Events - Daily
March 04, 2013 >>
|Monday, March 04|
Sebastian Maerkl, EPFL Lausanne, Large-scale single cell analysis
Observing cellular responses to perturbations is central to generating and testing hypothesis in biology. Time-lapse microscopy is a powerful tool for studying cellular phenotypes, but has been refractory to proteome-wide investigations. We developed a live-cell microarray integrated with a massively parallel microchemostat array to quantify microbial phenotypes in large-scale. Specifically, we quantified the spatio-temporal flux of the yeast proteome in response to environmental stresses by determining single-cell protein abundance and localisation changes in 4,085 GFP-tagged strains. Analysis of over 23,000 movies and 1.5 × 10^8 cells provided insight into the precise temporal orchestration of protein abundance and localisation changes in yeast. Highly dynamic re-location events are complementary to slow and persistent protein abundance changes, and together coordinate the cellular response on different time-scales. In particular, we observed that p-bodies rapidly form in response to UV-induced DNA/RNA damage. Through the precise spatio-temporal analysis of over 500 deletion - GFP-tagged strains we could determine that the p-body response is an intricate component of the DNA damage response pathway, and link it to other previously identified components. In summary, we developed a methodology for large-scale single-cell analysis and applied it to the characterisation of the stress response pathways in S. cerevisiae. Our approach is broadly applicable, and we have shown that other microbes such as E. coli, M. smegmatis, and S. pombe, can also be analysed on our platform.
Joseph Henry Room, Jadwin Hall · 12:00 p.m.– 1:00 p.m.
Job Dekker, U Mass, Chromosome folding and gene regulation
Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School
My laboratory studies how chromosomes are organized in three dimensions. The three-dimensional organization of the genome is critical for regulating gene expression by bringing genes in close spatial proximity to distal regulatory elements such as enhancers. We have developed powerful molecular approaches, based on our Chromosome Conformation Capture technology, to determine the folding of genomes at unprecedented resolution (Kb) and scale (genome-wide).
We have applied these methods to determine the spatial folding of 1% of the human genome (the ENCODE pilot regions) across a panel of cell lines. We discovered that chromosomes fold into extensive long-range interaction networks in which genes are interacting with distal gene regulatory elements. These results start to place genes and regulatory elements, that are often separated by large genomic distances, in three-dimensional context to reveal their functional relationships.
Our analysis of chromosome folding also revealed that chromosomes are compartmentalized in a series of “Topological Association Domains” (TADs) that are hundreds of Kb in size. Loci located within a TAD mingle freely, but interact far less frequently with loci located outside their TAD. TADs appear involved in gene expression, as we found that genes located within the same TAD tend to be co-expressed, but the mechanism(s) by which these domains affect gene regulation is still unknown. TADs represent novel universal and genetically encoded building blocks of chromosomes.
Carl Icahn Lab 101 · 4:15 p.m.– 5:15 p.m.