title: Comparative and functional analyses of LYL1 loci establish marsupial sequences as a model for phylogenetic footprinting.
abstract: Comparative genomic sequence analysis is a powerful technique for identifying regulatory regions in genomic DNA. However, its utility largely depends on the evolutionary distances between the species involved. Here we describe the screening of a genomic BAC library from the stripe-faced dunnart, Sminthopsis macroura, formerly known as the narrow-footed marsupial mouse. We isolated a clone containing the LYL1 locus, completely sequenced the 60.6-kb insert, and compared it with orthologous human and mouse sequences. Noncoding homology was substantially reduced in the human/dunnart analysis compared with human/mouse, yet we could readily identify all promoters and exons. Human/mouse/dunnart alignments of the LYL1 candidate promoter allowed us to identify putative transcription factor binding sites, revealing a pattern highly reminiscent of critical regulatory regions of the LYL1 paralogue, SCL. This newly identified LYL1 promoter showed strong activity in myeloid progenitor cells and was bound in vivo by Fli1, Elf1, and Gata2-transcription factors all previously shown to bind to the SCL stem cell enhancer. This study represents the first large-scale comparative analysis involving marsupial genomic sequence and demonstrates that such comparisons provide a powerful approach to characterizing mammalian regulatory elements.
authors.affiliation: Department of Haematology, Cambridge Institute for Medical Research, Cambridge University, Hills Road, Cambridge CB2 2XY, UK.
authors.forename: Michael A
authors.initials: MA
authors.lastname: Chapman
authors.forename: Fadi J
authors.initials: FJ
authors.lastname: Charchar
authors.forename: Sarah
authors.initials: S
authors.lastname: Kinston
authors.forename: Christine P
authors.initials: CP
authors.lastname: Bird
authors.forename: Darren
authors.initials: D
authors.lastname: Grafham
authors.forename: Jane
authors.initials: J
authors.lastname: Rogers
authors.forename: Frank
authors.initials: F
authors.lastname: Grützner
authors.forename: Jennifer A Marshall
authors.initials: JA
authors.lastname: Graves
authors.forename: Anthony R
authors.initials: AR
authors.lastname: Green
authors.forename: Berthold
authors.initials: B
authors.lastname: Göttgens
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D051792:Basic Helix-Loop-Helix Proteins; D002874:Chromosome Mapping; D004247:DNA; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000235:genetics*; D008394:Marsupialia / Q000235:genetics*; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009363:Neoplasm Proteins / Q000737:chemistry / Q000235:genetics*; D010802:Phylogeny; D011401:Promoter Regions, Genetic; D017386:Sequence Homology, Amino Acid; D012689:Sequence Homology, Nucleic Acid
chemical_list: D051792:Basic Helix-Loop-Helix Proteins; D004247:DNA; D004268:DNA-Binding Proteins; D009363:Neoplasm Proteins; C490130:Lyl1 protein, mouse