In followup to the Aspergillus RIP paper discussion, Jo Anne posted in the comments that her paper published in FGB about RIP in another asexual species of fungi also found that evidence for the meiosis-specific process of Repeat Induced Point-mutations (RIP).
I’m including a recapping as many of the talks as I remember. There were 6 concurrent sessions each afternoon so you have to miss a lot of talks. The conference was bursting at the seams as it was- at least 140 people had to be turned away beyond the 750 who attended.
If there was any theme in the conference it was “Hey we are all using these genome sequences we’ve been talking about getting”. I only found the overview talks that solely describe the genome solely a little dry as compared to those more focused on particular questions. I guess my genome palate is becoming refined.
A recent paper describes the discovery of 9 new introns in Saccharomyces cerevisiae by Ron Davis’s group at Stanford, using high density tiling arrays from Affymetrix. The arrays are designed for both strands allow the detection of transcripts transcribed from both strands. The arrays were also put to work by the Davis and Steinmetz labs to create a high density map of transcription in yeast and for polymorphism mapping from the Kruglyak lab.
Whole genome tiling arrays have also been employed in other fungi. For example, Anita Silâ€™s group at UCSF constructed a random tiling array for Histoplasma capsulatum and used it to identify genes responding to reactive nitrogen species. A similar approach was used in Cryptococcus neoformans to investigate temperature regulated genes using random sequencing clones.
As the technology has become cheaper, it may become sensible to use a tiling array to detect transcripts rather than ESTs when attempting to annotate a genome. In the Histoplasma work transcriptional units could be identified from hybridization alone. Some of the algorithms will need some work to correct incorporate this information, and the sensitivity and density of the array will influence this. These techniques can be part of a resequencing approaches or fast genotyping progeny from QTL experiments when the sequence from both parents is known (or at least enough of the polymorphims for the genetic map).
What is superior about the current Affymetrix yeast tiling array is the inclusion of both strands. This allows detection of transcripts from both strands. Several anti-sense transcripts in yeast have been discovered recently including in the IME4 locus through more classical approaches, but perhaps many more await discovery with high resolution transcriptional data from whole genome tiling arrays.