Endogenous retroviruses (ERVs) are ubiquitous genomic parasites originating from ancient infectious retroviruses, and constitute 8% of the human genome. Large-scale genomic studies have revealed ERVs as majorsourceoftranscriptionalregulatoryelementsinmammaliancells,suggestiveofanextensiveroleindriving theevolutionofgeneregulatorynetworksinbothhealthanddisease.However,thespecificconsequencesand biologicalsignificanceofERVregulatoryactivityremainscontroversialandnotwellunderstood.Theproposed researchseekstoinvestigateemergingrolesforERVsin(1)theevolutionofimmuneregulatorynetworksand (2) gene dysregulation in cancer. First, we will investigate a potentially fundamental role for ERVs driving regulatory evolution of innate immune responses in mammals, through genome-wide epigenetic and transcriptionalprofilingoftheinterferonresponseincellsderivedfromdiversemammalianspecies.Thisworkis positioned to uncover a recurrent role for ERVs in regulating immune pathways, which may reveal pervasive underappreciated differences in immune responses across species. In a second line of research, we seek to investigatehowtheepigeneticderepressionofERVsincancercontributestopathologicalgeneexpression.The transcriptional reactivation of ERVs is a hallmark of many cancers, but their potential contribution todisease remains poorly understood. We will investigate how reactivated ERVs might cause widespread regulatory dysfunction as a global source of cancer-specific promoters, enhancers, and noncoding RNAs. Focusing on colorectalcancerasamodel,wewillrepurposepooledCRISPRscreeningtoinvestigatehowreactivatedERVs regulate phenotypes contributing to oncogenesis. Our interdisciplinary approach synthesizes functional genomics, genome engineering, evolution, and disease to form a comprehensive platform for deciphering the consequencesofERVsonmammalianbiology.
Endogenousretrovirusesareremnantsofpastretroviralinfectionsandmakeup8%ofourgenomes.Thereis growingevidencethatthereactivationoftheseviralsequencesplaysanimportantroleinmanyhuman diseasesincludingcancerandautoimmunity.Thisproposalwillintegrategenomicanalysisandimmunological approachestoadvanceourunderstandingofhowtheseelementsimpactcellularfunctioninhealthand disease.
