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1. The ancestral chromatin landscape of land plants

   https://doi.org/10.1111/nph.19311  

   Hisanaga, Tetsuya; Wu, Shuangyang; Schafran, Peter; Axelsson, Elin; Akimcheva, Svetlana; Dolan, Liam; Li, Fay‐Wei; Berger, Frédéric (October 2023, New Phytologist)

   Summary Recent studies have shown that correlations between chromatin modifications and transcription vary among eukaryotes. This is the case for marked differences between the chromatin of the mossPhyscomitrium patensand the liverwortMarchantia polymorpha. Mosses and liverworts diverged from hornworts, altogether forming the lineage of bryophytes that shared a common ancestor with land plants. We aimed to describe chromatin in hornworts to establish synapomorphies across bryophytes and approach a definition of the ancestral chromatin organization of land plants.We used genomic methods to define the 3D organization of chromatin and map the chromatin landscape of the model hornwortAnthoceros agrestis.We report that nearly half of the hornwort transposons were associated with facultative heterochromatin and euchromatin and formed the center of topologically associated domains delimited by protein coding genes. Transposons were scattered across autosomes, which contrasted with the dense compartments of constitutive heterochromatin surrounding the centromeres in flowering plants.Most of the features observed in hornworts are also present in liverworts or in mosses but are distinct from flowering plants. Hence, the ancestral genome of bryophytes was likely a patchwork of units of euchromatin interspersed within facultative and constitutive heterochromatin. We propose this genome organization was ancestral to land plants. 

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2. The solid and liquid states of chromatin

   https://doi.org/10.1186/s13072-021-00424-5  

   Hansen, Jeffrey C.; Maeshima, Kazuhiro; Hendzel, Michael J. (October 2021, Epigenetics & Chromatin)

   Abstract The review begins with a concise description of the principles of phase separation. This is followed by a comprehensive section on phase separation of chromatin, in which we recount the 60 years history of chromatin aggregation studies, discuss the evidence that chromatin aggregation intrinsically is a physiologically relevant liquid–solid phase separation (LSPS) process driven by chromatin self-interaction, and highlight the recent findings that under specific solution conditions chromatin can undergo liquid–liquid phase separation (LLPS) rather than LSPS. In the next section of the review, we discuss how certain chromatin-associated proteins undergo LLPS in vitro and in vivo. Some chromatin-binding proteins undergo LLPS in purified form in near-physiological ionic strength buffers while others will do so only in the presence of DNA, nucleosomes, or chromatin. The final section of the review evaluates the solid and liquid states of chromatin in the nucleus. While chromatin behaves as an immobile solid on the mesoscale, nucleosomes are mobile on the nanoscale. We discuss how this dual nature of chromatin, which fits well the concept of viscoelasticity, contributes to genome structure, emphasizing the dominant role of chromatin self-interaction. 

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3. Chromatin assembly: Journey to the CENter of the chromosome

   https://doi.org/10.1083/jcb.201605005  

   Chen, Chin-Chi; Mellone, Barbara G. (July 2016, The Journal of Cell Biology)

   All eukaryotic genomes are packaged into basic units of DNA wrapped around histone proteins called nucleosomes. The ability of histones to specify a variety of epigenetic states at defined chromatin domains is essential for cell survival. The most distinctive type of chromatin is found at centromeres, which are marked by the centromere-specific histone H3 variant CENP-A. Many of the factors that regulate CENP-A chromatin have been identified; however, our understanding of the mechanisms of centromeric nucleosome assembly, maintenance, and reorganization remains limited. This review discusses recent insights into these processes and draws parallels between centromeric and noncentromeric chromatin assembly mechanisms. 

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4. Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin

   https://doi.org/10.1016/j.cell.2020.09.056  

   Ma, Sai; Zhang, Bing; LaFave, Lindsay M.; Earl, Andrew S.; Chiang, Zachary; Hu, Yan; Ding, Jiarui; Brack, Alison; Kartha, Vinay K.; Tay, Tristan; et al (November 2020, Cell)
5. CENP-N promotes the compaction of centromeric chromatin

   https://doi.org/10.1038/s41594-022-00758-y  

   Zhou, Keda; Gebala, Magdalena; Woods, Dustin; Sundararajan, Kousik; Edwards, Garrett; Krzizike, Dan; Wereszczynski, Jeff; Straight, Aaron F.; Luger, Karolin (April 2022, Nature Structural & Molecular Biology)

   Abstract The histone variant CENP-A is the epigenetic determinant for the centromere, where it is interspersed with canonical H3 to form a specialized chromatin structure that nucleates the kinetochore. How nucleosomes at the centromere arrange into higher order structures is unknown. Here we demonstrate that the human CENP-A-interacting protein CENP-N promotes the stacking of CENP-A-containing mononucleosomes and nucleosomal arrays through a previously undefined interaction between the α6 helix of CENP-N with the DNA of a neighboring nucleosome. We describe the cryo-EM structures and biophysical characterization of such CENP-N-mediated nucleosome stacks and nucleosomal arrays and demonstrate that this interaction is responsible for the formation of densely packed chromatin at the centromere in the cell. Our results provide first evidence that CENP-A, together with CENP-N, promotes specific chromatin higher order structure at the centromere. 

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