of DNA at defined locations. Here we report the development of a novel genomic array-based approach to DNaseI hypersensitive site mapping (ADHM) that permits precise, large-scale identification of such sites from as few as 5 million cells. Using ADHM we identified all previously recognized hematopoietic regulatory elements across 200 kb of the mouse T-cell acute lymphocytic leukemia-1 (Tal1) locus, and, in addition, identified two novel elements within the locus, which show transcriptional regulatory activity. We further validated the ADHM protocol by mapping the DNaseI hypersensitive sites across 250 kb of the human TAL1 locus in CD34(+) primary stem/progenitor cells and K562 cells and by mapping the previously known DNaseI hypersensitive sites across 240 kb of the human alpha-globin locus in K562 cells. ADHM provides a powerful approach to identifying DNaseI hypersensitive sites across large genomic regions. KW - array KW - dnasei KW - hypersensitive KW - prediction AU - Follows, George A AU - Dhami, Pawan AU - Göttgens, Berthold AU - Bruce, Alexander W AU - Campbell, Peter J AU - Dillon, Shane C AU - Smith, Aileen M AU - Koch, Christoph AU - Donaldson, Ian J AU - Scott, Mike A AU - Dunham, Ian AU - Janes, Mary E AU - Vetrie, David AU - Green, Anthony R PY - 2006/09/08/ UR - http://dx.doi.org/10.1101/gr.5373606 ER -