quire-lang / quire-lang blog: Recent posts

By far, the most common "missing" essential gene in yeast species closely related to S. cerevisiae is NBL1, which encodes a subunit of the chromosomal passenger complex involved in mitotic chromosome segregation. Importantly, NBL1 has two features that make it potentially difficult to identify: (1) NBL1 only spans 289 bases, and (2) NBL1 is one of the ~300 genes in S. cerevisiae that has an intron.... read more

It's really surprising that the core DNA replication gene POL12 , which encodes the beta subunit for DNA polymerase alpha, is missing from S. mikatae. (See previous blog post). Certainly one possibility is that POL12 is present, but some errors in either sequencing or annotation have caused it to be missed in our analysis. Thus, we will start the further investigation of essential genes from S. cerevisiae that are missing from related organisms with POL12. To review, we will first look at the essential gene ohnologs from the YGOB data in the most closely related species to S. cerevisiae: S. bayanus, S. kudriavzevii, and S. mikatae.... read more

Are the essential S. cerevisiae genes conserved in related species? Under the view that essential genes are core for the survival of a cell, conserved genes ought to be strictly conserved. However, many of the essential genes are sensitive to the genetic context; the lethality of many essential gene deletions can be suppressed by other mutations. For example, the lethality caused by deletion of the core DNA damage signaling genes MEC1, LCD2, and RAD53 can be suppressed by deletion of SML1, which encodes an inhibitor to ribonucleotide reductase. Similarly, deletion of DNA2, which is involved in Okazaki fragment maturation, is inviable, but this inviability can be suppressed by simultaneous deletion of PIF1.... read more

After the whole-genome duplication event leading the evolution of S. cerevisiae and related species, each of the genes that were essential would have been duplicated. The fates of each of these genes can be identified based on the knowledge of existing ohnologs (genes related by the whole-genome duplication), synthetic lethality data, and essentiality data.

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All organisms, including humans, have many genes that are essential for growth. The budding yeast Saccharomyces cerevisiae has around 6,000 genes and about 1,000 of them are essential. Essential genes in S. cerevisiae are involved in many core biological functions, such as DNA replication, transcription, translation, protein degradation, and maintenance of organelles.

Identifying essential S. cerevisiae genes
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This blog post shows an example of an easy quire analysis to extract self-self physical interactions identified in the budding yeast Saccharomyces cerevisiae from (an old) BioGRID database. The point of these blog posts is to show some of the motivation for the development of quire, not to explain the details of the language. For details on the quire language, see the documentation (>100 pages) in the provided .tgz file.... read more