Lectures and seminars The biases and mechanisms of regulatory DNA evolution and emergence

About the speaker

Dr Timothy Fuqua is a senior postdoc in the lab of Claudia Bank (University of Bern, Switzerland). His research broadly focuses on fitness landscapes, the evolution of gene expression, and the emergence of de novo functions, using experimental and computational approaches. Specifically, during his postdoc with Andreas Wagner (University of Zurich, Switzerland), he used high-throughput, experimental mutagenesis to create new bacterial promoters from different "flavors" of non-regulatory DNA, such as transposons (Fuqua and Wagner, Nat Comms 2025), repetitive AT-rich DNA (Fuqua et al., eLife 2024), and randomly synthesized DNA (Fuqua and Wagner, BiorXiv 2025), discovering trends and mechanisms underlying promoter emergence. During his PhD with Justin Crocker (EMBL, Germany), he developed robotics and microscopy pipelines (Fuqua et al., Sci Reps 2021) to screen mutagenesis libraries of Drosophila developmental enhancers (Fuqua et al., Nature 2020), discovering that enhancer evolution is biased and potentially constrained.

Selected publications

• De-novo promoters emerge more readily from random DNA than from genomic DNA. Fuqua and Wagner. BioRxiv (2025).
• The latent cis-regulatory potential of mobile DNA in Escherichia coli. Fuquaand Wagner. Nature Communications (2025).
• The emergence and evolution of gene expression in genome regions replete with regulatory motifs. Fuqua, Sun, and Wagner. eLife (2024).
• Dense and pleiotropic regulatory information in a developmental enhancer. Fuqua, Jordan, van Breugel, Halavatyi, Tischer, Polidoro, Abe, Tsai, Mann, Stern, and Crocker. Nature (2020).

Host: 

Department of Medical Biochemistry and Biophysics (contact: tamsinlindstrom@ki.se)