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1. Chromatin accessibility profiling methods

   https://doi.org/10.1038/s43586-020-00008-9  

   Minnoye, Liesbeth; Marinov, Georgi K.; Krausgruber, Thomas; Pan, Lixia; Marand, Alexandre P.; Secchia, Stefano; Greenleaf, William J.; Furlong, Eileen E.; Zhao, Keji; Schmitz, Robert J.; et al (December 2021, Nature Reviews Methods Primers)

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2. 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)

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   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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3. Fluid-like chromatin: Toward understanding the real chromatin organization present in the cell

   https://doi.org/10.1016/j.ceb.2020.02.016  

   Maeshima, Kazuhiro; Tamura, Sachiko; Hansen, Jeffrey C.; Itoh, Yuji (June 2020, Current Opinion in Cell Biology)
4. Analysis of three-dimensional chromatin packing domains by chromatin scanning transmission electron microscopy (ChromSTEM)

   https://doi.org/10.1038/s41598-022-16028-2  

   Li, Yue; Agrawal, Vasundhara; Virk, Ranya K.; Roth, Eric; Li, Wing Shun; Eshein, Adam; Frederick, Jane; Huang, Kai; Almassalha, Luay; Bleher, Reiner; et al (December 2022, Scientific Reports)

   Abstract Chromatin organization over multiple length scales plays a critical role in the regulation of transcription. Deciphering the interplay of these processes requires high-resolution, three-dimensional, quantitative imaging of chromatin structure in vitro . Herein, we introduce ChromSTEM, a method that utilizes high-angle annular dark-field imaging and tomography in scanning transmission electron microscopy combined with DNA-specific staining for electron microscopy. We utilized ChromSTEM for an in-depth quantification of 3D chromatin conformation with high spatial resolution and contrast, allowing for characterization of higher-order chromatin structure almost down to the level of the DNA base pair. Employing mass scaling analysis on ChromSTEM mass density tomograms, we observed that chromatin forms spatially well-defined higher-order domains, around 80 nm in radius. Within domains, chromatin exhibits a polymeric fractal-like behavior and a radially decreasing mass-density from the center to the periphery. Unlike other nanoimaging and analysis techniques, we demonstrate that our unique combination of this high-resolution imaging technique with polymer physics-based analysis enables us to (i) investigate the chromatin conformation within packing domains and (ii) quantify statistical descriptors of chromatin structure that are relevant to transcription. We observe that packing domains have heterogeneous morphological properties even within the same cell line, underlying the potential role of statistical chromatin packing in regulating gene expression within eukaryotic nuclei. 

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5. Genome-wide chromatin accessibility analysis unveils open chromatin convergent evolution during polyploidization in cotton

   https://doi.org/10.1073/pnas.2209743119  

   Han, Jinlei; Lopez-Arredondo, Damar; Yu, Guangrun; Wang, Yankun; Wang, Baohua; Wall, Sarah Brooke; Zhang, Xin; Fang, Hui; Barragán-Rosillo, Alfonso Carlos; Pan, Xiaoping; et al (November 2022, Proceedings of the National Academy of Sciences)

   Allopolyploidization, resulting in divergent genomes in the same cell, is believed to trigger a “genome shock”, leading to broad genetic and epigenetic changes. However, little is understood about chromatin and gene-expression dynamics as underlying driving forces during allopolyploidization. Here, we examined the genome-wide DNase I-hypersensitive site (DHS) and its variations in domesticated allotetraploid cotton (Gossypium hirsutumandGossypium barbadense, AADD) and its extant AA (Gossypium arboreum) and DD (Gossypium raimondii) progenitors. We observed distinct DHS distributions betweenG. arboreumandG. raimondii. In contrast, the DHSs of the two subgenomes ofG. hirsutumandG. barbadenseshowed a convergent distribution. This convergent distribution of DHS was also present in the wild allotetraploidsGossypium darwiniiandG. hirsutumvar.yucatanense, but absent from a resynthesized hybrid ofG. arboreumandG. raimondii, suggesting that it may be a common feature in polyploids, and not a consequence of domestication after polyploidization. We revealed that putativecis-regulatory elements (CREs) derived from polyploidization-related DHSs were dominated by several families, including Dof, ERF48, and BPC1. Strikingly, 56.6% of polyploidization-related DHSs were derived from transposable elements (TEs). Moreover, we observed positive correlations between DHS accessibility and the histone marks H3K4me3, H3K27me3, H3K36me3, H3K27ac, and H3K9ac, indicating that coordinated interplay among histone modifications, TEs, and CREs drives the DHS landscape dynamics under polyploidization. Collectively, these findings advance our understanding of the regulatory architecture in plants and underscore the complexity of regulome evolution during polyploidization. 

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