Supramolecular multilayer organization of chromosomes: possible functional roles of planar chromatin in gene expression and DNA replication and repair

Abstract

Experimental evidence indicates that the chromatin filament is self‐organized into a multilayer planar structure that is densely stacked in metaphase and unstacked in interphase. This chromatin organization is unexpected, but it is shown that diverse supramolecular assemblies, including dinoflagellate chromosomes, are multilayered. The mechanical strength of planar chromatin protects the genome integrity, even when double‐strand breaks are produced. Here, it is hypothesized that the chromatin filament in the loops and topologically associating domains is folded within the thin layers of the multilaminar chromosomes. It is also proposed that multilayer chromatin has two states: inactive when layers are stacked and active when layers are unstacked. Importantly, the well‐defined topology of planar chromatin may facilitate DNA replication without entanglements and DNA repair by homologous recombination.

Higher-order interfiber interactions in the self-assembly of benzene-1,3,5-tricarboxamide-based peptides in water

“…Supramolecular interactions of higher orders, such as assembly of collagen fibrils, amyloids, and nucleic acids, are especially interesting and involve changes in the material's bulk properties. [2][3][4][5] Mimicking such interactions in aqueous media with synthetic supramolecular systems remains a formidable task due to the complex and frequently counterintuitive self-assembly mechanisms. 6 In the last few decades multiple supramolecular systems with hierarchical self-assembly were reported, including coordination complexes, [7][8][9] porphyrins, 10 different peptides [11][12][13][14] including di-and tri-peptides with different motifs; 15,16 as well as synthetic 17,18 and natural 19,20 polymers.…”

“…Supramolecular interactions of higher orders, such as assembly of collagen fibrils, amyloids, and nucleic acids, are especially interesting and involve changes in the material's bulk properties. 2–5 Mimicking such interactions in aqueous media with synthetic supramolecular systems remains a formidable task due to the complex and frequently counterintuitive self-assembly mechanisms. 6 …”

About classical molecular genetics, cytogenetic and molecular cytogenetic data not considered by Genome Reference Consortium and thus not included in genome browsers like UCSC, Ensembl or NCBI

“…At least one could deduce from that study [17] that there might be roughly (if Xp represents ~ 2% if human genome) overall ~ 700 GTG-light and 650 GTG-dark bands in the whole human genome, which wait for their alignment with sequencing data. In the light of the description of TADs [6] and work of Joan-Ramon Daban [7] this has to be considered earlier or later. Also an important clue to learn from this work [16][17][18], is that in GTG-light bands, being less condensed than GTG-dark ones, there should be less DNA included than in more condensed dark ones.…”

“…Recent insights from 'second-' and 'third-generationsequencing' approaches [5] highlighted furthermore by discovery of inter-and intrachromosomal interactions, and more specifically the TADs (topologically associating domains) [6], that chromosome structure is extremely important for genome function, and if impaired for diseases [5,6]. Most recently, insight from electron microscopy combined with cytogenetic, molecular cytogenetic and molecular genetic data led to a complete new understanding of the chromosome structure itself [7]. As stated by Joan-Ramon Daban: "Experimental evidence indicates that the chromatin filament is self-organized into a multilayer planar structure that is densely stacked in metaphase and unstacked in interphase.…”

“…He suggests "that the chromatin filament in the loops and topologically associating domains is folded within the thin layers of the multilaminar chromosomes. It is also proposed that multilayer chromatin has two states: inactive when layers are stacked and active when layers are unstacked" [7].…”