Molecular Biology and Evolution, Vol 10, 186-204, Copyright © 1993 by Society for Molecular Biology and Evolution
G Bernardi
Vertebrate genomes are mosaics of isochores--namely, of long (> 300 kb),
compositionally homogeneous DNA segments that can be subdivided into a
small number of families characterized by different GC levels. In the human
genome (which is representative of a number of mammalian genomes, and, more
broadly, of the genomes of warm-blooded vertebrates), the compositional
range of isochores is 30%-60% GC, and five families of isochores have been
identified: two GC-poor families, L1 and L2, together representing 62% of
the genome, and three GC-rich families, H1, H2, and H3, representing 22%,
9%, and 3%, respectively (the remaining 4% of the genome is formed by
satellite and ribosomal DNA). Gene concentration is strikingly nonuniform,
being highest in the H3 isochore family, lowest in the L1 + L2 families,
and intermediate in the H1 + H2 families. The H3 family corresponds to
T(elomeric) bands of metaphase chromosomes, and the L1 + L2 families
correspond to G(iemsa) bands, whereas R(everse) bands comprise both GC-poor
and GC-rich isochores. The compositional distributions of large genome
fragments, of exons (and their codon positions), and of introns are
correlated with each other. They represent compositional patterns and are
very different between the genomes of cold- and warm-blooded vertebrates,
mainly in that the former are much less heterogeneous in base composition
and never reach the highest GC levels attained by the latter. Only
relatively small compositional differences are found among the genomes of
either cold- or warm-blooded vertebrates. Compositional patterns allow one
to define two modes in genome evolution: a conservative mode, with no
compositional change, and a transitional (or shifting) mode, with
compositional changes. The conservative mode can be observed among either
cold- or warm-blooded vertebrates. The transitional mode comprises both
major and minor compositional changes. In vertebrate genomes, the major
changes are associated with the appearance of GC-rich and very GC-rich
isochores in mammalian and avian genomes. Mutational biases play a role in
both modes of compositional evolution. According to one viewpoint, the
fixation of compositionally biased mutations is responsible for the
transitional mode of evolution of bacterial genomes; in the conservative
mode of evolution of vertebrates, they accomplish their role in conjunction
with differences either in chromatin structures that modulate replication
errors or in chromatin transcriptional activities that may lead to various
extents of repair-DNA synthesis.(ABSTRACT TRUNCATED AT 400 WORDS)
REVIEW ARTICLE
The vertebrate genome: isochores and evolution
Laboratoire de Genetique Moleculaire, Institut Jacques Monod, Paris, France.
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