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1. Nanoscale chromatin imaging and analysis platform bridges 4D chromatin organization with molecular function

   https://doi.org/10.1126/sciadv.abe4310  

   Li, Yue; Eshein, Adam; Virk, Ranya K.A.; Eid, Aya; Wu, Wenli; Frederick, Jane; VanDerway, David; Gladstein, Scott; Huang, Kai; Shim, Anne R.; et al (January 2021, Science Advances)

   null (Ed.)

   Extending across multiple length scales, dynamic chromatin structure is linked to transcription through the regulation of genome organization. However, no individual technique can fully elucidate this structure and its relation to molecular function at all length and time scales at both a single-cell level and a population level. Here, we present a multitechnique nanoscale chromatin imaging and analysis (nano-ChIA) platform that consolidates electron tomography of the primary chromatin fiber, optical super-resolution imaging of transcription processes, and label-free nano-sensing of chromatin packing and its dynamics in live cells. Using nano-ChIA, we observed that chromatin is localized into spatially separable packing domains, with an average diameter of around 200 nanometers, sub-megabase genomic size, and an internal fractal structure. The chromatin packing behavior of these domains exhibits a complex bidirectional relationship with active gene transcription. Furthermore, we found that properties of PDs are correlated among progenitor and progeny cells across cell division. 

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2. Explicit ion modeling predicts physicochemical interactions for chromatin organization

   https://doi.org/10.7554/eLife.90073  

   Lin, Xingcheng; Zhang, Bin (January 2024, eLife)

   Molecular mechanisms that dictate chromatin organization in vivo are under active investigation, and the extent to which intrinsic interactions contribute to this process remains debatable. A central quantity for evaluating their contribution is the strength of nucleosome-nucleosome binding, which previous experiments have estimated to range from 2 to 14k_BT. We introduce an explicit ion model to dramatically enhance the accuracy of residue-level coarse-grained modeling approaches across a wide range of ionic concentrations. This model allows for de novo predictions of chromatin organization and remains computationally efficient, enabling large-scale conformational sampling for free energy calculations. It reproduces the energetics of protein-DNA binding and unwinding of single nucleosomal DNA, and resolves the differential impact of mono- and divalent ions on chromatin conformations. Moreover, we showed that the model can reconcile various experiments on quantifying nucleosomal interactions, providing an explanation for the large discrepancy between existing estimations. We predict the interaction strength at physiological conditions to be 9k_BT, a value that is nonetheless sensitive to DNA linker length and the presence of linker histones. Our study strongly supports the contribution of physicochemical interactions to the phase behavior of chromatin aggregates and chromatin organization inside the nucleus. 

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3. Chromatin conformation, gene transcription, and nucleosome remodeling as an emergent system

   https://doi.org/10.1126/sciadv.adq6652  

   Almassalha, Luay M; Carignano, Marcelo; Liwag, Emily Pujadas; Li, Wing Shun; Gong, Ruyi; Acosta, Nicolas; Dunton, Cody L; Gonzalez, Paola Carrillo; Carter, Lucas M; Kakkaramadam, Rivaan; et al (January 2025, Science Advances)

   In single cells, variably sized nanoscale chromatin structures are observed, but it is unknown whether these form a cohesive framework that regulates RNA transcription. Here, we demonstrate that the human genome is an emergent, self-assembling, reinforcement learning system. Conformationally defined heterogeneous, nanoscopic packing domains form by the interplay of transcription, nucleosome remodeling, and loop extrusion. We show that packing domains are not topologically associated domains. Instead, packing domains exist across a structure-function life cycle that couples heterochromatin and transcription in situ, explaining how heterochromatin enzyme inhibition can produce a paradoxical decrease in transcription by destabilizing domain cores. Applied to development and aging, we show the pairing of heterochromatin and transcription at myogenic genes that could be disrupted by nuclear swelling. In sum, packing domains represent a foundation to explore the interactions of chromatin and transcription at the single-cell level in human health. 

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4. Chromatin fiber breaks into clutches under tension and crowding

   https://doi.org/10.1093/nar/gkac725  

   Liu, Shuming; Lin, Xingcheng; Zhang, Bin (August 2022, Nucleic Acids Research)

   Abstract The arrangement of nucleosomes inside chromatin is of extensive interest. While in vitro experiments have revealed the formation of 30 nm fibers, most in vivo studies have failed to confirm their presence in cell nuclei. To reconcile the diverging experimental findings, we characterized chromatin organization using a residue-level coarse-grained model. The computed force–extension curve matches well with measurements from single-molecule experiments. Notably, we found that a dodeca-nucleosome in the two-helix zigzag conformation breaks into structures with nucleosome clutches and a mix of trimers and tetramers under tension. Such unfolded configurations can also be stabilized through trans interactions with other chromatin chains. Our study suggests that unfolding from chromatin fibers could contribute to the irregularity of in vivo chromatin configurations. We further revealed that chromatin segments with fibril or clutch structures engaged in distinct binding modes and discussed the implications of these inter-chain interactions for a potential sol–gel phase transition. 

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5. Mature chromatin packing domains persist after RAD21 depletion in 3D

   https://doi.org/10.1126/sciadv.adp0855  

   Li, Wing Shun; Carter, Lucas M; Almassalha, Luay Matthew; Gong, Ruyi; Pujadas-Liwag, Emily M; Kuo, Tiffany; MacQuarrie, Kyle L; Carignano, Marcelo; Dunton, Cody; Dravid, Vinayak; et al (January 2025, Science Advances)

   Understanding chromatin organization requires integrating measurements of genome connectivity and physical structure. It is well established that cohesin is essential for TAD and loop connectivity features in Hi-C, but the corresponding change in physical structure has not been studied using electron microscopy. Pairing chromatin scanning transmission electron tomography with multiomic analysis and single-molecule localization microscopy, we study the role of cohesin in regulating the conformationally defined chromatin nanoscopic packing domains. Our results indicate that packing domains are not physical manifestation of TADs. Using electron microscopy, we found that only 20% of packing domains are lost upon RAD21 depletion. The effect of RAD21 depletion is restricted to small, poorly packed (nascent) packing domains. In addition, we present evidence that cohesin-mediated loop extrusion generates nascent domains that undergo maturation through nucleosome posttranslational modifications. Our results demonstrate that a 3D genomic structure, composed of packing domains, is generated through cohesin activity and nucleosome modifications. 

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