Run Full-Enhancer Scanner
- Addressing the problem of non-conserved elements within enhancers using 'Full-enhancer scanner'
To identify less conserved elements in enhancers that match elements within CSBs, use is made of the program 'Full-enhancer scanner.' Previous studies have demonstrated that certain enhancers, particularly those controlling the dynamic expression of developmental genes, contain multiple DNA-binding sites for one or more specific transcription factors. Comparative studies of orthologous enhancers have also revealed that within a binding site cluster individual DNA-binding sites can undergo turnover. The program Full-enhancer scanner aligns a limited group of cis-Decoder tags (cDTs) to an EvoPrint (including both the conserved and non-conserved bases).
- Generating a 'Full-enhancer scan'
Full-enhancer scanner program searches for sequences within EvoPrinted enhancers that cDT-scanner analysis has determined to be required for enhancer function and are also multiply repeated but not positionally conserved. For this alignment, cDTs present within an enhancer can be curated from the tabular output of cDT-scanner termed 'Results from cDT scan.' Care should be taken to take both the forward direction cDTs and the reverse-complements. These cDTs should be copy-pasted into the upper window of Full-enhancer scanner. The EvoPrint that was initially scanned by cDT-scanner is pasted in the lower window. Selecting the 'Align' option aligns the input cDTs to both the CSB sequences (in upper case) and to the interblock sequence (in lower case) of an EvoPrint, thus generating an alignment to both conserved and non-conserved sequences within an enhancer.
- Example of Full-enhancer scanner
The sequence AATCCTTTCG (see upper case blue highlight below) is present as a CSB in the even-skipped stripe 1 enhancer (Fujioka et al. 1999) and is also present in the giant #10 enhancer construct that drivers anterior expression of giant (Schroeder et al. 2004). Full-enhancer scanner reveals that this 10 bp sequence is present two additional times (illustrated in lower case with blue highlight) within the intra-block sequences of the eve. Interestingly, this CSB contains the consensus binding sequence for Tramtrack (TCCT), a regulator of segmental gene expression (Fairall et al. 1993). The underlined portion, containing the consensus Tramtrack site, is also found several additional times associated with this enhancer element. EvoDifference analysis (an EvoPrinter subroutine) reveals that the 5' most inter-block AATCCTTTCG is conserved in all Drosophila species except D. ananassae and the 3' inter-block repeat is absent in 6 of the 10 species used to generate the EvoP.
- Contact information
Please feel free to contact Dr. Thomas Brody at brodyt@ninds.nih.gov or Dr. Ward Odenwald at odenwaldw@ninds.nih.gov if you have any questions about EvoPrinter or its applications.
Discover multispecies conserved sequences using EvoPrinter.
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