Functional characterization of the Harbi1 and Naif1 transposon-derived genes in vertebrates

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Spatio-temporal coordination of eukaryotic gene expression relies on transcriptional and post-transcriptional regulatory networks. Although some of the components and function of these networks have been elucidated, the mechanisms by which such intricate circuits originate and evolve remain poorly understood. Significant fractions of eukaryotic genomes are composed of transposable elements (TEs) that are able to move and replicate in the genome. TEs are best viewed as genomic parasites with no apparent adaptive value to the host cell in which they reside. Thus, in the absence of selective pressure to maintain mobility, the vast majority of TEs has become transpositionally inactivated over evolutionary time, and has been viewed as "junk DNA" without any apparent cellular function. However, it is being increasingly realized that the spread of TEs in the genome likely played a key role in the evolution of novel gene functions. For example, through an evolutionary process termed "domestication" TE-derived transposase proteins have been recurrently recruited into cellular pathways as regulatory elements. Harbi1 and Naif1 are highly conserved genes in vertebrates that have been derived from an ancient PIF/Harbinger transposon in a common ancestor of jawed vertebrates some 500 million years ago. Conservation of these genes implies that they have been under selection for important cellular functions, and their phylogenetic relationship suggests that both are involved in the same molecular pathway. Naif1 has been implicated in apoptotic functions. Our preliminary data suggest that Naif1 is a DNA-binding protein that promotes nuclear import of Harbi1, where it may recruit Harbi1 to genomic sites through protein-protein interactions. Sequence conservation of the catalytic domain of Harbi1 suggests that it might have retained nuclease activity. However, the role(s) of these two genes in cellular homeostasis and organismal development have been enigmatic. In this project we leverage biochemical assays in vitro, genome-wide ChIP and transcriptional profiling in cultured cells ex vivo, and phenotyping of knockout (KO) animals in the zebrafish model in vivo to understand and functionally annotate these genes and the genetic networks they regulate. The project will greatly contribute to our understanding of the mechanisms and roles of TEs as an important force in the creation of genetic novelty.