In early online, UCSD's Bing Ren used chIP-chip to locate promoters, enhancers, and insulators across the human genome in multiple cell types. They found over 55,000 potential transcriptional enhancers, and that while the chromatin state at promoters and CTCF-binding at insulators doesn't change much across cell types, enhancers show highly cell-type-specific histone modification patterns and genome-wide, cell-type-specific gene expression programs. In other work, a team has engineered light-sensitive fusion proteins that trigger neurons to fire on individual signaling pathways within cells. Targeting these proteins, called optoXRs, to the pleasure center in the brains of mice, they were able to control the animals' behavior using pulses of light.
In work in this week's issue, scientists look at the population genomics of domestic and wild yeasts, tackling the genome sequences of over 70 isolates of the baker's yeast Saccharomyces cerevisiae and its closest relative, Saccharomyces paradoxus. They looked at variation in gene content, SNPs, insertions and deletions, copy number, and transposable elements. In contrast to the strictly geographical delineation of S. paradoxus, "the population structure of S. cerevisiae consists of a few well-defined, geographically isolated lineages and many different mosaics of these lineages," they say.
Princeton researchers have performed a genome-wide SNP survey on S. cerevisiae. Using tiling arrays to compare SNPs across 63 strains, they found 1.89 million SNPs, which were grouped into 101,343 distinct segregating sites. They also identified 3,985 deletion events of greater than 200 base pairs among the surveyed strains.
Scientists have created a map of the genome-wide occupancy of nucleosomes on purified yeast genomic DNA based on the DNA sequence preferences of the nucleosomes. In vitro, they found nucleosome depletion at many transcription factor binding sites and around gene start and end sites. To confirm their results, they performed a micrococcal nuclease-independent experiment that measured the relative affinity of nucleosomes for 40,000 double-stranded, 150-base-pair oligonucleotides and then built a computational model of nucleosome sequence preference in C. elegans in vitro that they say is "significantly correlated with in vivo nucleosome occupancy."