title: Comprehensive analysis of transcript start sites in ly49 genes reveals an unexpected relationship with gene function and a lack of upstream promoters.
abstract: Comprehensive analysis of the transcription start sites of the Ly49 genes of C57BL/6 mice using the oligo-capping 5'-RACE technique revealed that the genes encoding the "missing self" inhibitory receptors, Ly49A, C, G, and I, were transcribed from multiple broad regions in exon 1, in the intron1/exon2 region, and upstream of exon -1b. Ly49E was also transcribed in this manner, and uniquely showed a transcriptional shift from exon1 to exon 2 when NK cells were activated in vitro with IL2. Remarkably, a large proportion of Ly49E transcripts was then initiated from downstream of the translational start codon. By contrast, the genes encoding Ly49B and Q in myeloid cells, the activating Ly49D and H receptors in NK cells, and Ly49F in activated T cells, were predominantly transcribed from a conserved site in a pyrimidine-rich region upstream of exon 1. An ∼200 bp fragment from upstream of the Ly49B start site displayed tissue-specific promoter activity in dendritic cell lines, but the corresponding upstream fragments from all other Ly49 genes lacked detectable tissue-specific promoter activity. In particular, none displayed any significant activity in a newly developed adult NK cell line that expressed multiple Ly49 receptors. Similarly, no promoter activity could be found in fragments upstream of intron1/exon2. Collectively, these findings reveal a previously unrecognized relationship between the pattern of transcription and the expression/function of Ly49 receptors, and indicate that transcription of the Ly49 genes expressed in lymphoid cells is achieved in a manner that does not require classical upstream promoters.
authors.affiliation: The Institute of Cell and Molecular Biosciences, The Medical School, Newcastle, United Kingdom.
authors.forename: Frances
authors.initials: F
authors.lastname: Gays
authors.forename: Alan S C
authors.initials: AS
authors.lastname: Koh
authors.forename: Katarzyna M
authors.initials: KM
authors.lastname: Mickiewicz
authors.forename: Jonathan G
authors.initials: JG
authors.lastname: Aust
authors.forename: Colin G
authors.initials: CG
authors.lastname: Brooks
mesh_terms: D000818:Animals; D002478:Cells, Cultured; D005091:Exons / Q000235:genetics; D005455:Fluorescent Antibody Technique; D051379:Mice; D055650:NK Cell Lectin-Like Receptor Subfamily A / Q000235:genetics*; D011401:Promoter Regions, Genetic / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D024363:Transcription Initiation Site
chemical_list: D055650:NK Cell Lectin-Like Receptor Subfamily A