Characterizing the genetic and epigenetic landscape of transposable elements in African populations

Transposable elements (TEs) comprise nearly half of the human genome. They play a key role in gene regulation, genome stability and evolution, and there is emerging evidence of links to disease. However, their functional impact in humans is poorly understood, particularly in African populations where genomic diversity is highest. This project addresses a fundamental gap: the lack of genetic and epigenetic maps of TEs in diverse African genomes. Using Oxford Nanopore sequencing, I will characterize TE diversity and base-resolution blood DNA methylation across 600 genomes from three African populations covering East, West and Southern Africa. Four interlinked work packages will generate long-read sequencing datasets; map TE genetic and epigenetic variation; probe their potential regulatory function using AI foundation models to predict effects on gene expression and chromatin states; and quantify genetic and environmental influences through cis-mQTL mapping and analysis of early environmental exposures. I will generate the first, fully-annotated, open access African TE atlas, offering new insights into TE biology and providing a foundation for investigating links to disease susceptibility. By advancing African representation in functional genomics and building equitable partnerships, this project will contribute to a more globally inclusive understanding of TEs and their role in genome regulation.