title: Identifying gene regulatory elements by genomic microarray mapping of DNaseI hypersensitive sites.
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.
authors.affiliation: Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 2XY, United Kingdom. gf246@cam.ac.uk
authors.forename: George A
authors.initials: GA
authors.lastname: Follows
authors.forename: Pawan
authors.initials: P
authors.lastname: Dhami
authors.forename: Berthold
authors.initials: B
authors.lastname: Göttgens
authors.forename: Alexander W
authors.initials: AW
authors.lastname: Bruce
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Campbell
authors.forename: Shane C
authors.initials: SC
authors.lastname: Dillon
authors.forename: Aileen M
authors.initials: AM
authors.lastname: Smith
authors.forename: Christoph
authors.initials: C
authors.lastname: Koch
authors.forename: Ian J
authors.initials: IJ
authors.lastname: Donaldson
authors.forename: Mike A
authors.initials: MA
authors.lastname: Scott
authors.forename: Ian
authors.initials: I
authors.lastname: Dunham
authors.forename: Mary E
authors.initials: ME
authors.lastname: Janes
authors.forename: David
authors.initials: D
authors.lastname: Vetrie
authors.forename: Anthony R
authors.initials: AR
authors.lastname: Green
mesh_terms: D000465:Algorithms; D000818:Animals; D051792:Basic Helix-Loop-Helix Proteins / Q000235:genetics; D003850:Deoxyribonuclease I / Q000378:metabolism*; D005069:Evaluation Studies as Topic; D023281:Genomics / Q000379:methods*; D006801:Humans; D051379:Mice; D046228:Microarray Analysis / Q000379:methods*; D011518:Proto-Oncogene Proteins / Q000235:genetics; D050436:Regulatory Elements, Transcriptional / Q000235:genetics*; D015183:Restriction Mapping / Q000379:methods*; D000073942:T-Cell Acute Lymphocytic Leukemia Protein 1; D044767:Ubiquitin-Protein Ligases / Q000235:genetics
chemical_list: D051792:Basic Helix-Loop-Helix Proteins; D003850:Deoxyribonuclease I; D011518:Proto-Oncogene Proteins; D000073942:T-Cell Acute Lymphocytic Leukemia Protein 1; D044767:Ubiquitin-Protein Ligases; C489366:Tal1 protein, mouse; C489657:LRSAM1 protein, human