The Detailed 3D Multi-Loop Aggregate/Rosette Chromatin Architecture and Functional Dynamic Organization of the Human and Mouse Genomes

Abstract

Background:The dynamic three-dimensional chromatin architecture of genomes and its co-evolutionary connection to its function-the storage, expression, and replication of genetic information-is still one of the central issues in biology. Here, we describe the much debated 3D architecture of the human and mouse genomes from the nucleosomal to the megabase pair level by a novel approach combining selective high-throughput high-resolution chromosomal interaction capture (T2C), polymer simulations, and scaling analysis of the 3D architecture and the DNA sequence. Results:The genome is compacted into a chromatin quasi-fibre with ~5 ± 1 nucleosomes/11 nm, folded into stable ~30-100 kbp loops forming stable loop aggregates/rosettes connected by similar sized linkers. Minor but significant variations in the architecture are seen between cell types and functional states. The architecture and the DNA sequence show very similar fine-structured multi-scaling behaviour confirming their co-evolution and the above. Conclusions:This architecture, its dynamics, and accessibility, balance stability and flexibility ensuring genome integrity and variation enabling gene expression/regulation by self-organization of (in)active units already in proximity. Our results agree with the heuristics of the field and allow "architectural sequencing" at a genome mechanics level to understand the inseparable systems genomic properties.

A Guided Protocol for Array Based T2C: A High‐Quality Selective High‐Resolution High‐Throughput Chromosome Interaction Capture

“…However, these suggestions are not very well supported by the underlying experimental (raw) data. In contrast, with the introduction of T2C , we were able to show that the chromatin quasi‐fiber forms small stable loops of ∼30–100 kbp that form stable multi‐loop aggregates/rosettes connected by linkers of similar sizes as the loops (Knoch & Grosveld, ; Knoch et al., ). Additionally, the already above mentioned novel in vivo FCS approach came to the same conclusion (Wachsmuth et al., ).…”

“…Additionally, more structural factors such as CTCF and/or cohesin play a role here (Zuin et al., , and references therein), which seems obvious also from co‐evolutionary considerations. Since the 3D architecture, its dynamics, and accessibility found by us (Knoch & Grosveld, ; Knoch et al., ; Wachsmuth et al., ) balances stability and flexibility ensuring genome integrity and variation enabling gene expression/regulation by self‐organization of (in‐)active units already in proximity, sheds new light on these functional aspects. Nevertheless, the detailed 3D architecture under various circumstances, the local factors involved, the functional variations, and many more aspects give still rise to a huge number of questions yet to be answered.…”

“…The structure and function of genomes obviously co‐evolved as an inseparable system allowing the physical storage, replication, and expression of genetic information (Knoch, Münkel, & Langowski, ; Cremer & Cremer, ; Knoch, ; Knoch, ; Kolovos et al., ). However, only recently all missing architectural levels — the chromatin quasi‐fiber and its folding into stable multi‐loop aggregates/rosettes connected by a linker — could be determined in general by us using our novel and superior selective high‐resolution, high‐throughput chromosome interaction capture — T2C (targeted chromatin capture; Knoch & Grosveld, ; Knoch et al., ; Wachsmuth, Knoch, & Rippe, ). Together with the fast progress in genome engineering (e.g.…”

“…Jinek et al., ), biology has now really reached the genomic era. Nevertheless, the dynamic three‐dimensional higher‐order architecture of genomes, their spatial and temporal modifications and/or relation to functional multidimensional interaction and regulatory networks have yet to be determined in detail (Cremer & Cremer, ; Jhunjhunwala et al., ; Rauch et al., ; Knoch et al., ; Wachsmuth et al., ). In respect to possible settings and directions of thoughts for the design of T2C experiments, in the following a detailed overview of the history of the architecture and function of the cell nucleus is presented exemplifying the complexity of considerations to be involved.…”

“…Moreover, the fine‐structured multi‐scaling long‐range correlation behavior of the DNA sequence also predicts a compacted chromatin fiber (Knoch et al., ; Knoch, ; Knoch, ; Knoch et al., ). With T2C we were, however, able to show that nucleosomes form in general a quasi‐fiber with a differential compaction of ∼5 ± 1 nucleosomes/11 nm (Knoch & Grosveld, ; Knoch et al., ). This is in agreement with a novel in vivo fluorescence correlation spectroscopy (FCS) approach measuring the dynamics of chromatin (Wachsmuth et al., ).…”