Title: Characterization and Quantification of the Human Endogenous Retrovirus Transcriptome
Presenter: Matthew Bendall, PhD candidate
Mentors: Keith A. Crandall, PhD; Douglas F. Nixon, MD, PhD
Abstract: The human genome is host to thousands of Human Endogenous Retroviruses (HERVs) – proviral remnants of ancient exogenous retroviral infections – that altogether comprise almost 8% of the human genome. Several lines of evidence suggest that HERVs may in fact play an important role in human biology. Currently, single-locus quantification of repetitive element transcription using next-generation sequencing (NGS) is a major technological challenge. Two important limitations have prevented this technique from being widely adopted. First, the precise location and structure of HERV elements in the genome is largely unknown; and second, computational algorithms for mapping sequence reads to repetitive elements have not been developed. In this dissertation, I aim to resolve these two challenges by creating a reference set of HERV elements in the human genome and developing a computational approach to accurately quantify HERV expression. I will use these tools to investigate HERV expression in neurodevelopment, psychiatry, and embryonic development.