A Consistent Systems Mechanics Model of the 3D Architecture and Dynamics of Genomes
Tobias Knoch · IntechOpen eBooks · 2019
Already for thousands of years mankind is aware of inheritance and its manipulation by mating and breeding. The discovery of the cell nucleus by A. van Leeuwenhook in the 17th century marks a start to elucidate the epically discussed evolutionary transfer of information in detail. Now after more than 170 years of research on the 3D architecture and dynamics of genomes and the co-evolved interaction networks of regulatory elements creating genome function - i.e. the storage, replication, and expression of genetic information—a consistent systems statistical mechanics genomics framework emerges for the first time. Obviously the structure and function of genomes co-evolved as an inseparable system allowing the physical storage, expression, and replication of genetic information. The DNA double helix and the nucleosome had been determined structurally at the very highest level already, including genome sequences and epigenetic histone modifications. That chromosomes form territories with functional relevant positioning within the cell nucleus and that chromosomal subdomains exist has been also determined to a fair degree of detail. Only recently, however, we were finally able to fill the much debated gap in-between by establishing that nucleosomes compact into a quasi-fibre folded into stable loops which form stable multi-loop aggregates/rosettes connected by linkers and hence creating chromosome arms and entire chromosomes. Interestingly, this has lead immediately to a consistent and cross-proven systems statistical mechanics genomic framework which is balancing stability/flexibility ensuring genome integrity, enabling expression/regulation of genetic information, as well as genome replication - all this in evolutionary perspectives as the natural outcome of Darwinian natural selection and Lamarkian self-referenced manipulation. Thus, genotype and phenotype are multilisticly entangled and beyond are embedded in genome ecology i(!)n- and environments. This not only opens the door to a true universal sequencing of genetic information, but also is the key for a general understanding of genomes, their function and evolution, as well as for applied diagnostics and treatment of disease, for future genome manipulation and engineering efforts, as far as the creation of artificial or extra-terrestrial live contexts.