Mobile DNA short and long interspersed elements (SINEs and LINEs) are distinct fragments of DNA that are capable of copied movement to other regions of the genome. As non-autonomous elements, SINEs achieve retrotransposition by exploiting enzymatic functions of LINEs. Mobile element insertions (MEIs) are profound mediators of genomic variation and are associated to human disease, particularly the Alu and L1 elements that continue to generate new insertions. The dog has emerged as an important model system for mapping of disease variants, leading to discoveries of disease-associated human orthologs. Understanding the diversity in this understudied model species, especially in context of disease, should present an exceptional resource in health-related comparative genomics. The canine SINEC_Cf subfamily, like Alu in humans, has undergone recent expansion, with thousands of bimorphic copies among individuals. In dogs, unique SINEC_Cf insertions have been directly linked to phenotypes from narcolepsy and centronuclear myopathy to coat coloring and body size. However, whole-genome analysis of SINEC biology and impact is very limited. Moreover, virtually nothing is known of the recently active canid LINE, L1-Y_Cf, in its own transposition or to SINEC, though there are ~30 intact L1_Cf copies in the CanFam3.1 boxer reference, including bimorphic sites. Our preliminary data indicate >32,109 bimorphic SINEC copies in a global set of dogs and related canids, including ~23,166 from the `Cf' subfamily alone, and thousands from otherwise `inactive' SINEC subfamilies. We also find ~15,703 bimorphic L1-Y_Cf, including ~150 putative full-length copies. Finally, we directly tested a single non-reference L1-Y_Cf cloned from a breed dog, demonstrating bona fide activity in a cellular-based retrotransposition assay. These findings suggest recent movement of canine MEIs. We hypothesize that canine MEI activities have substantially contributed to phenotypes observed in genomic variation and disease in dogs. We will address this hypothesis in an approach that combines computational and molecular genomics, utilizing a unique combination of experts in genomic variation and mobile element biology offered at the University of Michigan. We will comprehensively characterize canine MEIs in the following specific aims: 1. Identification and characterization of non-reference MEIs from a diverse panel of dogs and related canids utilizing whole genome sequence data and computational genomics. 2. Molecular characterization of canid LINE retrotransposition potential and the corresponding effects to mobilization and movement of non-autonomous SINEs in dogs. The training leverages expertise at the University of Michigan in computational and experimental analyses of genomic variation. They complement and augment my own research background and will provide training in approaches required to understand the impact of MEIs on a genome wide scale.
The canine has emerged as an important model system for insight to mechanisms of human disease. Ongoing activities from mobile elements in the genome are known to cause human disease. We propose to characterize related elements in dogs that similarly contribute to variation and disease phenotypes. This will allow improved understanding of how canine mobile elements influence genetic variation in this model system.
| Wildschutte, Julia Halo; Williams, Zachary H; Montesion, Meagan et al. (2016) Discovery of unfixed endogenous retrovirus insertions in diverse human populations. Proc Natl Acad Sci U S A 113:E2326-34 |
| Wildschutte, Julia H; Baron, Alayna; Diroff, Nicolette M et al. (2015) Discovery and characterization of Alu repeat sequences via precise local read assembly. Nucleic Acids Res 43:10292-307 |
