Lab run by Mustafa Mir studying transcription and nuclear organization using live imaging at University of Pennsylvania, Children's Hospital of Philadelphia, and Howard Hughes Medical Institute. mir-lab.com
Mir Lab
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Samantha Fallacaro in the @mirlab.bsky.social defends her thesis tomorrow!
7/🧵 We hope SPARK will allow users to assess whether the clusters they observe can be explained by DNA binding and diffusion kinetics, rather than higher-order phenomena like condensate formation.
1/🧵 Can transcription factor condensate formation be explained without phase separation? Our new preprint introduces SPARK, a simulation tool that reproduces condensate behavior (clustering, fusion, FRAP) from diffusion & binding kinetics alone. Movie: 60 sec FRAP sim www.biorxiv.org/content/10.6...
Video
8/🧵 SPARK was developed by @pennengineering.bsky.social bioengineering graduate student Manya Kapoor @manyakapoor.bsky.social and inspired by our recent experimental results on Pol II (www.nature.com/articles/s41...) and Dorsal clustering (www.biorxiv.org/content/10.1...)
3/🧵 SPARK recapitulates the clustering of transcription factors like Dorsal and Bicoid in Drosophila embryos, and Sox2 in mouse ES cells, despite explicitly excluding protein-protein interactions. (Dorsal clusters shown below)
5/🧵 To demonstrate that simulated data can recapitulate key emergent condensate properties we show that clusters arising from DNA binding can show fluorescence recovery after photobleaching at similar timescales as those reported for condensates. We also observe cluster fusion in simulated movies.
2/🧵 SPARK (Simulation of Protein Accumulation from Reaction Kinetics) takes in experimentally-measurable binding site information and molecular kinetic parameters and generates molecular trajectories. It outputs simulated microscope images under user-defined imaging conditions (mag, exposure, etc.)
Mir Lab
CAMB Graduate Group
Mir Lab
6/🧵 SPARK is packaged with a user-friendly GUI for those who want to gain intuition about how cluster properties emerge and also for use with high-performance computing for more involved simulations and parameter sweeps. Download software and user manual here: doi.org/10.5281/zeno...
Very proud of Samantha "S" Fallacaro the first student from our lab to defend their thesis! Check out her latest work (tinyurl.com/42hdfssz) where she shows that "hubs" formed by the transcription factor Dorsal are emergent features of binding kinetics, not higher-order regulatory assemblies.
4/🧵 In addition to simulating 3D time lapse movies, SPARK can also be used to render super-resolution data for comparison to published work. Image below shows a simulation of Sox2 clustering in mESCs
