Evoprinter

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The availability of genomic sequences for multiple nematode, Drosophila and vertebrate species opens up the possibility of examining in detail the changes that have occurred during the process of molecular evolution. Vertebrate species have evolved over the course of hundreds of millions of years, while the time frame for the divergence of Drosophila species ranges from a few million to more than 50 million years. EvoPrinter is a comparative genomics tool for assessing evolutionary divergence of protein-encoding genes as well as the non-coding sequences that regulate gene expression.

EvoPrinter is a tool for phylogenetic footprinting -- that is, the use of multi-species comparisons to discover unusually well-conserved regions in a set of orthologous DNA sequences. In Drosophila, the combined mutational histories of five or more species renders near base-pair resolution of conserved transcription factor DNA-binding sites, and essential amino acids are revealed by the nucleotide flexibility of the third base of their encoding codons. EvoPrinter is easy to use and affords a view of the evolutionary changes of any of your favorite genes.

EvoPrinter is used for discovering conserved DNA sequences that are shared among three or more orthologous DNAs (Odenwald et al., 2005). Only a single curated DNA sequence is required to initiate the rapid comparative analysis. Generated from multiple pairwise BLAT alignments (Kent, 2002), an EvoPrint presents an ordered, uninterrupted representation of evolutionarily resilient sequences within the user's DNA of interest. By superimposing the different species evolutionary histories, the combined 'in silico' mutagenic force reveals DNA sequences that are essential for gene expression and function.

EvoPrinterHD is a 2nd-generation comparative tool that automatically superimposes higher-resolution alignments to give an enhanced view of sequence conservation between evolutionarily distant species. Currently available for 5 nematode, 12 Drosophila and 20 vertebrate genomes, EvoPrinterHD employs a modified BLAT algorithm (enhanced-BLAT) to facilitate the discovery of short conserved sequence blocks. Enhanced-BLAT represents three superimposed BLAT alignments of the same genomic sequence that were generated using different search and alignment parameters. When alignments between evolutionarily distant genomes are compared, enhanced-BLAT detects up to 75% more conserved bases than identified by original BLAT alignments. The new program also queries 3 different enhanced-BLAT alignments from each genome to identify sequence rearrangements and/or duplications, in addition to detecting sequencing gaps. EvoPrinterHD currently holds over 112 billion bp of indexed genomes in memory and has the flexibility of selecting a subset of genomes for analysis. An EvoDifferences profile is also generated to portray conserved sequences that are uniquely lost in any one of the orthologs. Finally, EvoPrinterHD incorporates options that allow for (1) superimposition of multiple enhanced BLATs to highlight all conserved sequences when orthologous DNAs contain rearrangements; (2) re-initiation of the analysis using a different genome's aligning region as the reference DNA to detect species-specific changes in less-conserved regions and (3) rapid extraction and curation of conserved cis-regulatory sequences.

Analysis of cis-regulatory modules or enhancers reveals that they contain evolutionarily conserved sequences commonly called Multi-species Conserved Sequences (MCSs). These MCSs are made up of multiple Conserved Sequence Blocks (CSBs). cis-DECODER is suite of alignment programs that scans CSBs, identified by the phylogenetic footprinting tool EvoPrinter, generating an alignment of sequence elements (termed cis-Decoder tags or cDTs) common to enhancers of different genes. cis-DECODER analysis of well-characterized enhancers identifies both known transcription factor binding sites and novel sequence elements.

Alignment of hundreds of CSBs from both similarly regulating enhancers and functionally different enhancers assures that conserved cis-regulatory elements shared by as few as two enhancers are identified and included in the analyses. cDT-scans show that most CSBs have a modular organization made up of smaller overlapping/interlocking sequence elements that align with CSBs of other enhancers. A typical CSB is made up of both enhancer type-specific sequence elements and common elements that are found in enhancers with different regulatory functions. More than half of all of the shared CSB sequence elements do not correspond to known transcription factor DNA-binding sites and can therefore be considered functionally novel.

References

• Odenwald WF, Rasband W, Kuzin A and Brody T. (2005). EvoPrinter, a multigenomic comparative tool for rapid identification of functionally important DNA. Proc. Natl. Acad. Sci. 102: 14700-5. [1]
• Kent WJ. (2002). BLAT-- the BLAST-like alignment tool. Genome Res. 12: 656-64. [2]
• Brody T, Rasband W, Baler K, Kuzin A, Kundu M, Odenwald WF. (2007). cis-Decoder discovers constellations of conserved DNA sequences shared among tissue-specific enhancers. Genome Biol. 8(5): R7. [3]