Project 8: The stress response: a universal integrating module? (Rando) (#39-46) We studied chromatin structure and function by using a novel microarray to determine nucleosome positions at 20-bp resolution. Chromatin plays a critical role in regulating any processes that take place on DNA, including transcription, replication, DNA repair, and chromosome segregation. Measuring chromatin structure at high resolution over genomic scales allowed us to describe a number of surprising features of yeast chromatin: 1) most of the genome is found in well positioned, rather than delocalized, nucleosomes16, 2) the pattern of histone modification is much less complex and much less instructive than advocates of the histone code had proposed: the 12 different histone modifications occur in two grouped sets, transcription-independent modifications marking promoters and transcription-dependent ones in the transcribed region17, and the acetylation of lysines on H4 primarily affects transcription by modulating overall charge18;3) promoters have a 200 base pair long nucleosome-free region where transcription starts16;this region is flanked by two well positioned nucleosomes that contain the H2A variant Htz1 and are hypo-acetylated at specific lysines19;4) nucleosomes exchange rapidly at promoters and at known chromatin boundary elements;histone replacement rates over coding regions correlate with polymerase density20. In total, this work reveals that the chromatin structure of yeast promoters is more stereotyped and dynamic than was previously thought. The technological advances inspired similar studies in higher organisms, such as humans, where the analysis of chromatin structure promises important insights into developmental processes, such as stem cell differentiation, and into diseases with an epigenetic component, such as cancer. Oliver Rando, the PI, was a Bauer Fellow and is now Assistant Professor of Biochemistry and Molecular Biology at U Mass Worcester. New project 8: Sociobiology at the genetic level: cooperation and conflict in microbes (Foster) (#47-50) Using microbes as models for sociogenomics, we investigate the genetic and genomic basis of two key social traits: biofilm formation in the pathogen Pseudomonas aeruginosa3*, and production of invertase, a foraging enzyme, in budding yeast40. Our goal is to characterize evolutionary cooperation and conflict in microbial social traits at both the genetic and phenotypic level, using a combination of empirical and theoretical approaches. Our first year has seen the successful development of four study systems: 1) Biofilm formation in the pathogenic bacterium P. aeruginosa. We find biofilm increases and gene expression patterns change when genetically distinct strains of P. aeruginosa meet, consistent with a competitive response to the presence of foreign genotypes. This shows that one cannot fully understand microbial behaviors from single clone studies. 2) An individual-based simulation of biofilm development. We find that slime production in biofilms can benefit the slime-producers by pushing their descendents up into the nutrient- and oxygen-rich regions of the biofilm41. 3) Secretion of invertase (which breaks down sucrose) and phosphatase (which converts organic phosphate to inorganic phosphate) by the yeast Saccharomyces cerevisiae as cooperative traits (in collaboration with A. Murray). 4) Flocculation as a social escape response in yeast (in collaboration with K. Verstrepen). This year has changed our perspective of these species by showing the central role that evolutionary conflict plays in their behaviors. The notion that conflict drives microbial behaviors is central to both the correct interpretation of lab results, and to the treatment and avoidance of infections, which are nearly always associated with microbial group behaviors. Kevin Foster became a Bauer Fellow in 2005 and joined CMB in 2006.

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National Institute of General Medical Sciences (NIGMS)
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