Statistical and high-throughput models of enhancer function and evolution

Harvard University, Cambridge MA

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Abstract

Project Summary This diversity supplement proposes to train Mr. Christian Burns, an African American master’s student, in modern methods of comparative genomics and genome biology. African Americans are severely underrepresented in evolutionary biology and this supplement will assist Mr. Burns in reaching his goal of gaining admission to a top PhD program and furthering his career towards becoming a faculty at an R1 university. Our main Aim is to train Mr. Burns in basic skills in genome biology, including long-read genome sequencing, assembly, annotation and comparative analysis. This training will be accomplished through a research project building on recent work in the PI laboratory that revealed dramatic differences in transposable element (TE) abundance in two closely related, cryptic species of thrushes (family Turdidae). Catharus bicknelli and C. minimus are estimated to have diverged only ~15,000 years before present, yet exhibit up to 10% difference in TE abundance depending on the TE subfamily. This project will expose Mr. Burns to cutting-edge approaches in bioinformatics, including PacBio HiFi genome assembly, assembly quality assessment, genome alignment, TE abundance and annotation, and pangenome analysis. This project is related to the parent proposal because of the well-known relationship between enhancer origin and function and TE proliferation: many TEs in vertebrate genomes are discovered to underlie enhancers with diverse functions in multiple tissues. The parent proposal is focused on understanding how changes in evolutionary rate of enhancers can be estimated and tied to changes in function through high throughput enhancer assays, and this supplement will complement Aim 2 of the parent grant by exploring possible connections between TE proliferation and the origin of novel enhancer functions. Mr. Burns will receive in-depth mentoring focusing on four areas critical to achieving his career goals: Finding your voice in science; the importance of writing; acquisition of technical skills; and envisioning and planning for a future in STEM. Together these research and mentoring activities will strengthen the career prospects of Mr. Burns in evolutionary biology and equip him with lasting technical and conceptual skills to allow him to achieve his career goals.