We used hybridization chain reaction fluorescence in situ hybridization (HCR-FISH) to study RNA localization in ex vivo skeletal muscle fibers. We find that mRNAs from many genes are distributed nearly uniformly across muscle fibers, despite discovering that diffusion of RNA away from nuclei is severely restricted in muscle. By automated image analysis and stochastic simulation, we discover that frequent directed transport of RNA along microtubules is required to disperse RNAs across the fiber.
Our manuscript is live! Check it out on bioRxiv.
All code used in this study for image analysis and RNA transport simulation is written in Python.
- General image analysis pipeline
- Detection of Z-disk/microtubule intersections (ZMIs)
- Simulation of RNA transport
- Examples
- Modules
