Meiotic recombination is a fundamental genetic and evolutionary process, initiated by the deliberate infliction of numerous double strand breaks (DSBs) on the genome. In most mammals, these DSBs are specified by PRDM9, which binds DNA through a zinc finger (ZF) array and makes two histone modifications that together serve to recruit the DSB machinery. In these species, the ZF binding affinity is rapidly-evolving. Intriguingly, PRDM9 is not only found in mammals but throughout vertebrates, and may be directing meiotic recombination there too. Despite its broad phylogenetic distribution, the gene has been lost independently many times; in these cases, the determinants of DSB location are less well understood but are associated with promoter features. We propose four analyses that address these gaps in our understanding:
Aim 1. Do non-mammalian species with an intact PRDM9 use it to direct recombination? We will test this hypothesis in corn snakes, a vertebrate species that carries a complete and rapidly-evolving PRDM9. We will infer a genetic map from linkage disequilibrium (LD) data as well as by End- seq, a recently-developed approach to assay meiotic DSB frequencies in the genome. We will also collect genomic data about salient histone marks, chromatin accessibility and expression levels. These data will help us to establish if PRDM9 is used to direct recombination. The generality of our findings will be evaluated by building and examining an LD-based map in a fish species with an intact PRDM9, the Northern pike.
Aim 2. What mechanisms direct the location of DSBs in species lacking an intact PRDM9? Here, we will focus on two vertebrates: zebra finches, which (like other birds) lack PRDM9 entirely, and swordtail fish, which lack the two N-terminal domains. We will combine existing LD-based genetic maps with data that we will collect on DSB frequencies, salient histone marks, chromatin accessibility, and expression levels. We will then ask which genomic features influence local recombination rates and if they also play a role in species with an intact PRDM9.
Aim 3. What genes co-evolve with PRDM9? We will test 246 candidate genes for their co-evolution with PRDM9 across the vertebrate phylogeny. As a byproduct, we will make available a pipeline to identify orthologs of interest.
Aim 4. What drives the evolution of PRDM9 binding? To answer this question, we developed a generative model, from PRDM9 binding to population dynamics. We will extend our model, notably to characterize conditions for the loss of PRDM9, and test key predictions with genomic and comparative data. Thus, we will combine population genetic, phylogenetic and experimental approaches in four vertebrate species to learn how DSBs are localized in the genome and how and why the mechanism differs among taxa.

Public Health Relevance

Meiotic recombination is a fundamental genetic and evolutionary process, whose successful completion is necessary for the production of egg and sperm. How meiotic recombination events are directed to the genome varies across vertebrates and remains poorly understood. By combining approaches from population genetics, genomics and phylogenetics, we will elucidate how recombination events are localized in the genome and how and why the mechanism differs across taxa.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
2R01GM083098-09
Application #
10121188
Study Section
Genetic Variation and Evolution Study Section (GVE)
Program Officer
Janes, Daniel E
Project Start
2007-09-17
Project End
2024-12-31
Budget Start
2021-01-15
Budget End
2021-12-31
Support Year
9
Fiscal Year
2021
Total Cost
Indirect Cost
Name
Columbia University (N.Y.)
Department
Biology
Type
Graduate Schools
DUNS #
049179401
City
New York
State
NY
Country
United States
Zip Code
10027
Schumer, Molly; Xu, Chenling; Powell, Daniel L et al. (2018) Natural selection interacts with recombination to shape the evolution of hybrid genomes. Science 360:656-660
Smith, Joel; Coop, Graham; Stephens, Matthew et al. (2018) Estimating Time to the Common Ancestor for a Beneficial Allele. Mol Biol Evol 35:1003-1017
Baker, Zachary; Schumer, Molly; Haba, Yuki et al. (2017) Repeated losses of PRDM9-directed recombination despite the conservation of PRDM9 across vertebrates. Elife 6:
Aeschbacher, Simon; Selby, Jessica P; Willis, John H et al. (2017) Population-genomic inference of the strength and timing of selection against gene flow. Proc Natl Acad Sci U S A 114:7061-7066
Buffalo, Vince; Mount, Stephen M; Coop, Graham (2016) A Genealogical Look at Shared Ancestry on the X Chromosome. Genetics 204:57-75
Bradburd, Gideon S; Ralph, Peter L; Coop, Graham M (2016) A Spatial Framework for Understanding Population Structure and Admixture. PLoS Genet 12:e1005703
Wei, Shan; Williams, Zev (2016) Rapid Short-Read Sequencing and Aneuploidy Detection Using MinION Nanopore Technology. Genetics 202:37-44
Elyashiv, Eyal; Sattath, Shmuel; Hu, Tina T et al. (2016) A Genomic Map of the Effects of Linked Selection in Drosophila. PLoS Genet 12:e1006130
Moorjani, Priya; Sankararaman, Sriram; Fu, Qiaomei et al. (2016) A genetic method for dating ancient genomes provides a direct estimate of human generation interval in the last 45,000 years. Proc Natl Acad Sci U S A 113:5652-7
Ralph, Peter L; Coop, Graham (2015) The Role of Standing Variation in Geographic Convergent Adaptation. Am Nat 186 Suppl 1:S5-23

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