Project Grant R35GM155272

CO-EVOLUTIONARY DYNAMICS BETWEEN TRANSPOSABLE ELEMENTS AND THEIR HOSTS - PROJECT SUMMARY GENOME STABILITY IS NECESSARY FOR FERTILITY AND HEALTH. TRANSPOSABLE ELEMENTS DISRUPT GENOME STABILITY BY SELFISHLY REPLICATING WITHIN HOST GENOMES, PRODUCING INSERTIONS THAT DISRUPT FUNCTIONAL SEQUENCES AND CAUSE ECTOPIC RECOMBINATION. TRANSPOSABLE ELEMENTS ARE WIDESPREAD ACROSS EUKARYOTES, AND CAN OCCUPY A SUBSTANTIAL PORTION OF THE GENOME. ORGANISMS DEFEND AGAINST TRANSPOSABLE ELEMENT INVASION WITH A COMPLEX SYSTEM BASED ON SMALL RNA. ESSENTIALLY, SMALL RNA PRODUCED FROM TRANSPOSABLE ELEMENTS (TERMED PIRNA) IS USED AS A GUIDE TO CLEAVE TRANSPOSABLE ELEMENT TRANSCRIPTS AND DIRECT EPIGENETIC SILENCING. IN MOST ORGANISMS, EXEMPLIFIED BY DROSOPHILA, THERE ARE SEPARATE SYSTEMS FOR TE SUPPRESSION IN SOMATIC AND GERMLINE CELLS - SOMATIC SUPPRESSION IS ACHIEVED LARGELY BY A SINGLE CANONICALLY TRANSCRIBED LOCUS. GERMLINE SUPPRESSION IS ACHIEVED BY MANY REDUNDANT LOCI WHICH PRODUCE PIRNA THROUGH NON-CANONICAL TRANSCRIPTION. MUCH OF WHAT WE KNOW ABOUT THE FUNCTION OF THE PIRNA SYSTEM HAS BEEN DERIVED FROM CAREFULLY EXECUTED EXPERIMENTS IN DEVELOPMENTAL BIOLOGY, WHERE TYPICALLY A SINGLE GENOTYPE OF DROSOPHILA MELANOGASTER IS USED. SOME OF THE GENERALIZATIONS FROM THIS WORK ARE THAT REGIONS OF THE GENOME THAT PRODUCE PIRNA ARE LARGE AND CONSERVED. FURTHERMORE, THE PRIMARY SUPPRESSION SYSTEM IS THOUGHT TO BE PIRNA TARGETED HETEROCHROMATIN OR TRANSCRIPT DEGRADATION, DESPITE AT LEAST ONE TE BEING SUPPRESSED BY ALTERNATIVE SPLICING. MY LAB RECENTLY HAS MADE DISCOVERIES THAT BRING SOME OF THESE CONCLUSIONS INTO QUESTION - FOR EXAMPLE MANY GERMLINE PIRNA CLUSTERS APPEAR TO BE GENOTYPE SPECIFIC. EVEN THE LARGEST AND MOST PROLIFIC PIRNA REGION IDENTIFIED IN THE ORIGINAL DEVELOPMENTAL BIOLOGY EXPERIMENTS APPEARS TO BE UNIMPORTANT FOR PIRNA PRODUCTION IN SOME GENOTYPES. IN ADDITION, THE PRIMARY LOCUS RESPONSIBLE SOMATIC SUPPRESSION WAS THOUGHT TO BE DEEPLY CONSERVED BUT WE FOUND IT TO BE EVOLUTIONARILY LABILE, HAVING DUPLICATED IN DROSOPHILA SIMULANS AND POTENTIALLY FUNCTIONALLY DIVERSIFIED. LASTLY, ALTERNATIVE SPLICING OF MANY TES APPEARS TO OCCUR, BUT WE KNOW NOTHING ABOUT HOW FUNCTIONALLY IMPORTANT THIS IS FOR TE SUPPRESSION. THIS HAS PROFOUND IMPLICATIONS FOR FITNESS VARIATION IN POPULATIONS OF INDIVIDUALS FROM DROSOPHILA TO HUMANS. THE CONSEQUENCES OF TRANSPOSABLE ELEMENT MOBILIZATION ARE DIRE, YET THE SYSTEM WHICH SUPPRESSES THEM EVOLVES RAPIDLY AND IS NOT WELL CONSERVED BETWEEN EVEN CLOSELY RELATED SPECIES. MY LAB WILL WORK TO UNDERSTAND THE FORCES THAT GENERATE AND MAINTAIN VARIATION IN THE PRODUCTION OF PIRNA IN THE DEFENSE AGAINST TRANSPOSABLE ELEMENTS, THE EVOLUTION OF PIRNA PRODUCING REGIONS, AND THE EVOLUTION OF ALTERNATIVE MECHANISMS OF TRANSPOSABLE ELEMENT SUPPRESSION. THE PROPOSED WORK REPRESENTS ADVANCES IN A NUMBER OF FIELDS, INCLUDING POPULATION GENETICS, POST- TRANSCRIPTIONAL REGULATION, TRANSCRIPTIONAL REGULATION, ALTERNATIVE SPLICING, AND SMALL RNA BIOLOGY. TAKEN TOGETHER, THIS RESEARCH WILL OFFER A UNIFIED PICTURE OF THE EVOLUTION OF HOST DEFENSE SYSTEMS AGAINST TRANSPOSABLE ELEMENTS WHICH CAN BE EXTENDED INTO HUMANS AND OTHER ECONOMICALLY IMPORTANT SYSTEMS.