 Congratulations to Michele, Hugo, and Asmita from the lab and Simon (Mirny lab) on the publication of their preprint in Science! This was a wonderful collaboration with Christoph Zechner and Leonid Mirny's group as well as former colleagues Claudia, Gina, and Stanley from Berkeley, where we developed a range of new experimental, microscopy, image analysis, Bayesian inference, and 3D polymer modeling approaches to directly visualize and quantify the dynamics of the structural chromatin loops that fold the human genome into domains. We show that the chromatin loops formed by CTCF and cohesin are both dynamic and short-lived (~10-30 min median lifetime) and quite rare (only present ~3-6.5% of the time) using Fbn2 as our model system. This has functional implications for how these loops may regulate downstream processes such as gene expression regulation. For more information, please see:
A representative movie and summary sketch are further shown below.  Huge credit to Michele, Hugo, Simon, and Asmita for putting all of this together! 
Congratulations to Asmita whose protocol paper is now published in Methods in Molecular Biology. Asmita wrote this step-by-step protocol to help anyone interested in Single-Particle Tracking (SPT) get started with SPT experiments and how to analyze the data. The focus is on transcription factors in mammalian cells, but we also discuss key considerations to avoid common biases in SPT and how to optimize the experiments in general. Finally, we discuss how to analyze "fastSPT" data with Spot-On. Read the full protocol here: https://link.springer.com/protocol/10.1007%2F978-1-0716-2140-0_9
New preprint: Dynamics of CTCF and cohesin mediated chromatin looping revealed by live-cell imaging2/1/2022
We are thrilled to share our preprint on the dynamics of chromatin looping. Using 3D Super-Resolution Live-Cell Imaging, we visualize the CTCF/cohesin-mediated loops that hold together TADs and loop domains for the first time in living cells. Surprisingly, these loops are both highly dynamic (median lifetime of ~10-30 min) and very rare (~3-6.5%). Instead of a stable loop, our results establish a highly dynamic view of TADs and loops where TADs exists predominantly in a partially extruded conformation. Read more here. Data here. Code here. This was a team effort and only possible due to the amazing lead from Michele, Hugo, Simon, and Asmita who lead the project and put it all together during a global pandemic! This was a collaborative project with Leonid Mirny (MIT Physics) and Christoph Zechner (Max Planck, Dresden) and the project began in Berkeley in collaboration with Gina Dailey, Claudia Cattoglio, and TH Stanley Hsieh.  
Congratulations to Harvey and Hugo on their new preprint on how DNA loop extrusion may mediate DNA double-strand break repair! Here's the abstract: DNA double-strand breaks (DSBs) occur every cell cycle and must be efficiently repaired. Non-homologous end joining (NHEJ) is the dominant pathway for DSB repair in G1-phase. The first step of NHEJ is to bring the two DSB ends back into proximity (synapsis). However, although synapsis is generally assumed to occur through passive diffusion, we show here that passive diffusion is unlikely to be consistent with the speed and efficiency of NHEJ observed in cells. Instead, we hypothesize that DNA loop extrusion facilitates synapsis. By combining experimentally constrained simulations and theory, we show that the simplest loop extrusion model only modestly facilitates synapsis. Instead, a loop extrusion model with targeted loading of loop extruding factors (LEFs), a small portion of long-lived LEFs as well as LEF stabilization by boundary elements and DSB ends achieves fast synapsis with near 100% efficiency. We propose that loop extrusion plays an underappreciated role in DSB repair. Check out BioRxiv for the full article!
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