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Microbiology @ SILS
Research Groups

DNA & RNA Interaction Lab

The DNA & RNA Interaction Lab (d.r.n.a) studies how RNA and DNA interactions shape bacterial gene regulation and chromosome organisation. We combine new experimental methods with data-driven analysis to uncover non-canonical regulatory mechanisms in bacteria.

What we do

We are interested in how RNA and DNA interactions control bacterial gene expression and cell physiology. Our focus is on non-coding RNAs, RNA-binding proteins and DNA-associated factors that together orchestrate translation, stress responses and cellular decisions. We study these processes in a range of bacterial systems, with relevance for infection biology, microbiome function and microbial biotechnology.

How we do it

Experimental approaches

We develop and use methods to capture RNA–RNA, RNA–protein and RNA–DNA contacts directly inside cells, and combine these with deep sequencing and multi-omics readouts. This allows us to map regulatory interactions at high resolution. Our work includes bacterial genetics, physiology, stress responses and infection-relevant models.

Data-driven analysis

We use unsupervised learning and other machine-learning approaches to detect structure in large, multidimensional datasets without strong prior assumptions. This helps us identify unexpected regulatory modules and chromosomal organisations. The lab values open, reproducible analysis workflows and close collaboration between experimental and computational team members.

Team

Daphne Denaijere

Daphne Denaijere

Research technician

Emma Bouvy

Emma Bouvy

Research Analyst

Selected publications

  • Teichmann L, Wenne M, Luitwieler S, Dugar G, et al.. Genetic adaptation to amoxicillin in Escherichia coli. PLOS One (2025).

  • Han Y, Wang B, Agnolin A, Dugar G, Hamoen LW. Ribosome pausing in amylase-producing Bacillus subtilis during long fermentation. Microbial Cell Factories (2025).

  • Wang B, Kes MBMJ, van den Berg van Saparoea ACH, Dugar G, Hamoen LW. Increasing enzyme production via LonA inactivation in Bacillus subtilis. Microbial Cell Factories (2024).

  • Dugar G, Hofmann A, Heermann DW, Hamoen LW. A chromosomal loop anchor mediating bacterial genome organisation. Nature Genetics (2022).Link

  • Jiao C, Sharma S, Dugar G, et al.. Noncanonical crRNAs enabling multiplexable RNA detection by Cas9. Science (2021).