More Like this

1. Polymer Modeling Reveals Interplay between Physical Properties of Chromosomal DNA and the Size and Distribution of Condensin-Based Chromatin Loops

   https://doi.org/10.3390/genes14122193  

   Kolbin, Daniel; Walker, Benjamin L; Hult, Caitlin; Stanton, John Donoghue; Adalsteinsson, David; Forest, M Gregory; Bloom, Kerry (December 2023, Genes)

   Transient DNA loops occur throughout the genome due to thermal fluctuations of DNA and the function of SMC complex proteins such as condensin and cohesin. Transient crosslinking within and between chromosomes and loop extrusion by SMCs have profound effects on high-order chromatin organization and exhibit specificity in cell type, cell cycle stage, and cellular environment. SMC complexes anchor one end to DNA with the other extending some distance and retracting to form a loop. How cells regulate loop sizes and how loops distribute along chromatin are emerging questions. To understand loop size regulation, we employed bead–spring polymer chain models of chromatin and the activity of an SMC complex on chromatin. Our study shows that (1) the stiffness of the chromatin polymer chain, (2) the tensile stiffness of chromatin crosslinking complexes such as condensin, and (3) the strength of the internal or external tethering of chromatin chains cooperatively dictate the loop size distribution and compaction volume of induced chromatin domains. When strong DNA tethers are invoked, loop size distributions are tuned by condensin stiffness. When DNA tethers are released, loop size distributions are tuned by chromatin stiffness. In this three-way interaction, the presence and strength of tethering unexpectedly dictates chromatin conformation within a topological domain. 

   more » « less
2. Chromosome segregation in a minimal bacterial cell driven by SMC protein complexes

   https://doi.org/10.1002/pro.70604  

   Maytin, Andrew K; Gilbert, Benjamin R; Luthey‐Schulten, Zaida (June 2026, Protein Science)

   Abstract Minimal bacterial cells such as JCVI‐Syn3A provide a powerful system for uncovering the essential mechanisms of chromosome organization and segregation. Lacking canonical systems such as Min and ParABS, JCVI‐Syn3A relies primarily on structural maintenance of chromosomes (SMC) protein complexes for partitioning. Here, we investigate a four‐dimensional (4D; three spatial dimensions plus time) polymer‐based model of the JCVI‐Syn3A chromosome (543 kbp) that captures replication and partitioning dynamics across the full cell cycle. Our simulations reproduce chromosome segregation mediated by SMC‐driven loop extrusion and reveal how segregation depends on the number of SMC complexes, their translocation speed, and their dwell time on DNA. A systematic parameter scan shows that segregation is strongly predicted by the effective loop coverage, which represents the expected fraction of the chromosome extruded into loops. We generate contact maps for stationary‐phase cells to directly connect our simulations with 3C experiments, and for replicating chromosomes throughout the cell cycle to provide new, testable predictions for synchronized cell populations. Our results suggest that SMC protein complexes and topoisomerases can drive chromosome segregation in minimal cells without additional partitioning systems provided loop extrusion achieves sufficient genomic coverage. 

   more » « less
3. Tethering-facilitated DNA ‘opening’ and complementary roles of β-hairpin motifs in the Rad4/XPC DNA damage sensor protein

   https://doi.org/10.1093/nar/gkaa909  

   Paul, Debamita; Mu, Hong; Tavakoli, Amirrasoul; Dai, Qing; Chen, Xuejing; Chakraborty, Sagnik; He, Chuan; Ansari, Anjum; Broyde, Suse; Min, Jung-Hyun (October 2020, Nucleic Acids Research)

   null (Ed.)

   Abstract XPC/Rad4 initiates eukaryotic nucleotide excision repair on structurally diverse helix-destabilizing/distorting DNA lesions by selectively ‘opening’ these sites while rapidly diffusing along undamaged DNA. Previous structural studies showed that Rad4, when tethered to DNA, could also open undamaged DNA, suggesting a ‘kinetic gating’ mechanism whereby lesion discrimination relied on efficient opening versus diffusion. However, solution studies in support of such a mechanism were lacking and how ‘opening’ is brought about remained unclear. Here, we present crystal structures and fluorescence-based conformational analyses on tethered complexes, showing that Rad4 can indeed ‘open’ undamaged DNA in solution and that such ‘opening’ can largely occur without one or the other of the β-hairpin motifs in the BHD2 or BHD3 domains. Notably, the Rad4-bound ‘open’ DNA adopts multiple conformations in solution notwithstanding the DNA’s original structure or the β-hairpins. Molecular dynamics simulations reveal compensatory roles of the β-hairpins, which may render robustness in dealing with and opening diverse lesions. Our study showcases how fluorescence-based studies can be used to obtain information complementary to ensemble structural studies. The tethering-facilitated DNA ‘opening’ of undamaged sites and the dynamic nature of ‘open’ DNA may shed light on how the protein functions within and beyond nucleotide excision repair in cells. 

   more » « less
4. Replisomes restrict SMC translocation in vivo

   https://doi.org/10.1038/s41467-025-62596-y  

   Liao, Qin; Brandão, Hugo B; Ren, Zhongqing; Wang, Xindan (December 2025, Nature Communications)

   Abstract Structural maintenance of chromosomes (SMC) complexes organize genomes by extruding DNA loops, while replisomes duplicate entire chromosomes. These essential molecular machines must collide frequently in every cell cycle, yet how such collisions are resolved in vivo remains poorly understood. Taking advantage of the ability to load SMC complexes at defined sites in theBacillus subtilisgenome, we engineered head-on and head-to-tail collisions between SMC complexes and the replisome. Replisome progression was monitored by genome-wide marker frequency analysis, and SMC translocation was monitored by time-resolved ChIP-seq and Hi-C. We found that SMC complexes do not impede replisome progression. By contrast, replisomes restrict SMC translocation regardless of collision orientations. Combining experimental data with simulations, we determined that SMC complexes are blocked by the replisome and then released from the chromosome. Occasionally, SMC complexes can bypass the replisome and continue translocating. Our findings establish that the replisome is a barrier to SMC-mediated DNA-loop extrusion in vivo, with implications for processes such as chromosome segregation, DNA repair, and gene regulation that require dynamic chromosome organization in all organisms. 

   more » « less
5. Structural predictions of protein–DNA binding: MELD-DNA

   https://doi.org/10.1093/nar/gkad013  

   Esmaeeli, Reza; Bauzá, Antonio; Perez, Alberto (February 2023, Nucleic Acids Research)

   Abstract Structural, regulatory and enzymatic proteins interact with DNA to maintain a healthy and functional genome. Yet, our structural understanding of how proteins interact with DNA is limited. We present MELD-DNA, a novel computational approach to predict the structures of protein–DNA complexes. The method combines molecular dynamics simulations with general knowledge or experimental information through Bayesian inference. The physical model is sensitive to sequence-dependent properties and conformational changes required for binding, while information accelerates sampling of bound conformations. MELD-DNA can: (i) sample multiple binding modes; (ii) identify the preferred binding mode from the ensembles; and (iii) provide qualitative binding preferences between DNA sequences. We first assess performance on a dataset of 15 protein–DNA complexes and compare it with state-of-the-art methodologies. Furthermore, for three selected complexes, we show sequence dependence effects of binding in MELD predictions. We expect that the results presented herein, together with the freely available software, will impact structural biology (by complementing DNA structural databases) and molecular recognition (by bringing new insights into aspects governing protein–DNA interactions). 

   more » « less