The genome: an isochore ensemble and its evolution

Abstract

The genomes of eukaryotes are mosaics of isochores. These are long DNA stretches that are fairly homogeneous in base composition and that belong to a small number of families characterized by different ratios of GC to AT and different short-sequence patterns (i.e., different DNA structures that interact with different proteins). This genome organization led to two discoveries: (1) the genomic code, which refers to two correlations, that of the composition of coding and contiguous noncoding sequences, and that of coding sequences and the structural properties of the encoded proteins; and (2) the genome phenotypes, which correspond to the patterns of isochore families in the genomes. These patterns indicate that genome evolution may proceed either according to a conservative mode or to a transitional (isochore shifting) mode, apparently depending upon whether the environment is constant or shifting. According to the neoselectionist theory, natural selection is responsible for both modes.

A History of Genomic Structures: The Big Picture

“…Thus, the gene landscape (Cruveiller et al 2004 ) is a sophisticated feature that might have emerged with compositional heterogeneity in large genomes. A selective advantage associated with such a sophisticated organization of chromosomal territories might be found in the regulation system, allowing genes to be regulated spatially and temporally under different compositional contexts (different promoter and enhancer motifs) (Bernardi 2012 ). Differential levels of gene expression between the GC-poor and GC-rich compartments have been observed in humans (Arhondakis et al 2004(Arhondakis et al , 2011 and plants (Carels and Bernardi 2000a , b ).…”

“…7.12 ). Such a CDS distribution bias according to GC level led to the introduction of the concept of gene deserts, which are associated with GC-poor genomic fragments in which genes are rare (Bernardi 2012 ). Sets of genes can also be classifi ed as GC-poor or GC-rich according to their intron number and size (Carels and Bernardi 2000b ).…”

G4 motifs in human genes

“…Abundance of G4 motifs is independent of genomic environment Our genomes consist of large segments of fairly homogeneous guanine + cytosine content, defined as isochores 29 (also see Ref. 30). Although the concept of isochores was put forward long before the sequence of the genome was known, it has proven to be robust.…”

Overview of the creative genome: effects of genome structure and sequence on the generation of variation and evolution

“…The timing of replication at imprinted loci depends on the parent of origin 18 . Casper et al 19 note that some fragile sites may lie at transition between early and late replicating DNA, which also appear to be boundaries of isochores (described by Bernardi 7 as functionally distict blocks of differing G/C content in genomes).…”

“…Our understanding of genome organization and hierarchies of control are in their infancy, yet we are conversant with terms such as “locus control region,” 2 “allelic exclusion,” 3,4 “boundaries,”“insulators,” and “imprinting.” 5 It no longer is assumed that a DNA sequence functions identically wherever a researcher places it in the genome 6,7 . Some regions are gene rich, some are gene “deserts” 7 that burst with RNA transcripts, 8 while the creation of protein‐coding sequences from cryptogenes 9 makes it clear that there is much more for us to understand about recognition, integration, and storage of information in genomes.…”