The genome in space and time comes of age

References

• Brown R. Observations on the organs and mode of fecundation in Orchideae and asclepiadeae. Taylor, editor.London: Taylor, Transactions of the Linnean Society; 1831.
   Google Scholar
• Rabl C. « Über Zelltheilung ». Morpholo Jahrb. 1885;10:214330.
   Google Scholar
• Feulgen R, Rossenbeck H. « Mikroskopisch-Chemischer Nachweis Einer Nucleinsäure Vom Typus Der Thymonucleinsäure Und Die- Darauf Beruhende Elektive Färbung von Zellkernen in Mikroskopischen Präparaten. ». 1924;135(56):20348. doi: 10.1515/bchm2.1924.135.5-6.203
   Google Scholar
• Olins AL, Olins DE. « spheroid chromatin units (v bodies) ». Science. 1974;183(4122):33032. doi: 10.1126/science.183.4122.330
   Web of Science ®Google Scholar
• Tashiro S, Lanctôt C. « the international nucleome consortium ». Nucleus. 2015;6(2):8992. doi: 10.1080/19491034.2015.1022703
   Web of Science ®Google Scholar
• Marti-Renom MA, Almouzni G, Bickmore WA, et al. « challenges and guidelines toward 4D nucleome data and Model standards ». Nature Genet. 2018;50(10):135258. do i:
   Web of Science ®Google Scholar
• Cremer T, Cremer M, Hübner B, et al. « the interchromatin compartment participates in the structural and functional organization of the cell nucleus ». BioEssays. 2020;42(2):1900132. doi: 10.1002/bies.201900132
   Web of Science ®Google Scholar
• Gelléri M, Chen S-Y, Hübner B, et al. « true-to-scale DNA-density maps correlate with major accessibility differences between active and inactive chromatin ». Cell Rep. 2023;42(6):112567. doi: 10.1016/j.celrep.2023.112567
   PubMed Web of Science ®Google Scholar
• Mota-Gómez I, Antonio Rodríguez J, Dupont S, et al. « sex-determining 3D regulatory hubs revealed by genome spatial auto-correlation analysis ». 2022; bioRxiv. doi: 10.1101/2022.11.18.516861
   Google Scholar
• Madsen-Østerbye J, Abdelhalim M, Baudement M-O, et al. « local euchromatin enrichment in lamina-associated domains anticipates their repositioning in the adipogenic lineage ». Genome Bio. 2022;23(1):91. doi: 10.1186/s13059-022-02662-6
   PubMed Web of Science ®Google Scholar
• Sebestyén E, Marullo F, Lucini F, et al. « SAMMY-Seq reveals early alteration of Heterochromatin and deregulation of bivalent genes in Hutchinson-Gilford progeria syndrome ». Nat Commun. 2020;11(1):6274. do i:
   PubMed Web of Science ®Google Scholar
• Xie T, Danieli-Mackay A, Buccarelli M, et al. « Extreme Structural Heterogeneity Rewires Glioblastoma Chromosomes to Sustain Patient-Specific Transcriptional Programs ». 2023; bioRxiv. doi: 10.1101/2023.04.20.537702
   Google Scholar
• Fackelmayer FO, Dahm K, Renz A, et al. « nucleic-acid-binding properties of HnRNP-U/SAF-A, a Nuclear-Matrix Protein Which Binds DNA and RNA in vivo and in vitro ». Eur J Biochem. 1994;221(2):74957. doi: 10.1111/j.1432-1033.1994.tb18788.x
   Google Scholar
• Isiaka BN, Semple JI, Haemmerli A, et al. « cohesin forms fountains at active enhancers in C. Elegans ». 2023; bioRxiv. doi: 10.1101/2023.07.14.549011
   Google Scholar
• Tomás-Daza L, Rovirosa L, López-Martí P, et al. « low input capture hi-C (LiChi-C) identifies promoter-enhancer interactions at high-resolution ». Nat Commun. 2023;14(1):268.
   PubMed Web of Science ®Google Scholar
• Serra F, Nieto-Aliseda A, Fanlo L, et al. « P53 rapidly restructures 3D chromatin organization to trigger a transcriptional response ». 2023; bioRxiv. DOI:10.1101/2023.10.10.561663
   Google Scholar
• Aljahani A, Hua P, Karpinska MA, et al. « analysis of sub-kilobase chromatin topology reveals nano-scale regulatory interactions with variable dependence on cohesin and CTCF ». Nat Commun. 2022;13(1):2139. doi: 10.1038/s41467-022-29696-5
   PubMed Web of Science ®Google Scholar
• Shyam R, Aljahani A, Magdalena AK, et al. « the mediator complex regulates enhancer-promoter interactions ». Nat Struct Mol Biol. 2023;30(7):9911000. doi: 10.1038/s41594-023-01027-2
   Web of Science ®Google Scholar
• Mahrik L, Stefanovie B, Maresova A, et al. « the SAGA histone acetyltransferase module targets SMC5/6 to specific genes ». Epigenet Chromatin. 2023;16(1):6. doi: 10.1186/s13072-023-00480-z
   PubMed Web of Science ®Google Scholar
• Cortés-Mancera FM, Sarno F, Goubert D, et al. « gene-targeted DNA methylation: towards long-lasting reprogramming of gene expression? ». Adv Exp Med Biol. 2022;1389:51533. doi: 10.1007/978-3-031-11454-0_18
   Google Scholar
• Đorđević M, Stepper P, Feuerstein-Akgoz C, et al. « EpiCRISPR targeted methylation of arx gene initiates transient switch of mouse pancreatic alpha to insulin-producing cells ». Front Endocrinol (Lausanne). 2023;14:1134478. doi: 10.3389/fendo.2023.1134478
   PubMed Web of Science ®Google Scholar
• Logie E, Van Puyvelde B, Cuypers B, et al. « ferroptosis induction in multiple myeloma cells triggers DNA methylation and histone modification changes associated with cellular senescence ». Int J Mol Sci. 2021;22(22):12234. doi: 10.3390/ijms222212234
   PubMed Web of Science ®Google Scholar
• Stankevičius V, Gibas P, Masiulionytė B, et al. « selective chemical tracking of Dnmt1 catalytic activity in live cells ». Molecular Cell. 2022;82(5):1053–1065.e8. doi: 10.1016/j.molcel.2022.02.008
   PubMed Web of Science ®Google Scholar
• Beckman WF, Ángel Lermo Jiménez M, Moerland PD, et al. « 4sUDRB-Sequencing for Genome-Wide Transcription Bursting Quantification in Breast Cancer Cells ». bioRxiv. 2021. doi: 10.1101/2020.12.23.424175
   Google Scholar
• Kocanova S, Raynal F, Goiffon I, et al. « enhancer-driven local 3D chromatin domain folding modulates transcription in human mammary tumor cells ». 2023. bioRxiv. doi: 10.1101/2023.10.17.562690
   Google Scholar
• Shaban HA, Barth R, Recoules L, et al. « hi-D: nanoscale mapping of nuclear dynamics in single living cells ». Genome Bio. 2020;21(1):95. doi: 10.1186/s13059-020-02002-6
   PubMed Web of Science ®Google Scholar
• Salari H, Fourel G, Jost D. 2023. « transcription regulates the Spatio-Temporal Dynamics of Genes through micro-compartmentalization ». bioRxiv. doi: 10.1101/2023.07.18.549489.
   Google Scholar
• Anastasia C, Chatzantonaki E, Soupsana K, et al. « heterochromatin remodeling in embryonic stem cells proceeds through stochastic de-stabilization of regional steady-states ». Biochim Biophys Acta Gene Regul Mech. 2017;18606:66173. doi: 10.1016/j.bbagrm.2017.01.009
   Web of Science ®Google Scholar
• Gnan S, Flyamer IM, Klein KN, et al. « nuclear organisation and replication timing are coupled through RIF1–PP1 interaction ». Nat Commun. 2021;12(1):2910.
   PubMed Web of Science ®Google Scholar