Josep Comeron - US grants

The genetic information of most genes that code for proteins in eukaryotes is not contiguous but split into segments called 'exons' and 'introns'. Exons correspond to sequences with information for the amino acids of the encoded protein while introns are intervening sequences between exons that do not carry information for protein sequence. The number of introns in a gene varies considerably not only among different genes but also when comparing homologous genes between species. Nevertheless, little is known about the causes for intron presence and the evolution of exon-intron structures. Theoretical models of natural selection forecast that, all else being equal, genes with introns might exhibit a selective advantage compared to genes without introns, which would explain the prevalence of introns in most genomes. In this project the PI will investigate this possibility by applying population genetics techniques, both experimental and theoretical. To this purpose, the PI will obtain information of nucleotide variability within species (i.e., polymorphism) and between species (i.e., divergence) in several species of Drosophila and will estimate the efficacy of natural selection's taking advantage of advantageous mutations and eliminating deleterious mutations in four groups of genes classified according to the size of the coding sequence and intron presence/absence.

The results from the proposed work will be significant for the field of population genetics and it will give new insight into the forces involved in the evolution of introns and gene structures, and genome size and organization in eukaryotes.

DESCRIPTION (provided by applicant): This topic specifically targets developing a deep and diverse understanding of genetic maps and recombination within and between species, which is what our proposal intends to study. Project Title: Fine-scale recombination rate variation within and between Drosophila species. Over the past two decades the NIH, NSF, USDA, and DOE have invested billions of dollars into genomic sequencing. These genome projects have given us new insight into the biological basis of disease, led to the production of new diagnostic tools, and recently contributed to the development of high throughput resequencing technologies (HTseq) that are revolutionizing biomedical research. With these recent technological breakthroughs, researchers can resequence the full genome of any individual at costs approaching a "thousand dollar genome." The resultant data will usher in an era of "personalized medicine" by enhancing our understanding of what makes individuals unique, helping physicians tailor treatments to individuals, identifying new genetic determinants for the susceptibility, etiology, and pathogenesis of many diseases, and generally giving us a deeper understanding of biology. Making sense of this new found wealth of genomic data is the new challenge. Key unsolved questions are where does the biologically relevant variation reside and what are the structural, evolutionary, and genetic processes shaping this variation? Meiotic recombination lies at the nexus of these two questions. Genetic mapping remains one of our primary tools for uncovering meaningful associations between genetic and phenotypic variation. In most eukaryotes, recombination is critical for ensuring proper chromosome segregation, facilitating DNA repair, and providing a basis for genetic diversity. Recombination, by breaking up linkage relationships among loci, also allows different genomic regions to have different evolutionary histories. The results of this multi-PI, 2-year project will fill in a gap in our basic knowledge of one of the fundamental parameters in biology: recombination. The collection of genetic maps produced by this project will provide an unprecedented insight how recombination varies within and between populations and among species. Our data will be a critical resource for the large and heterogeneous scientific community interested in population genetics and whole genome association studies. PUBLIC HEALTH RELEVANCE: While whole genome association studies (WGA) have be successful in identifying a number of new loci associated with diseases and complex traits, such as diabetes, these loci only explain a fraction of the heritability of these traits. WGA studies, however, assume that recombination rates are invariant among individuals within species, an assumption that is either unjustified or untrue. The results of our comprehensive study on how recombination rates vary within populations of Drosophila - a commonly used model system for association studies - will reshape how human WGA are performed and lay out the foundation for a new generation of WGA models and tools.

Recombination promotes genetic diversity and the continuous adaptation of natural populations to ever-changing biotic and abiotic environments. These well-known advantages of recombination explain why most species reproduce through outcrossing. Significantly less attention has been paid to the fact that recombination rates are themselves a variable and evolving trait. Despite the profound importance of recombination in evolutionary and genetic studies, there is a significant gap in our basic knowledge of within-species natural variation in recombination. The PIs propose to take advantage of the unparalleled genetic and genomic tools available in the model system Drosophila melanogaster to conduct the first comprehensive study of intraspecific variation in recombination, from the description of where and how much recombination rates vary across genomes and among individuals of the same species, to the elucidation of the molecular causes and evolutionary consequences of this variation.

This study will provide a new paradigm within models of adaptation under suboptimal conditions by investigating a direct mechanistic link between increased recombination and stressful conditions, the very same circumstances where recombination may be most favorable. The PIs also propose a two-pronged approach to increase the participation of women and other underrepresented groups in science and education. They will organize a series of high school seminars, focusing on Evolution as a modern scientific discipline, and create a summer hands-on workshop for future educators. The workshop will focus on evolutionary and genomic concepts, with laboratory experience and experimental activities easily transferrable to secondary education settings. These seminars will enable the participants to confidently discuss contemporary issues related with evolution and modern genomic techniques (e.g., human and primate evolution, personalized medicine, etc.) in their classrooms.

Telomeres protect chromosome ends in eukaryotes. In the absence of telomerase, telomeres shorten, which eventually leads to senescence. Alternative lengthening of telomeres (ALT) is a recombination pathway that maintains eukaryotic telomeres in cells lacking telomerase. Notably, 15% of cancers take advantage of ALT to maintain their telomeres. Also, the anti-tumor effect that telomerase-inhibiting drugs have on some cancers is compromised due to activation of ALT. However, despite the relevance of ALT to cancer development and pro- gression, its mechanism remains elusive. In large part, this is because quantitative assessment of ALT is hin- dered by its highly stochastic nature. The focus of this research is to overcome this problem by combining ex- perimental molecular genetics with a modeling approach we call Population Genetic based Modeling (PGM). This approach not only accommodates, but actually exploits the stochasticity of ALT to enable quantitative as- sessments and modeling of the ALT mechanism. Due to the lack of convenient experimental system in mam- mals, studies will be carried out in yeast Saccharomyces cerevisiae, which previously proved to be a dependable and productive model system to characterize the underlying mechanism of ALT (break-induced replication (BIR)), to define genetic requirements, and to characterize outcomes of ALT. The first goal of the project is to model the process of telomere erosion in large yeast populations, which will be accomplished by a combination of molecular genetics and PGM. The resulting models will characterize the entire population?s telomere dynamics and will allow detection of even small cell subpopulations, including putative ALT precursors (cells that eventually give rise to ALT survivors). Secondly, a similar approach will provide the first quantitative assessment of ALT frequency. Finally, the connection between the pattern of telomere erosion and ALT survivor formation will be elucidated by assessing the effects of various genetic factors and environmental stressors on both telomere erosion and ALT survivor formation. In particular, the effect of mutations affecting the DNA damage-induced checkpoints, telomere capping, and DNA repair (with an emphasis on BIR genes) on the dynamics of telomere erosion and ALT survivor formation will be evaluated. Also, the effect of various environmental stressors, includ- ing ethanol, caffeine, as well as cadmium and arsenic, known to affect telomere length, will be assessed. To- gether, the proposed research will link the formation of ALT survivors with the mode of telomere erosion and will create a comprehensive and quantitative model of ALT, which will generate new hypotheses that will guide future research aimed at unraveling the entire mechanism of ALT progression. In addition, the results of this research will provide an opportunity to use telomere erosion and ALT formation as a new type of biosensor that can be used to assess the effects of various environmental assaults on genetic stability. Finally, it is expected that the approaches and results produced through this research in yeast will be applied in the future towards elucidating ALT in humans, and particularly its roles in cancer.