Mir Lab
@mirlab.bsky.social
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
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...
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.
@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.
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...
nature.com
Apratim (Appy) Mukherjee@mukherja.bsky.social · 11mo ago(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...
We are happy to have contributed single-molecule tracking and super-resolution imaging to this great work from Nik Sgourakis' lab. HLA-Shuttle restores antigen presentation in immunologically cold tumors enabling the identification of new targets for immunotherapy. www.science.org/doi/10.1126/...
HLA-Shuttle: A system for enhancing antigen presentation in immunologically cold tumors
HLA-Shuttle enhances production of HLA class I molecules in neuroblastoma, leading to the discovery of tumor-associated antigens.
science.org
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😊
WE ARE HIRING! The lab got the Packard AND an R35! Please spread this PostDoc Ad around! Philly and Upenn are a great place to live and work!
1/n We have an exciting new initiative at UPenn to provide custom advanced microscopy solutions: Advanced Core for Microscope Engineering (ACME): www.med.upenn.edu/cdbacme/ We are looking for a specialist to help run this new facility, job description is attached please help share widely!
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)
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...
biorxiv.org
Martino Ugolini and I wrote a review on how useful embryos are to understand the role of transcription bodies in gene expression. I am sure @mirlab.bsky.social, @harrisonflylab.bsky.social, @lennarthilbert.bsky.social and others would agree. Enjoy the read! portlandpress.com/biochemsoctr....
The role of transcription bodies in gene expression: what embryos teach us
Transcription does not occur diffusely throughout the nucleus but is concentrated in specific areas. Areas of accumulated transcriptional machinery have been called clusters, hubs, or condensates, whi...
portlandpress.com
In light of policies to defund biomedical research, and with judicial hearings happening today, we hope to highlight the many ways biomedical research improves people's lives, and to convey how damaging the proposed cuts would be... not just for us researchers, but for everyone.
Jakob von Moltke@jmoltke.bsky.social · last yr.Patrick Mitchell (@psmitchej.bsky.social), Thornton Thompson and I wrote an OpEd, with support from 650+ biomedical researchers across Washington State (450+ at time of submission). www.heraldnet.com/opinion/comm... List: www.moltkelab.com/s/NIH-OpEd-S...
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...
Big congratulations to our MD/PHD student @driaadigun.bsky.social on receiving a F31 award from NIGMS to "Illuminate the Molecular Mechanisms of Replication and Transcription Coordination" during zygotic genome activation and support her training.
#BPS2024 check out our lab's presentations & pls reach out if you want to chat! Posters:B128 (@littlescholar_ ) txn activator hubs, B195(@GHaywardLara ) repressive bodies. Talks: @mukherja PolII kinetics(13th,5:30 p 201AB), myself, on how hubs find their targets (14th,9:30a BRA)
Happy Halloween from the lab, all whom decided to dress like their very scary PI this year 🎃
