Sunday, April 24, 2011

Comparative Functional Genomics of the Fission Yeasts

Fresh off the press: An online version appeared on the Science Express website (pre-publication online release of Science articles). This is a genome paper where the main result is the sequencing of a genome. In this case, actually two new species, both related to the fission yeast, S. Pombe

(figure from Nick Rhind's website)

The fission yeast is well studied model organsim. As its name suggests, it divides in half during growth (unlike the budding yeast). It is also closer to humans than the budding yeast (aka Baker's yeast) in terms of many mechanisms. And so, many important discoveries in fission yeast in the areas of cell cycle, silenced genomic regions (heterochromatin) and other regions, were more directly related to mammalian cells.

(figure from )

The new world of genomes allows to compare related genomes and use these comparisons to understand what part of the genome are functional. Such comparative genomics has proved immensely fruitful. However, so far very few related species of S. pombe were sequenced. The sequencing of the new genomes, and functional annotations of the genes in the these two genomes provide fresh insights into S. pombe genetics. 

As you can see in this evolutionary tree that contains most of the currently sequenced yeast genomes, the "neighborhood" of S. cervisiae (bakers' yeast) and C. albicans (a species of Candida, a human pathogen) are well populated (horizontal branch lengths correspond to evolutionary distance). With the addition of S. japanicus and S. octosporus, the branch leading to S. pombe is now better explored.

(figure courtesy of Naomi and Ilan)

This project was spearheaded by Nick Rhind (UMass Medical School) and Chad Nusbaum (Broad Institute). Our contribution was in helping make sense of functional data and comparative analysis. Moran helped in identifying transcribed genes in the two new species based on samples collected at Aviv Regev's lab. She discovered many antisense transcripts that regulate some of the key genes in developmental decision making in these yeasts. Naomi and Ilan used comparative methods to find regulatory elements in these genomes, and showed how regulatory elements that are conserved throughout the tree of ascomycota yeasts change their function in these yeasts to match their life style.

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