**Legends Movie 1 and 2**

works of the last 170 years - by establishing that nucleosomes compact into a quasi-fibre which is folded into stable loops, forming stable multi-loop aggregates/rosettes connected by linkers creating chromosome arms and entire chromosomes [26, 27]. Although the heuristics of the field leads already to a sound basis, this could only be achieved - as we summarized here - by a highly integrated systems approach linking holistically i) a by far superior selective chromosome interaction (T2C) technique, ii) a novel *in vivo* FCS dynamic method, iii) a novel analytical approach and improved super-computer simulations, and iv) finally scaling analysis of the 3D-architecture and the DNA sequence itself. Including the heuristics of the field this leads to a consistent picture of genome organization, which match all the criteria necessary for storage, transcription, and replication as one would expect them as the outcome of Darwinian natural selection and Lamarkian self-referenced manipulation as shown here. In parallel, a multilistic systems statistical mechanics with uncertainty principles has emerged while reaching the fundamental resolution limits in the above holistic approach, which represents a theoretical framework which also reunites the overall far from thermodynamic equilibrium notion with local hierarchic substance stability. Beyond, the tight entanglement of genome levels having left footprints on all levels, has not only shown that genomes have evolved as an entire system, but also the multilistic entanglement between genotype and phenotype. Hence, the natural outcome of Darwinian natural selection and Lamarkian self-referenced manipulation is united in a genome ecology framework, which we consider a major step in the systems theory of life. Thus, this not only leads to a solid basis for sequencing genetic information holistically and thus for applied diagnostics and treatment of disease, as well as future genome manipulation and engineering efforts, but more importantly paves the path to a true understanding of genomes, their function and evolution, and thus of life in general - earthbound, extra-terrestrial, or artificial.

For supporting and influencing this long lasting work of T.A.K thanks go to: M. Wachsmuth, T. Weidemann, K. Fejes-Toth, M. Göker, R. Lohner, M. Stör, E. Spiess, K. Rippe, W. Waldeck, C. Cremer, T. Cremer, K. Erenpreisa, A. Ollins, D. Ollins, K. Sullivan, C. C. Murre, J. Skok, A. M. A. Imam, F. G. Grosveld, K. Egger, O. Zimina, and last but not least L. A. Knoch, as well as the German and International Societies for Human Ecology. T2C was invented by T.A.K. and F. G. Grosveld, with many thanks to M. Lesnussa, N. Kepper, A. Abuseiris, P. Kolovos, Jessica Zuin, R. W. W. Brouwer, H. J. G. van de Werken, W. F. J. van IJken, and Kerstin S. Wendt. This work was also part of the EpiGenSys consortium setup and coordinated by T.A.K., funded by ERASysBio+/FP7 and the national funding organizations (the Dutch Ministry for Science and Education, the Netherlands Science Organization, the UK Biotechnology and Biological Sciences Research Council, and the Bundesministerium für Bildung und Forschung (BMBF)). Further support came from the BMBF under grants # 01 KW 9602/2 (Heidelberg 3D Human Genome Study Group, German Human Genome Project), #01AK803A (German MediGRID), #01IG07015G (Services@MediGRID), as well as the Erasmus Medical Centre and the Hogeschool Rotterdam. The High-Performance Computing Center Stuttgart (HLRS; grant HumNuc), the Supercomputing Center Karlsruhe (SCC; grant ChromDyn), and the Computing Facility of the German Cancer Research Center (DKFZ) are thanked for access to their CRAY T3E and IBM SP2s in the initial part of this work. Thanks

**Acknowledgements**

86 Chromatin and Epigenetics

### Video files available at: https://bit.ly/34KCuxe

**Movie 1.** Brownian Dynamics simulated decondensation from a metaphase starting configuration of a simulated Multi-Loop-Subcompartment model with 126 kbp loops and linkers with segment length of 50 nm (~5.2 kb) [26]. The whole 750 ms long movie shows how abruptly the metaphase chromosome expands due to its high density while opening the linker, which is constrained/condensed/pulled into a loop in metaphase. Nevertheless, the rosettes form distinct chromatin territories in which the loops do not intermingle freely in contrast to other models (see Introduction) such as the RW/GL model (**Figure 2**). The final shape and form in a whole nucleus would be determined by the limitations the other adjacent chromosomes provide (for more details see [22]). The different densities during decondensation also resemble nicely the conditions of shorter linkers, general genome regions with higher densities, or also the variation of nuclear volumes. Notably, the intrinsic movement of the chromatin fibre is clearly taking place on the millisecond scale, and hence, obviously a topological preformed architecture would dissolve within seconds if it would not be stable [26, 27].

**Movie 2.** Brownian Dynamics simulation of the consensus architecture (i.e. with the real measured loop and linker sizes) of the of the IGF/H19 region at HS11p15.5–15.4 (**Figure 3**), with a segment length of 20 nm (~2.0 kbp; colours of loops like in **Figure 3** middle, with additional linkers at the beginning and end of the region in red; for details see [26]). The whole movie encompasses 146 ms and shows the high intrinsic dynamics of the loops and the loop aggregate/rosette. Obviously, the single subchromosomal domains are constrained by the subsequent subchromosomal domains. Hence, and also obviously a topological preformed architecture would dissolve within seconds if it would not be stable [26, 27]. Nevertheless, the loop aggregates/rosettes form distinct subchromosomal domains in which the loops do not intermingle freely in contrast to other models (see Introduction) such as the RW/GL model (**Figure 2**). The final shape and form in a whole nucleus would be determined by the limitations adjacent chromosomes provide (for more details see [22]).
