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...

@mukherja.bsky.social work on RNAPII clusters is in print today: www.nature.com/articles/s41... Congrats! TLDR: RNAPII clusters represent transcriptonally engaged molecules at single genes, not super-stochiometric assemblies. Please check it out and see the the thread below for a summary.

(2/3) Previously, we had only looked at one gene (hunchback). Here, we extend our study to 3 additional genes (eve, snail, and sog), sister chromatids, and include multiple controls (non-transcribing loci and control spots) to more definitively claim single-cluster association with individual genes.

(3/3) We also include new simulations showing cluster visibility over background is mediated by # of engaged polymerases at a locus. Our data + sim. show that RNAPII clusters do not require higher-order assembly mechanisms and reflect local accumulations of transcriptionally engaged polymerases.

Huge props to our grad student @manyakapoor.bsky.social for developing the simulations and the new MS2 analysis amongst other things! We also thank the transcription community for their invaluable feedback and always welcome further discussion😊

(1/3) Excited to post our updated pre-print! We show RNAPII clusters are simply collections of polymerase molecules stably engaged at single genes & cluster intensity is strongly correlated with txn output during Drosophila embryogenesis. www.biorxiv.org/content/10.1...