Organization of Nucleotide Sequences in the Chicken Genome

Abstract

The four major components of chicken D N A were prepared by density gradient centrifugation and characterized in several basic properties: relative amounts, d G + d C content, buoyant densities, compositional heterogeneity, and reassociation kinetics. While the relative amounts and the compositions of the major components of chicken DNA were similar to those found in mammalian genomes, their compositional hetei-ogeneities were found to be narrower. The relative amounts of interspersed repeated and unique sequences were strikingly different in different components and also different from those found in the corresponding major components of mouse and human DNAs. If one takes into consideration that major D N A components (a) account for practically all of main-band D N A and (b) derive by preparative breakage from very long DNA segments of fairly homogeneous composition, the isochores, our findings indicate that the distribution of interspersed repeats is different in different chromosomal regions and is species-specific.Equilibrium density gradient centrifugation in the presence of DNA ligands has been applied in our laboratory to investigate the nucleotide sequence organization of the genomes of eukaryotes and, more particularly, of vertebrates [I -81. This approach has led us, so far, to several conclusions. The first one is that, neglecting satellite and minor components, the genomes of higher, warm-blooded vertebrates can be resolved into four families of fragments, the major DNA components. Two of these components (not resolved in some species) represent about two thirds of the main-band D N A and have densities in the range 1.697-1.702 g/cm3, whereas the other two represent about 25 "/, and 10 "/, and have densities of 1.704 and 1.708 g/cm3, respectively.Both the relative amounts and the buoyant densities of the major components show little variation in different mammalian and avian genomes. In contrast, DNAs from lower, cold-blooded vertebrates have buoyant densities which are, in most cases, in the same range as the light components of warm-blooded vertebrates; these DNAs d o not show the compositional heterogeneity of DNAs from higher vertebrates and cannot be resolved into families of fragments equivalent to the major components mentioned above.The second conclusion is that the four major components of warm-blooded vertebrates are families of DNA fragments derived, by preparative breakage, from very long DNA segments (3 x lo5 residues in the mouse genome) fairly homogeneous in base composition, the isochores, possibly corresponding to chromosomal bands. Furthermore, unique, interspersed repeated and foldback sequences show a different distribution in the major components of mouse and human DNAs, and also in corresponding major components of these mammalian DNAs. The first finding points to a sequence interspersion pattern which varies in different chromosomal regions; the second one to an unsuspected variety of sequence arrangements in mammals.In the present work we have investigated the basic propertie...

The distribution of interspersed repeats is nonuniform and conserved in the mouse and human genomes.

“…The results showed very significant differences and a high species specificity in the relative amounts of the various kinetic classes-particularly of the interspersed repeated sequences-among the four components (6). Nonuniformity and species specificity in the distribution of repeated sequences also have been shown in the four major components of the chicken genome (7).…”

Target Site Preferences of Subgroup C Rous Sarcoma Virus Integration into the Chicken DNA

“…Obviously, some of these features are interdependent. In both mammals and birds, gene-rich regions tend to be GC-rich [25][26][27]. However, the apparent under-representation of insertions into microchromosomes is surprising, as chicken microchromosomes have, in general, an increased GC content, more CpG islands, and higher gene density [ 28,29].…”

“…The basic compositional properties of avian genomes are comparable to mammalian genomes [25][26][27]. In both the human and chicken genome, gene-rich regions are concentrated in GC-rich isochores.…”

Compositional Gene Landscapes in Vertebrates

“…The discovery of isochores was accompanied by the identification, and physical isolation, of a small number of DNA components of increasing GC level in several vertebrate species (Macaya et al 1976;Cuny et al 1981;Olofsson and Bernardi 1983;Bernardi et al 1985). The isochores from which the DNA derived were correspondingly allocated, in each species, to a small number of isochore families: five in human, four in mouse, six in chicken, and two in Xenopus.…”

“…Approximate locations corresponding to components of bulk DNA (Olofsson and Bernardi 1983;Bernardi et al 1985), as calculated from the relation GC3 = 2.64 GC ‫מ‬ 64 ): 40%, 51.4%, 59.3%, 67.2%, 75.9%, and 87.8% GC3.…”