Exon and Intron Base Compositions Differ

KEY CONCEPTS
-The four “rules” for DNA base composition are the first and second parity rules (both also known as Chargaff’s rules), the cluster rule, and the GC rule. Exons and introns can be distinguished on the basis of all rules except the first.
-The second parity rule suggests an extrusion of structured stem-loop segments from duplex DNA, which would be greater in introns.
-The rules relate to genomic characteristics, or “pressures,” that constitute the genome phenotype.
In the 1940s, Erwin Chargaff initiated studies of DNA base composition that led to four “rules,” beginning with the first parity rule for duplex DNA (see the chapter titled Genes Are DNA and Encode RNAs and Polypeptides). This rule applies to most regions of DNA, including both exons and introns. Base A in one strand of the duplex is matched by a complementary base (T) in the other strand, and base G in one strand of the duplex is matched by a complementary base (C) in the other strand. By extension, the rule applies not only to single bases but also to dinucleotides, trinucleotides, and oligonucleotides. Thus, GT pairs with its reverse complement AC, and ATG pairs with its reverse complement CAT.
In addition to the well-known first parity rule, later work by Chargaff led him to propose a second parity rule. The little-known second parity rule is that, to a close approximation, there are equal amounts of A and T, and equal amounts of C and G, in each single strand of the duplex. Like the first parity rule, this extends to oligonucleotide sequences: For example, in a very long strand there are approximately equal numbers of AC and TG dinucleotides. The reasons for the existence of this rule are not clear, but sequencing of many genomes has shown it to be nearly universally true. The second parity rule applies more closely to introns than to exons, partly due to a further rule—purines tend to cluster on one DNA strand and pyrimidines tend to cluster on the other. This cluster rule as applied to exons is that the purines, A and G, tended to be clustered in one DNA strand of the DNA duplex (usually the nontemplate strand) and these are complemented by clusters of the pyrimidines, T and C, in the template strand.
The fact that in single-stranded DNA an oligonucleotide is accompanied in series by equal quantities of its reverse complementary oligonucleotide suggests that duplex DNA has the potential to extrude folded stem-loop structures, the stems of which can display base parity and the loops of which can display some degree of base clustering. Indeed, the potential for such secondary structure is found to be greater in introns than in exons, especially in exons under positive selection pressure .
Finally, there is the GC rule, which is that the overall proportion of G+C in a genome (GC content) tends to be a species-specific character (although individual genes within that genome tend to have distinctive values). The GC content tends to be greater in exons than in introns. Chargaff’s four rules are seen to relate to characters or “pressures” that are intrinsic to the genome, contributing to what was termed the genome phenotype .

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