Arnaud Perrin

Genomic Exploration of the Hemiascomycetous Yeasts: 4. The genome of Saccharomyces cerevisiae revisited

Since its completion more than 4 years ago, the sequence of Saccharomyces cerevisiae has been extensively used and studied. The original sequence has received a few corrections, and the identification of genes has been completed, thanks in particular to transcriptome analyses and to specialized studies on introns, tRNA genes, transposons or multigene families. In order to undertake the extensive comparative sequence analysis of this program, we have entirely revisited the S. cerevisiae sequence using the same criteria for all 16 chromosomes and taking into account publicly available annotations for genes and elements that cannot be predicted. Comparison with the other yeast species of this program indicates the existence of 50 novel genes in segments previously considered as ‘intergenic’ and suggests extensions for 26 of the previously annotated genes.

Polymorphism in mouse and human class I H-2 and HLA genes is not the result of random independent point mutations

Sufficient mouse H-2 and human HLA class I gene sequences have become available to make a statistical analysis of nucleotide variations within the multigene families possible. In the H-2 and HLA families, a group of four H-2K allelic sequences and three HLA-A sequences were compared with a group of four non-H-2 and three non-HLA-A sequences, respectively. Simple calculations show that nucleotide variations in each group do not occur in a random independent fashion. It is therefore possible that a number of mutations are “concerted” between the subgroups. Interestingly, these concerted mutations are clustered and distributed almost exclusively in the 5′ end of H-2 and HLA genes, which is very rich in GC nucleotides, and where the dinucleotide CpG is particularly frequent. The general concept of unequal repair is proposed as the basis of a model which is supported by these observations.

[5] In Vitro fragmentation of yeast chromosomes and yeast artificial chromosomes at artificially inserted sites and applications to genome mapping

Publisher Summary Techniques for large-scale genome mapping, cloning, and sequencing have been developed in the bakers yeast, Saccharomyces cerevisiae , a particularly suitable model and tool for such experiments for several reasons. The discovery of endonucleases cutting very rarely (meganucleases) and encoded by mobile group I introns has permitted to develop new tools for genome mapping that are particularly well suited to the case of yeast chromosomes and yeast artificial chromosomes (YACs). The chapter discusses the use of intron-encoded endonucleases for site-directed chromosomal fragmentation and its applications to the physical mapping of intact yeast chromosomes, YACs, or fragments thereof. The methods described in the chapter include the integration of I- Sce I recognition sites in yeast chromosomes and in YACs, the preparation of yeast DNA in agarose plugs for PFGE after I- Sce I and/or I- Ppo I digestion, the purification of chromosome fragments and the labeling of chromosomal DNA probes in agarose plugs, and the hybridization of cosmid, plasmid, or λ clones with chromosome fragments. The examples of the applications of such methods are also summarized in the chapter.