title: APTE: identification of indirect read-out A-DNA promoter elements in genomes.
abstract: BACKGROUND
  Transcriptional regulation is normally based on the recognition by a transcription factor of a defined base sequence in a process of direct read-out. However, the nucleic acid secondary and tertiary structure can also act as a recognition site for the transcription factor in a process known as indirect read-out, although this is much less understood. We have previously identified such a transcriptional control mechanism in early Xenopus development where the interaction of the transcription factor ilf3 and the gata2 promoter requires the presence of both an unusual A-form DNA structure and a CCAAT sequence. Rapid identification of such promoters elsewhere in the Xenopus and other genomes would provide insight into a less studied area of gene regulation, although currently there are few tools to analyse genomes in such ways.
  
  
  RESULTS
  In this paper we report the implementation of a novel bioinformatics approach that has identified 86 such putative promoters in the Xenopus genome. We have shown that five of these sites are A-form in solution, bind to transcription factors and fully validated one of these newly identified promoters as interacting with the ilf3 containing complex CBTF. This interaction regulates the transcription of a previously uncharacterised downstream gene that is active in early development.
  
  
  CONCLUSIONS
  A Perl program (APTE) has located a number of potential A-form DNA promotor elements in the Xenopus genome, five of these putative targets have been experimentally validated as A-form and as targets for specific DNA binding proteins; one has also been shown to interact with the A-form binding transcription factor ilf3. APTE is available from http://www.port.ac.uk/research/cmd/software/ under the terms of the GNU General Public License.
authors.forename: David C
authors.initials: DC
authors.lastname: Whitley
authors.forename: Valeria
authors.initials: V
authors.lastname: Runfola
authors.forename: Peter
authors.initials: P
authors.lastname: Cary
authors.forename: Liliya
authors.initials: L
authors.lastname: Nazlamova
authors.forename: Matt
authors.initials: M
authors.lastname: Guille
authors.affiliation: Biophysics Laboratories, School of Biological Sciences, Institute of Biomedical and Biomolecular Science, University of Portsmouth, King Henry Building, King Henry I Street, Portsmouth PO1 2DY, UK. garry.scarlett@port.ac.uk.
authors.forename: Garry
authors.initials: G
authors.lastname: Scarlett
mesh_terms: D000818:Animals; D001483:Base Sequence; D044704:DNA, A-Form / Q000235:genetics* / Q000378:metabolism; D050989:GATA2 Transcription Factor / Q000235:genetics / Q000378:metabolism; D005786:Gene Expression Regulation; D016678:Genome / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D050779:Nuclear Factor 90 Proteins / Q000378:metabolism; D011401:Promoter Regions, Genetic / Q000235:genetics*; D012984:Software; D014981:Xenopus / Q000235:genetics / Q000378:metabolism; D029867:Xenopus Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: D044704:DNA, A-Form; D050989:GATA2 Transcription Factor; C494714:GATA2 protein, Xenopus; D050779:Nuclear Factor 90 Proteins; D029867:Xenopus Proteins