title: Identifying putative promoter regions of Hermansky-Pudlak syndrome genes by means of phylogenetic footprinting.
abstract: HPS is an autosomal recessive disorder characterized by oculocutaneous albinism and prolonged bleeding. Eight human genes are described resulting in the HPS subtypes 1-8. Certain HPS proteins combine to form Biogenesis of Lysosome-related Organelles Complexes (BLOCs), thought to function in the formation of intracellular vesicles such as melanosomes, platelet dense bodies, and lytic granules. Specifically, BLOC-2 contains the HPS3, HPS5 and HPS6 proteins. We used phylogenetic footprinting to identify conserved regions in the upstream sequences of HPS3, HPS5 and HPS6. These conserved regions were verified to have in vitro transcription activation activity using luciferase reporter assays. Transcription factor binding site analyses of the regions identified 52 putative sites shared by all three genes. When analysis was limited to the conserved footprints, seven binding sites were found shared among all three genes: Pax-5, AIRE, CACD, ZF5, Zic1, E2F and Churchill. The HPS3 conserved upstream region was sequenced in four patients with decreased fibroblast HPS3 RNA levels and only one HPS3 mutation in the coding exons and surrounding exon/intron boundaries; no mutation was found. These findings illustrate the power of phylogenetic footprinting for identifying potential regulatory regions in non-coding sequences and define the first putative promoter elements for any HPS genes.
authors.affiliation: Section on Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Horia
authors.initials: H
authors.lastname: Stanescu
authors.forename: Tyra G
authors.initials: TG
authors.lastname: Wolfsberg
authors.forename: R Travis
authors.initials: RT
authors.lastname: Moreland
authors.forename: Mariam H
authors.initials: MH
authors.lastname: Ayub
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Erickson
authors.forename: Wendy
authors.initials: W
authors.lastname: Westbroek
authors.forename: Marjan
authors.initials: M
authors.lastname: Huizing
authors.forename: William A
authors.initials: WA
authors.lastname: Gahl
authors.forename: Amanda
authors.initials: A
authors.lastname: Helip-Wooley
mesh_terms: D002352:Carrier Proteins / Q000235:genetics*; D018983:DNA Footprinting; D017930:Genes, Reporter; D022861:Hermanski-Pudlak Syndrome / Q000235:genetics*; D006801:Humans; D047908:Intracellular Signaling Peptides and Proteins / Q000235:genetics*; D011401:Promoter Regions, Genetic
chemical_list: D002352:Carrier Proteins; C432680:HPS3 protein, human; C493900:HPS5 protein, human; C493901:HPS6 protein, human; D047908:Intracellular Signaling Peptides and Proteins