Isochore (genetics)

In genetics, an isochore is a large region of DNA (greater than 300 kb) with a high degree uniformity in guanine (G) and cytosine (C): G- C and C-G (collectively GC content).

Bernardi and colleagues first uncovered the compositional non-uniformity within vertebrate genomes using thermal melting and density gradient centrifugation. The DNA fragments extracted by the gradient centrifugation were later termed "isochores", which was subsequently defined as "very long (much greater than 200 KB) DNA segments" that "are fairly homogeneous in base composition and belong to a small number of major classes distinguished by differences in guanine-cytosine (GC) content". Subsequently, the isochores "grew" and were claimed to be ">300 kb in size." The theory proposed that isochore’s composition varied markedly between "warm-blooded" (homeotherm) vertebrates and "cold-blooded" (poikilotherm) vertebrates and later became known as the isochore theory.

The isochore theory purported that the genome of "warm-blooded" vertebrates (mammals and birds) are mosaics of long isochoric regions of alternating GC-poor and GC-rich composition, as opposed to the genome of "cold-blooded" vertebrates (fishes and amphibians) that were supposed to lack GC-rich isochores. These findings were explained by the thermodynamic stability hypothesis, attributing genomic structure to body temperature. GC-rich isochores were purported to be a form of adaptation to environmental pressures, as an increase in genomic GC-content could protect DNA, RNA, and proteins from degradation by heat.

Despite its attractive simplicity, the thermodynamic stability hypothesis has been repeatedly shown to be in error . Many authors showed the absence of a relationship between temperature and GC-content in vertebrates, while others showed the existence of GC-rich domains in "cold-blooded" vertebrates such as crocodiles, amphibians, and fish.

The isochore theory was the first to identify the nonuniformity of nucleotide composition within vertebrate genomes and predict that the genome of "warm-blooded" vertebrates such as mammals and birds are mosaic of isochores (Bernardi et al. 1985). The human genome, for example, was described as a mosaic of alternating low and high GC content isochores belonging to five compositional families, L1, L2, H1, H2, and H3, whose corresponding ranges of GC contents were said to be <38%, 38%-42%, 42%-47%, 47%-52%, and >52%, respectively.

The main predictions of the isochore theory are that:

Two opposite explanations that endeavored to explain the formations of isochores were vigorously debated as part of the neutralist-selectionist controversy. The first view was that isochores reflect variable mutation processes among genomic regions consistent with the neutral model. Alternatively, isochores were posited as a result of natural selection for certain compositional environment required by certain genes. Several hypotheses derive from the selectionist view, such as the thermodynamic stability hypothesis and the biased gene conversion hypothesis. Thus far, none of the theories provides a comprehensive explanation to the genome structure, and the topic is still under debate.

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