Biology subjects

Grosse-Holz, S.

Publications and source records attributed to Grosse-Holz, S..

5 recordsLinked to original sources

bioRxiv2025

Chromatin Dynamics are Highly Subdiffusive Across Seven Orders of Magnitude

Chromatin dynamics control the timescales of essential biological processes including DNA damage repair and activation of gene promoters by distal enhancers. Prior chromatin dynamics studies have reported widely varying degrees of subdiffusion, likely due to technical limitations. Here, we integrate MINFLUX--a recently developed single particle tracking method capable of achieving microsecond time resolution--with traditional tracking methodologies. We tracked chromatin dynamics across seven orders of magnitude in time in both human and mouse cells and found strongly subdiffusive dynamics ( [~] 0.3). These dynamics are only mildly sensitive to perturbations of transcription, histone acetylation, and topoisomerase II, while loop extrusion has a constraining effect. Search times under these observed dynamics are extremely short for nearby loci (<100 nm), but almost impossibly long over larger distances (>1 {micro}m). These findings have important implications for processes involving two locus contacts such as enhancer-promoter search and double-strand break repair.

biophysics↗

bioRxiv2025

Genome-wide absolute quantification of chromatin looping

3D genomics methods such as Hi-C and Micro-C have uncovered chromatin loops across the genome and linked these loops to gene regulation. However, these methods only measure 3D interaction probabilities on a relative scale. Here, we overcome this limitation by using live imaging data to calibrate Micro-C in mouse embryonic stem cells, thus obtaining absolute looping probabilities for 36,804 chromatin loops across the genome. We find that the looped state is generally rare, with a mean probability of 2.3% and a maximum of 26% across the quantified loops. On average, CTCF-CTCF loops are stronger than loops between cis-regulatory elements (3.2% vs. 1.1%). Our findings can be extended to human stem cells and differentiated cells under certain assumptions. Overall, we establish an approach for genome-wide absolute loop quantification and report that loops generally occur with low probabilities, generalizing recent live imaging results to the whole genome.

biophysics↗

bioRxiv2023

Scale-free models of chromosome structure, dynamics, and mechanics

The nucleus of a cell contains its genetic information in the form of chromatin: polymers of DNA and associated proteins. The physical nature of this polymer system is yet to be understood. Orthogonal experimental approaches probing chromosome structure, dynamics, and mechanics typically suggest the existence of scaling relationships, leading to the widespread use of scale-free, or fractal, models to represent interphase chromosomes. However, currently, there is no single physical model consistent with all reported scaling exponents. Here, we consider the space of possible scale-free models of chromosome structure, dynamics, and mechanics, and examine the fundamental connections between these physical properties. We demonstrate the existence of two algebraic relationships between the scaling exponents---connecting structure with dynamics, and dynamics with mechanics, respectively---outlining the necessary physical conditions for a model to match specific exponent values. Applied to values reported in metazoans, our theory identifies the family of models consistent with all observed scalings, which notably excludes the classical Rouse, Zimm, and fractal globule polymer models. Our theory highlights dynamic correlations between distal genomic loci as necessary to reconnect seemingly contra-dictory measurements. Consequently, we propose new experiments to narrow down the space of possible models. We expect this framework to serve as a guide for understanding past and future measurements, and for building new physical models of interphase chromosomes.

biophysics↗

bioRxiv2021

Dynamics of CTCF and cohesin mediated chromatin looping revealed by live-cell imaging

Animal genomes are folded into loops and topologically associating domains (TADs) by CTCF and cohesin, but whether these loops are stable or dynamic is unknown. Here, we directly visualize chromatin looping at the Fbn2 TAD in mouse embryonic stem cells using super-resolution live-cell imaging and quantify looping dynamics by Bayesian inference. Our results are consistent with cohesin-mediated loop extrusion in cells, and with CTCF both stopping and stabilizing cohesin. Surprisingly, the Fbn2 loop is both rare and dynamic, with a looped fraction of ~3-6.5% and a median loop lifetime of ~10-30 minutes. Instead of a stable loop, our results establish a highly dynamic view of TADs and loops where the Fbn2 TAD exists predominantly in a partially extruded conformation. This dynamic and quantitative view of TADs may facilitate a mechanistic understanding of their functions.

biophysics↗

bioRxiv2021

Live-cell micromanipulation of a genomic locus reveals interphase chromatin mechanics

Our understanding of the physical principles organizing the genome in the nucleus is limited by the lack of tools to directly exert and measure forces on interphase chromosomes in vivo and probe their material nature. Here, we present a novel approach to actively manipulate a genomic locus using controlled magnetic forces inside the nucleus of a living human cell. We observe viscoelastic displacements over microns within minutes in response to near-picoNewton forces, which are well captured by a Rouse polymer model. Our results highlight the fluidity of chromatin, with a moderate contribution of the surrounding material, revealing the minor role of crosslinks and topological effects and challenging the view that interphase chromatin is a gel-like material. Our new technology opens avenues for future research, from chromosome mechanics to genome functions.

biophysics↗