Genome-wide protein-DNA interaction site mapping using a double strand DNA-specific cytosine deaminase
Gallagher, L. A.; Velazquez, E.; Peterson, S. B.; Charity, J. C.; Hsu, F.; Radey, M. C.; Gebhardt, M. J.; de Moraes, M. H.; Penewit, K. M.; Kim, J.; Andrade, P. A.; LaFramboise, T.; Salipante, S. J.; de Lorenzo, V.; Wiggins, P. A.; Dove, S. L.; Mougous, J.
Show abstract
DNA-protein interactions (DPIs) are central to such fundamental cellular processes as transcription and chromosome maintenance and organization. The spatiotemporal dynamics of these interactions dictate their functional consequences; therefore, there is great interest in facile methods for defining the sites of DPI within cells. Here, we present a general method for mapping DPI sites in vivo using the double stranded DNA-specific cytosine deaminase toxin DddA. Our approach, which we term DddA-sequencing (3D-seq), entails generating a translational fusion of DddA to a DNA binding protein of interest, inactivating uracil DNA glycosylase, modulating DddA activity via its natural inhibitor protein, and DNA sequencing for genome-wide DPI detection. We successfully applied this method to three Pseudomonas aeruginosa transcription factors that represent divergent protein families and bind variable numbers of chromosomal locations. 3D-seq offers several advantages over existing technologies including ease of implementation and the possibility to measure DPIs at single-cell resolution.
Matching journals
The top 6 journals account for 50% of the predicted probability mass.
Similar papers in this journal
Similar papers in this journal
Similar papers in this journal
- The conserved transcriptional regulator CdnL is required for metabolic homeostasis and morphogenesis in Caulobacter 96%
- The glutathione import system satisfies the Staphylococcus aureus nutrient sulfur requirement and promotes interspecies competition. 95%
- Evaluation of the fitness benefit conferred by RNA cis-regulators to Streptococcus pneumoniae during infection 95%
Similar papers in this journal
- Amoxicillin-resistant Streptococcus pneumoniae can be resensitized by targeting the mevalonate pathway as indicated by sCRilecs-seq 96%
- Periplasm homeostatic regulation maintains spatial constraints essential for cell envelope processes and cell viability 96%
- A simple mechanism for integration of quorum sensing and cAMP signalling in V. cholerae 96%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.