Apratim (Appy) Mukherjee

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😊

(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.

(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.

(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...

Transcription factor hubs exhibit gene-specific properties that tune expression The spatial and temporal control of gene expression relies on transcription factors binding to and occupying their target sites. Transcription factor hubs - localized, high-concentration microenvironm...

1/n: Excited to share our new preprint. We find that Dorsal transcription factor hubs exhibit gene-specific biophysical properties that tune transcriptional output. Read here: www.biorxiv.org/content/10.1.... Project was led by amazing graduate student Samantha Fallacaro (not on bsky)

1/n Excited to share our new preprint! Using live imaging in Drosophila embryos, we show that RNA Pol II clusters switch from sites of initiation to elongation during zygotic genome activation and that they are stably associated with an active gene: www.biorxiv.org/content/10.1...

Super cool!