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1. DNA methylation-based high-resolution mapping of long-distance chromosomal interactions in nucleosome-depleted regions

   https://doi.org/10.1038/s41467-024-48718-y  

   Li, Yi; Lee, James; Bai, Lu (May 2024, Nature Communications)

   NA (Ed.)

   Abstract 3C-based methods have significantly advanced our understanding of 3D genome organization. However, it remains a formidable task to precisely capture long-range chromosomal interactions between individual loci, such as those between promoters and distal enhancers. Here, we presentMethyltransferaseTargeting-based chromosomeArchitectureCapture (MTAC), a method that maps the contacts between a target site (viewpoint) and the rest of the genome in budding yeast with high resolution and sensitivity. MTAC detects hundreds of intra- and inter-chromosomal interactions within nucleosome-depleted regions (NDRs) that cannot be captured by 4C, Hi-C, or Micro-C. By applying MTAC to various viewpoints, we find that (1) most long-distance chromosomal interactions detected by MTAC reflect tethering by the nuclear pore complexes (NPCs), (2) genes co-regulated by methionine assemble into inter-chromosomal clusters near NPCs upon activation, (3) mediated by condensin, the mating locus forms a highly specific interaction with the recombination enhancer (RE) in a mating-type specific manner, and (4) correlation of MTAC signals among NDRs reveal spatial mixing and segregation of the genome. Overall, these results demonstrate MTAC as a powerful tool to resolve fine-scale long-distance chromosomal interactions and provide insights into the 3D genome organization. 

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2. Statistical mechanics of chromosomes: in vivo and in silico approaches reveal high-level organization and structure arise exclusively through mechanical feedback between loop extruders and chromatin substrate properties

   https://doi.org/10.1093/nar/gkaa871  

   He, Yunyan; Lawrimore, Josh; Cook, Diana; Van Gorder, Elizabeth Erin; De Larimat, Solenn Claire; Adalsteinsson, David; Forest, M Gregory; Bloom, Kerry (October 2020, Nucleic Acids Research)

   null (Ed.)

   Abstract The revolution in understanding higher order chromosome dynamics and organization derives from treating the chromosome as a chain polymer and adapting appropriate polymer-based physical principles. Using basic principles, such as entropic fluctuations and timescales of relaxation of Rouse polymer chains, one can recapitulate the dominant features of chromatin motion observed in vivo. An emerging challenge is to relate the mechanical properties of chromatin to more nuanced organizational principles such as ubiquitous DNA loops. Toward this goal, we introduce a real-time numerical simulation model of a long chain polymer in the presence of histones and condensin, encoding physical principles of chromosome dynamics with coupled histone and condensin sources of transient loop generation. An exact experimental correlate of the model was obtained through analysis of a model-matching fluorescently labeled circular chromosome in live yeast cells. We show that experimentally observed chromosome compaction and variance in compaction are reproduced only with tandem interactions between histone and condensin, not from either individually. The hierarchical loop structures that emerge upon incorporation of histone and condensin activities significantly impact the dynamic and structural properties of chromatin. Moreover, simulations reveal that tandem condensin–histone activity is responsible for higher order chromosomal structures, including recently observed Z-loops. 

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3. Chemically Induced Chromosomal Interaction (CICI) method to study chromosome dynamics and its biological roles

   https://doi.org/10.1038/s41467-022-28416-3  

   Du, Manyu; Zou, Fan; Li, Yi; Yan, Yujie; Bai, Lu (December 2022, Nature Communications)

   Abstract Numerous intra- and inter-chromosomal contacts have been mapped in eukaryotic genomes, but it remains challenging to link these 3D structures to their regulatory functions. To establish the causal relationships between chromosome conformation and genome functions, we  develop a method, Chemically Induced Chromosomal Interaction (CICI), to selectively perturb the chromosome conformation at targeted loci. Using this method, long-distance chromosomal interactions can be induced dynamically between intra- or inter-chromosomal loci pairs, including the ones with very low Hi-C contact frequencies. Measurement of CICI formation time allows us to probe chromosome encounter dynamics between different loci pairs across the cell cycle. We also conduct two functional tests of CICI. We perturb the chromosome conformation near a DNA double-strand break and observe altered donor preference in homologous recombination; we force interactions between early and late-firing DNA replication origins and find no significant changes in replication timing. These results suggest that chromosome conformation plays a deterministic role in homology-directed DNA repair, but not in the establishment of replication timing. Overall, our study demonstrates that CICI is a powerful tool to study chromosome dynamics and 3D genome function. 

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4. Loops and the activity of loop extrusion factors constrain chromatin dynamics

   https://doi.org/10.1091/mbc.E23-04-0119  

   Bailey, Mary Lou; Surovtsev, Ivan; Williams, Jessica F.; Yan, Hao; Yuan, Tianyu; Li, Kevin; Duseau, Katherine; Mochrie, Simon G.; King, Megan C. (July 2023, Molecular Biology of the Cell)

   Bloom, Kerry (Ed.)

   The chromosomes—DNA polymers and their binding proteins—are compacted into a spatially organized, yet dynamic, three-dimensional structure. Recent genome-wide chromatin conformation capture experiments reveal a hierarchical organization of the DNA structure that is imposed, at least in part, by looping interactions arising from the activity of loop extrusion factors. The dynamics of chromatin reflects the response of the polymer to a combination of thermal fluctuations and active processes. However, how chromosome structure and enzymes acting on chromatin together define its dynamics remains poorly understood. To gain insight into the structure-dynamics relationship of chromatin, we combine high-precision microscopy in living Schizosaccharomyces pombe cells with systematic genetic perturbations and Rouse model polymer simulations. We first investigated how the activity of two loop extrusion factors, the cohesin and condensin complexes, influences chromatin dynamics. We observed that deactivating cohesin, or to a lesser extent condensin, increased chromatin mobility, suggesting that loop extrusion constrains rather than agitates chromatin motion. Our corresponding simulations reveal that the introduction of loops is sufficient to explain the constraining activity of loop extrusion factors, highlighting that the conformation adopted by the polymer plays a key role in defining its dynamics. Moreover, we find that the number of loops or residence times of loop extrusion factors influence the dynamic behavior of the chromatin polymer. Last, we observe that the activity of the INO80 chromatin remodeler, but not the SWI/SNF or RSC complexes, is critical for ATP-dependent chromatin mobility in fission yeast. Taking the data together, we suggest that thermal and INO80-dependent activities exert forces that drive chromatin fluctuations, which are constrained by the organization of the chromosome into loops. 

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5. A data-driven chromatin model reveals spatial and dynamic features of genome organization

   https://doi.org/10.1073/pnas.2530583123  

   Oliveira_Junior, Antonio B; Mello, Matheus F; Oliveira, Ronaldo J; Dodero-Rojas, Esteban; Brahmachari, Sumitabha; Contessoto, Vinícius G; Onuchic, José N (January 2026, Proceedings of the National Academy of Sciences)

   Compacting chromatin within the cellular nucleus presents a significant challenge for biology. Chromosomes must be both condensed and spatially organized to enable essential processes such as transcription and replication. Chromosome conformation capture experiments (e.g., Hi-C) provide valuable information about the spatial organization and, therefore, the connectivity between different genomic regions. These experiments inspired polymer models that describe the physical mechanism of the chromosomal energy landscape. The Full-Inversion Chromatin model (FI-Chrom), a data-driven approach for modeling genome organization, uses Hi-C contact maps to infer pairwise interaction potentials between all chromosomal loci. It combines Graphics Processing Unit (GPU)-accelerated simulations with efficient training of tens of millions of parameters derived from the maximum-entropy principle to determine 3D structures of chromosomes that accurately reproduce Hi-C-like data. FI-Chrom does not make any a priori assumptions regarding chromosome architecture, making it applicable to any chromosome conformation capture experiment. Its derived structural ensembles capture all essential features from the short- and long-range interactions of typical chromosome organization, such as segregated compartments, chromosome territories, and fully or partially formed loops. Although Hi-C contains only structural information, FI-Chrom extends these data by revealing an emergent dynamical mechanism encoded in the inferred energy landscape. For example, simulations show that chromatin loops are not static architectural features but rather transient structural elements. Statistical analyses further indicate that loops confined within a single compartment occur more frequently than those spanning multiple compartments, highlighting the dynamic and compartment-dependent nature of chromatin organization. 

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