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Reposted by Manya Kapoor

Mir Lab @mirlab.bsky.social · 07/06/2026

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...

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Reposted by Manya Kapoor

Mir Lab @mirlab.bsky.social · 20/03/2026

@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.

nature.com

A single cluster of RNA Polymerase II molecules is stably associated with active genes - Nature Communications

Live molecular-scale imaging in fly embryos shows that a single RNA Polymerase II cluster stays bound to active genes during transcription. Cluster formation requires initiation, and intensity represe...

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Reposted by Manya Kapoor

Apratim (Appy) Mukherjee @mukherja.bsky.social · 18/09/2025

(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.

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Reposted by Manya Kapoor

Apratim (Appy) Mukherjee @mukherja.bsky.social · 18/09/2025

(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.

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Reposted by Manya Kapoor

Apratim (Appy) Mukherjee @mukherja.bsky.social · 18/09/2025

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😊

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Reposted by Manya Kapoor

Apratim (Appy) Mukherjee @mukherja.bsky.social · 18/09/2025

(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...

biorxiv.org

A single cluster of RNA Polymerase II molecules is stably associated with active genes

In eukaryotic nuclei, transcription is associated with the clustering of RNA Polymerase II (RNAPII) molecules. The mechanisms underlying cluster formation, their interactions with genes, and their imp...

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