title: TSS seq based core promoter architecture in blood feeding Tsetse fly (Glossina morsitans morsitans) vector of Trypanosomiasis.
abstract: BACKGROUND
  Transcription initiation regulation is mediated by sequence-specific interactions between DNA-binding proteins (transcription factors) and cis-elements, where BRE, TATA, INR, DPE and MTE motifs constitute canonical core motifs for basal transcription initiation of genes. Accurate identification of transcription start site (TSS) and their corresponding promoter regions is critical for delineation of these motifs. To this end, the genome scale analysis of core promoter architecture in insects has been confined to Drosophila. The recently sequenced Tsetse fly genome provides a unique opportunity to analyze transcription initiation regulation machinery in blood-feeding insects.
  
  
  RESULTS
  A computational method for identification of TSS in newly sequenced Tsetse fly genome was evaluated, using TSS seq tags sampled from two developmental stages namely; larvae and pupae. There were 3134 tag clusters among which 45.4% (1424) of the tag clusters mapped to first coding exons or their proximal predicted 5'UTR regions and 1.0% (31) tag clusters mapping to transposons, within a threshold of 100 tags per cluster. These 1393 non transposon-derived core promoters had propensity for AT nucleotides. The -1/+1 and 1/+1 positions in D. melanogaster, and G. m. morsitans had propensity for CA and AA dinucleotides respectively. The 1393 tag clusters comprised narrow promoters (5%), broad with peak promoters (23%) and broad without peak promoters (72%). Two-way motif co-occurrence analysis showed that the MTE-DPE pair is over-represented in broad core promoters. The frequently occurring triplet motifs in all promoter classes are the INR-MTE-DPE, TATA-MTE-DPE and TATA-INR-DPE. Promoters without the TATA motif had higher frequency of the MTE and INR motifs than those observed in Drosophila, where the DPE motif occur more frequently in promoters without TATA motif. Gene ontology terms associated with developmental processes were overrepresented in the narrow and broad with peak promoters.
  
  
  CONCLUSIONS
  The study has identified different motif combinations associated with broad promoters in a blood-feeding insect. In the case of TATA-less core promoters, G.m. morsitans uses the MTE to compensate for the lack of a TATA motif. The increasing availability of TSS seq data allows for revision of existing gene annotation datasets with the potential of identifying new transcriptional units.
authors.affiliation: South African MRC Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa. sarah@sanbi.ac.za.
authors.forename: Sarah
authors.initials: S
authors.lastname: Mwangi
authors.affiliation: Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA. geoffrey.attardo@yale.edu.
authors.forename: Geoffrey
authors.initials: G
authors.lastname: Attardo
authors.affiliation: Department of Medical Genome Sciences, University of Tokyo, Tokyo, Japan. ysuzuki@k.u-tokyo.ac.jp.
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Suzuki
authors.affiliation: Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA. serap.aksoy@yale.edu.
authors.forename: Serap
authors.initials: S
authors.lastname: Aksoy
authors.affiliation: South African MRC Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa. alan@sanbi.ac.za.
authors.forename: Alan
authors.initials: A
authors.lastname: Christoffels
mesh_terms: D000818:Animals; D001482:Base Composition; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D020451:Contig Mapping; D049750:Genome, Insect; D023281:Genomics; D007303:Insect Vectors; D058977:Molecular Sequence Annotation; D059372:Nucleotide Motifs; D011401:Promoter Regions, Genetic; D024363:Transcription Initiation Site; D014345:Trypanosoma; D014352:Trypanosomiasis / Q000635:transmission; D014370:Tsetse Flies / Q000235:genetics* / Q000469:parasitology