Mir Lab

1/ Our paper, “Enhancer binding kinetics explain transcription factor hub formation,” is now published! Here we set out to understand why transcription factors form bright clusters or “hubs” in the nucleus, and whether those hubs actually control gene activity. tinyurl.com/38uf8348

8/ More broadly, our results suggest that not every bright nuclear cluster needs to be explained by a new higher-order structure or condensate. In many cases (stay tuned for more), protein-chromatin interactions, viewed through the microscope, are enough to create the appearance of a persistent hub.

1/ Our paper, “Enhancer binding kinetics explain transcription factor hub formation,” is now published! Here we set out to understand why transcription factors form bright clusters or “hubs” in the nucleus, and whether those hubs actually control gene activity. tinyurl.com/38uf8348

6/ Single-molecule tracking let us measure Dorsal’s binding and diffusion directly. When we put those kinetics into simulations (tinyurl.com/yc3tehe5), together with enhancer binding-site number, we could reproduce the enrichment and persistence of the hubs we saw experimentally.

1/ Our paper, “Enhancer binding kinetics explain transcription factor hub formation,” is now published! Here we set out to understand why transcription factors form bright clusters or “hubs” in the nucleus, and whether those hubs actually control gene activity. tinyurl.com/38uf8348

4/ We then asked whether stronger or longer-lived hubs predict transcription. Surprisingly, they mostly don’t. At a given enhancer, hub enrichment and persistence are only weakly related to transcriptional burst properties.

1/ Our paper, “Enhancer binding kinetics explain transcription factor hub formation,” is now published! Here we set out to understand why transcription factors form bright clusters or “hubs” in the nucleus, and whether those hubs actually control gene activity. tinyurl.com/38uf8348

2/ To do this, we combined high-resolution live imaging of developing Drosophila embryos, single-molecule tracking, and computational modeling to watch the transcription factor Dorsal (grey in video) interact with target (sog, sna) and a non-target gene (hb) in real time.

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...

7/🧵 We hope SPARK will allow users to assess whether the clusters they observe can be explained by DNA binding and diffusion kinetics, rather than higher-order phenomena like condensate formation.

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...

5/🧵 To demonstrate that simulated data can recapitulate key emergent condensate properties we show that clusters arising from DNA binding can show fluorescence recovery after photobleaching at similar timescales as those reported for condensates. We also observe cluster fusion in simulated movies.

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...

3/🧵 SPARK recapitulates the clustering of transcription factors like Dorsal and Bicoid in Drosophila embryos, and Sox2 in mouse ES cells, despite explicitly excluding protein-protein interactions. (Dorsal clusters shown below)

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...

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!

4/n We are seeking a microscope specialist/engineer. The role will include developing and implementing new microscope hardware, control software, customized analysis pipelines as well as collaborating with core users.

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!

2/n: ACME is co-directed by myself (Mustafa Mir), Melike Lakadamyali @melikel.bsky.social (www.lakadamyali-lab.com), Yihui Shen (www.imaging-systems-metabolism-lab.com), and Andrea Stout @aleestoutphd.bsky.social (www.med.upenn.edu/cdbmicroscopycore)

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)

8/n: We suggest that enhancers encode the biophysical properties of transcription factor hubs (intensity and stability) through binding affinities and cofactors. Hub properties dictate gene occupancy and transcriptional kinetics, suggesting hubs are active executors of enhancer-encoded regulation.

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)

6/n: Hub presence at a gene is correlated with increased transcription burst amplitude, Pol II loading rate, and total output. Surprisingly, transient interactions between Dorsal hubs and hunchback (lacking Dorsal binding) boosts transcription in ventral nuclei where Dorsal concentration is highest

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)

4/n: Next we examined Dorsal hub interactions at two target genes with distinct Dorsal occupancy and enhancer grammars, snai and sog, and as a negative control examined hunchback which has no dorsal sites.

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)

2/n: Transcription factor hubs (dense local accumulations) regulate gene expression by promoting the frequency of binding. They are often discussed as having uniform properties based on protein sequence and concentration. We wondered if their biophysical properties vary in a gene dependent manner.

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...

Major oversight in my earlier postdoc: This work was led by our wonderful postdoc @mukherja.bsky.social who also built the microscope that enabled these experiments

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...

6/n Using simultaneous imaging of nascent transcription and Pol II clusters we found that a single cluster remains associated with an active gene during a transcription burst and the intensity of the cluster is highly correlated in real time with the amount of nascent transcription.

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...

4/n We found that Pol II clusters undergo a transformation as the zygotic genome is activated. From initially being mostly composed of molecules engaged in transcription initiation to becoming hotspots of elongating molecules.

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...

2/n Since their discovery in the 1990's the functional roles and mechanisms of formation of RNAPII clusters have been heavily investigated. Models have ranged from transcription factories containing many genes to condensates that transiently "kiss” active genes.