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Major advances have
been made in understanding the evolution of transcriptional regulation using
microevolutionary and macroevolutionary experimental approaches. The roles of
stabilising selection and compensatory changes in an enhancer region have been
elucidated in Drosophila. The molecular dynamics of regulatory alleles have
been studied in plants. Evidence is accumulating for the involvement of regulatory
evolution in morphological changes between closely related species, as well
as in major changes of body plans. (Diethard Tautz. Curr Opin
Genet Dev. 2000 Oct;10(5):575-9. Review)
We want to find the variation of promoter and upstream region affect the body development of insects at embryo.
The sequences used come in files that contain two or more FastA formatted sequences of Drosophila melanogaster, named EP________. These come from Genbank and a database called EPD (Eukaryotic promoter database) and were collected to study polymorphism in regulatory sequence in D. melanogaster in genes for which the transcription start site has been experimentally determined (currently only a small number of genes fulfill this criterion).
Then we needed to test a) if sequences with no polymorphism and with polymorphism have equal numbers of predicted transcription factor binding sites, and b) if more, equal, or less polymorphic sites are located within potential transcription factor binding sites in the sequences found polymorphism.
We use those two tools:
http://www.ebi.ac.uk/clustalw/
- make alignments.
http://genomatix.gsf.de/free_services/ - Matinspector to find predicted binding
sites for transcription factors. ex.
1. How to decide the correct transcription bind site
2. very conservative
3. http://flybase.bio.indiana.edu/genes/
- to look at the specific entries of genes and experimental
data/papers that report on those.Á@