The “Genomic Code”: DNA Pervasively Moulds Chromatin Structures Leaving no Room for “Junk”

Abstract

The chromatin of the human genome was analyzed at three DNA size levels. At the first, compartment level, two “gene spaces” were found many years ago: A GC-rich, gene-rich “genome core” and a GC-poor, gene-poor “genome desert”, the former corresponding to open chromatin centrally located in the interphase nucleus, the latter to closed chromatin located peripherally. This bimodality was later confirmed and extended by the discoveries (1) of LADs, the Lamina-Associated Domains, and InterLADs; (2) of two “spatial compartments”, A and B, identified on the basis of chromatin interactions; and (3) of “forests and prairies” characterized by high and low CpG islands densities. Chromatin compartments were shown to be associated with the compositionally different, flat and single- or multi-peak DNA structures of the two, GC-poor and GC-rich, “super-families” of isochores. At the second, sub-compartment, level, chromatin corresponds to flat isochores and to isochore loops (due to compositional DNA gradients) that are susceptible to extrusion. Finally, at the short-sequence level, two sets of sequences, GC-poor and GC-rich, define two different nucleosome spacings, a short one and a long one. In conclusion, chromatin structures are moulded according to a “genomic code” by DNA sequences that pervade the genome and leave no room for “junk”.

Plant Tolerance to Drought Stress with Emphasis on Wheat

“…In vertebrates, the genome was shown to be organized into two major components with specific functionalities [82] according to guanine plus cytosine (GC) content. The base changes during vertebrate evolution were such that the GC-poor compartment remained poor in cold-blooded vertebrates (fishes, amphibians, reptiles), but their GC-rich compartment became even richer in GC during their transition to warm-blooded vertebrates (mammals and birds).…”

“…The base changes during vertebrate evolution were such that the GC-poor compartment remained poor in cold-blooded vertebrates (fishes, amphibians, reptiles), but their GC-rich compartment became even richer in GC during their transition to warm-blooded vertebrates (mammals and birds). This compositional transition led to a range of functional adaptations at the molecular level [82]. The effect of this major transition [83] on the genome structure of modern species of both groups can still be observed through GC composition at the regional level, which led Bernardi to coin the term isochores in 2007 for DNA stretches larger than 300 Kbp that do not vary by more than an average standard deviation of ~2% GC [84].…”

Phospho-Tau and Chromatin Landscapes in Early and Late Alzheimer’s Disease

“…Condensed chromatin or heterochromatin is formed by 30 nm fibers or greater degree of packing with tight contacts between nucleosomes; it is rich in AT bases and poor in GC bases [20]. Heterochromatin mainly contains non-coding DNA sequences, especially repetitive sequences such as α, β, γ, I, II, and II satellite sequences; micro-, mini-, and macro-satellites; and diverse transposon types [13].…”

Differences in Alu vs L1-rich chromosome bands underpin architectural reorganization of the inactive-X chromosome and SAHFs

“…(reviewed in: Li and Shen, 2023; Solovei et al, 2016). Routine cytogenetic banding can delineate ∼800 alternating light and dark G-bands, but individual bands may contain smaller segments corresponding to distinct GC or AT isochores (Bernardi, 2021). Why our genome maintains such a large fraction of repeated sequences (∼45%), and why L1 and Alu sequences are organized in cytologically visible mega-structures (chromosome bands) is not well understood.…”