Heterochromatin causes compartmentalization of inverted and standard nuclei
Solovei, I., Thanisch, Okay. & Feodorova, Y. How one can govern the nucleus: divide and impera. Curr. Opin. Cell Biol. 40, 47-59 (2016).
Domains related to van Steensel, B. & Belmont, A. S. Lamina: hyperlinks to chromosome structure, heterochromatin and gene repression. Cell 169, 780-791 (2017).
Bonev, B. & Cavalli, G. Group and performance of the 3D genome. Nat. Rev. Broom. 17: 661-678 (2016).
Jerabek, H. & Heermann, D. W. How the chromatin loop and the nuclear envelope fixation have an effect on the group of the genome in eukaryotic cell nuclei. Int. Rev. Cell Mol. Biol. 307, 351-381 (2014).
Jost, D., Carrivain, P., Cavalli, G. & Vaillant, C. Modeling the folding of the epigenome: formation and dynamics of topologically related chromatin domains. Nucleic Acids Res. 42, 9553-9561 (2014).
Lee S., S., Tashiro, A. Awazu and A. Kobayashi. A brand new software of the section subject technique to know the mechanisms of the reorganization of the nuclear structure. J. Math. Biol. 74, 333-354 (2017).
Di Pierro, M., Zhang, B., Aiden, E.L., Wolynes, P.G. and Onuchic, J. N. Transferable mannequin for chromosome structure. Proc. Natl Acad. Sci. USA 113, 12168-12173 (2016).
Nuebler, J., Fudenberg, G., Imakaev, M., Abdennur, N. and Mirny, L. A. Chromatin. Group by a sport of loop extrusion and compartmental segregation. Proc. Natl Acad. Sci. USA 115, E6697 to E6706 (2018).
van de Werken, H.J.G. et al. Small chromosomal areas place themselves autonomously in accordance with their class of chromatin. Genome Res. 27, 922 to 933 (2017).
Larson, A.G. et al. The formation of liquid droplets by HP1α suggests a task in section separation in heterochromatin. Nature 547, 236-240 (2017).
Strom, A. R. et al. Section separation results in the formation of the heterochromatin area. Nature 547, 241-245 (2017).
Machida, S. et al. Structural foundation of human HP1 heterochromatin formation. Mol. Cell 69, 385-397 (2018).
Ganai, N., Sengupta, S. and Menon, G. I. Positioning chromosomes from segregation primarily based on exercise. Nucleic Acids Res. 42, 4145-4159 (2014).
Grosberg, A.Y. & Joanny, J.-F. Out-of-equilibrium statistical mechanics of particle mixtures in touch with completely different thermostats. Phys. Rev. E 92, 032118 (2015).
Smrek, J. and Kremer, Okay. Small variations in exercise end in section separation in active-passive polymer blends. Phys. Rev. Lett. 118, 098002 (2017).
Stevens, T.J. et al. 3D buildings of particular person mammalian genomes studied by unicellular Hello-C. Nature 544, 59-64 (2017).
Hilbert, L. et al. Transcription organizes euchromatin just like an energetic microemulsion. Pre-print at https://www.biorxiv.org/content material/10.1101/234112v2 (2018).
Zheng, X. et al. The lamins manage the worldwide genome in three dimensions from the nuclear periphery. Mol. Cell 71, 802-815 (2018).
Solovei, I. et al. The nuclear structure of photoreceptor rod cells suits the visible evolution of mammals. Cell 137, 356-368 (2009).
Solovei, I. et al. LBR and laminate A / C sequentially bind peripheral heterochromatin and inversely regulate differentiation. Cell 152, 584-598 (2013).
Eberhart, A. et al. Epigenetics of eu and heterochromatin within the inverted and standard nuclei of the mouse retina. Chromosome Res. 21, 535-554 (2013).
Tan, L., Xing, D., Chang, C.-H., Li, H. and Xie, X. S. Three-dimensional genomic buildings of distinctive sensory neurons in mouse visible and olfactory techniques. Nat. Struct. Mol. Biol. 26, 297-307 (2019).
Imakaev, M. et al. The iterative correction of Hello-C knowledge reveals the traits of chromosome group. Nat. Strategies 9, 999-1003 (2012).
Or, H. D. et al. ChromEMT: visualization of the 3D construction of chromatin and compaction in interphase and mitotic cells. Science 357, eaag0025 (2017).
Choo, Okay. H. A. The Centromere (Oxford Univ Press, 1997).
Rubinstein, M. and Colby, R. H. Polymer Physics (Oxford Univ Press, 2003).
Biggs, R., Liu, P.Z., Stephens, A.D., and Marko, J.F. Results of modifying post-translational modifications of histones on the construction and mechanics of the mitotic chromosome. Mol. Biol. Cell 30, 820-827 (2019).
Helmlinger, D. et al. Ataxin-7 expanded glutamine alters recruitment of TFTC / STAGA and chromatin construction resulting in photoreceptor dysfunction. PLoS Biol. four, e67 (2006).
Tang, S.-J. Chromatin group by repetitive parts (CORE): genomic precept of the upper order construction of chromosomes. Genesis 2, 502-515 (2011).
Rosa, A. & Everaers, R. Construction and dynamics of interphase chromosomes. PLOS Comput. Biol. four, e1000153 (2008).
Solovei, I. Fluorescence in situ hybridization (FISH) on tissue cryosections. in Strategies Mol. Biol. 659, 71-82 (2010).
Eberhart, A., Kimura H., Leonhardt H., B. & Solovei, I. Dependable detection of epigenetic histone markings and nuclear proteins in tissue cryosections. Chromosome Res. 20, 849-858 (2012).
Cremer, M. et al. Multicolored 3D Fluorescent In Situ Hybridization for Interphase Chromosome Imaging. Mol. Biol. 463, 205-239 (2018).
Walter, J. et al. To many colours in FISH on interphase nuclei preserved in 3D. Cytogenet. Genome Res. 114, 367-378 (2006).
Feodorova, Y., Koch, M., S. Bultman, S. Michalakis and S. Solovei, I. Speedy and dependable technique for the dissociation of the retina and the separation of the perikarya photoreceptor rod of grownup mice. MethodsX 2, 39-46 (2015).
Cohen, T.V. et al. The Lamin B receptor underneath transcriptional management of C / EBPε is required for the morphological however non-functional maturation of neutrophils. Hum. Mol. Broom. 17, 2921-2933 (2008).
Naumova, N. et al. Group of the mitotic chromosome. Science 342, 948-953 (2013).
Heinz, S. et al. Easy combos of lineage-determining transcription components optimize the cis-regulatory parts vital for the identities of macrophages and B cells. Mol. Cell 38, 576-589 (2010).
Nora, E.P. et al. Focused degradation of CTCF dissociates the native isolation of chromosomal domains from genomic compartmentalization. Cell 169, 930-944 (2017).
Flyamer, I.M. et al. Hello-C mononuclear reveals a singular reorganization of chromatin throughout the oocyte to zygote transition. Nature 544, 110-114 (2017).
Crane, E. et al. Transforming of the chromosome X topology attributable to the condensate throughout the compensation of the dosage. Nature 523, 240-244 (2015).
Eastman, P. et al. OpenMM four: A reusable, extensible, hardware-independent library for prime efficiency molecular simulation. J. Chem. Comput Concept. 9, 461-469 (2013).
Eastman, P. et al. OpenMM 7: speedy improvement of excessive efficiency algorithms for molecular dynamics. PLOS Comput. Biol. 13, e1005659 (2017).
Abdennur, N. & Mirny, L. Cooler: Evolutionary storage for Hello-C knowledge and different genomically labeled matrices. Pre-print on https://www.biorxiv.org/content material/10.1101/557660v1 (2019).
Shultz, L. D. et al. Mutations on the mouse ichthyosis locus are discovered within the laminamine B receptor gene: a single-gene mannequin for the Pelger-Huet human anomaly. Hum. Mol. Broom. 12, 61-69 (2003).
Dixon, J. R. et al. Topological domains in mammalian genomes recognized by evaluation of chromatin interactions. Nature 485, 376-380 (2012).
Rao, S.P. S. et al. A 3D map of the human genome at decision in kilobases reveals the rules of the chromatin loop. Cell 159, 1665-1680 (2014).
Schwarzer, W. et al. Two impartial modes of chromatin group revealed by the elimination of cohesin. Nature 551, 51-56 (2017).
Grant, C.E., Bailey, T.L. and Noble, W.S.FIMO: Prevalence seek for a given motive. Bioinformatics 27, 1017-1018 (2011).
Schmidt, D. et al. Enlargement waves of retrotransposons reshape the group of the genome and the binding of CTCF in a number of mammalian lineages. Cell 148, 335-348 (2012).
Kerpedjiev, P. et al. HiGlass: visible exploration and internet evaluation of genomic interplay maps. Genome Biol. 19, 125 (2018).
Zhang, Y. et al. Spatial group of the mouse genome and its position in recurrent chromosomal translocations. Cell 148, 908-921 (2012).
Lin, Y.C. et al. World adjustments in nuclear gene positioning and intra and interdomain genomic interactions that orchestrate the destiny of B. Nat. Immunol. 13, 1196-1204 (2012).
Kizilyaprak, C., Spehner, D., Devys D., and Schultz P., P. An in vivo group of mouse rod photoreceptor chromatin is correlated with adjustments in histone. PLoS ONE 5, e11039 (2010).