EvoPrinter and cis-Decoder analysis reveals putative C. elegans cis-regulatory sequences at base-pair resolution

Sequence conservation of non-coding DNA has been of great value for identification and characterization of cis-regulatory elements. The comparative genomic alignment tools EvoPrinter (Yavatkar et al., 2008) and cis-Decoder (Brody et al., 2007) can be used to identify and analyze nematode cis-regulatory DNA. EvoPrinter output identifies conserved sequence blocks (CSBs) as they exist in the species of interest. cis-Decoder discovers repeat motifs within CSBs and identifies conserved elements among functionally related enhancers.

EvoPrinter is currently formatted for five nematode genomes. In the example reported here, a relaxed EvoPrint displays in color-coded fashion the conserved sequences in a putative C. elegans enhancer located 5’ of the start of egl-46 transcription. Black uppercase letters represent bases conserved in all species, while colored sequences are present in all species except C. remanei, C. briggsae, C. brenneri or C. japonica. Most, if not all, invertebrate and vertebrate enhancers contain CSB clusters.

EvoPrinter->cis-Decoder analysis of nematode developmental genes reveals many contain flanking cis-regulatory regions that are made up of CSB clusters, which harbor repeat identity elements that can aid in the identification of other functionally related enhancers.

Figures

Figure 1: cis-Decoder analysis of this cluster discovers repeat and palindromic sequence elements among the CSBs (palindromic sequence – yellow; HOX sites – red; bHLH sites – turquoise).

References

Brody T, Rasband W, Baler K, Kuzin A, Kundu M, and Odenwald, WF. (2007). cis-Decoder discovers constellations of conserved DNA sequences shared among tissue-specific enhancers. Genome Biol. 8, R75.

Yavatkar AS, Lin Y, Ross J, Fann Y, Brody T, and Odenwald WF. (2008). Rapid detection and curation of conserved DNA via enhanced-BLAT and EvoPrinterHD analysis. BMC Genomics 9, 106.