Isochore (genetics)
Encyclopedia
In genetics, an isochore is a large region of DNA
(greater than 300 KB) with a high degree uniformity in G-C and C-G (collectively GC) which tends to have more genes, higher local melting or denaturation
temperatures, and different flexibility. Overall, isochores are largely homogeneous in GC content in contrast to the heterogeneity of the entire genome.
There are five families of isochores ranging in overall GC content:
In vertebrates, gene expression is tissue-dependent and the genome is heterogeneous in terms of GC content. Bernardi et.al (1985,1988) have shown that vertebrate genomes are a mosaic composed of GC-rich regions and GC-poor regions, and some GC-rich regions have a GC content of about 60% and some GC-poor regions about 30%. Each of these GC-rich or GC-poor regions may be as long as 300kb and contain many functional genes. These GC-rich or GC-poor regions are called isochores.
There are four major groups of isochores (two GC-rich and two GC-poor isochores) in warm-blooded vertebrates such as mammals and birds, but in cold-blooded vertebrates GC-rich isochores are rare or nearly absent. The boundary between the GC-rich and GC-poor isochores is known to be quite narrow (Ikemura and Aota 1988).
The origin of isochores in vertebrates has been a subject of controversy, and no consensus has been reached at the present time. The reader who is interested in this subject may refer to Wolfe et al. (1989), Holmquist and Filipski (1994) and Bernardi (1995). However, it is important to note that the genes located in different isochores are expected to have different patterns of codon usage biases and since codon usage bias affects the rate of nucleotide substitution (Shields et al. 1988; Sharp et al. 1989), they may evolve at different rates.
Isochores have been described using CsCl
ultracentrifugation.
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
(greater than 300 KB) with a high degree uniformity in G-C and C-G (collectively GC) which tends to have more genes, higher local melting or denaturation
Denaturation (biochemistry)
Denaturation is a process in which proteins or nucleic acids lose their tertiary structure and secondary structure by application of some external stress or compound, such as a strong acid or base, a concentrated inorganic salt, an organic solvent , or heat...
temperatures, and different flexibility. Overall, isochores are largely homogeneous in GC content in contrast to the heterogeneity of the entire genome.
There are five families of isochores ranging in overall GC content:
- The L1 and L2 have a low GC-content of < 40% and have few genes
- The H1 has a GC content of ~47%
- The H2 has a GC content of ~52%
- The H3 has the highest GC content of > 52% and has the highest density of genes.
In vertebrates, gene expression is tissue-dependent and the genome is heterogeneous in terms of GC content. Bernardi et.al (1985,1988) have shown that vertebrate genomes are a mosaic composed of GC-rich regions and GC-poor regions, and some GC-rich regions have a GC content of about 60% and some GC-poor regions about 30%. Each of these GC-rich or GC-poor regions may be as long as 300kb and contain many functional genes. These GC-rich or GC-poor regions are called isochores.
There are four major groups of isochores (two GC-rich and two GC-poor isochores) in warm-blooded vertebrates such as mammals and birds, but in cold-blooded vertebrates GC-rich isochores are rare or nearly absent. The boundary between the GC-rich and GC-poor isochores is known to be quite narrow (Ikemura and Aota 1988).
The origin of isochores in vertebrates has been a subject of controversy, and no consensus has been reached at the present time. The reader who is interested in this subject may refer to Wolfe et al. (1989), Holmquist and Filipski (1994) and Bernardi (1995). However, it is important to note that the genes located in different isochores are expected to have different patterns of codon usage biases and since codon usage bias affects the rate of nucleotide substitution (Shields et al. 1988; Sharp et al. 1989), they may evolve at different rates.
Isochores have been described using CsCl
Caesium chloride
Caesium chloride is the inorganic compound with the formula CsCl. This colorless solid is an important source of caesium ions in a variety of applications. Its crystal structure forms a major structural type where each caesium ion is coordinated by 8 chlorine ions...
ultracentrifugation.
External links
- GC-Profile — a free, open source program used to visualize isochores in a given genome.
- EMBOSSEMBOSSEMBOSS is an acronym for European Molecular Biology Open Software Suite. EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology and bioinformatics user community...
isochore— a free, open source program used to plot isochores in DNA sequences.