Botany online 1996-2004. No further update, only historical document of botanical science!

Repeated (repetitive) DNA, Nonrepeated DNA, Active Genes

Towards the end of the 1960th it became clear that the genomes of eucaryotes contain in contrast to procaryotic genomes a high percentage of non-coding, usually repetitive nucleotide sequences (repetitive DNA). The kinetics of the renaturation of isolated, ‘melted’ DNA revealed the first indications. Melting of DNA means the denaturation of the DNA double strand into its two complementary single strands as a result of the dissolving of the hydrogen bonds due to heat. The single strands re-associate after cooling down. The old state (DNA double helices) is re-established, the DNA is renatured. The velocity of re-association depends on the amount of complementary single strands and thus on the complexity of the mixture of DNA, the genome.

If the nucleotide sequences of a large eucaryotic genome (with a hypothetical 1012 base pairs) would display no similarities, then the probability that a fragment of single-stranded DNA (with a hypothetical length of 1000 nucleotides) would find its complementary partner piece would be 1:0.5 x 10-9. It would thus take weeks or even month before the random thermal movements would lead to the formation of the first DNA double strands. 

Reality is different. A considerable amount of such single-stranded DNA fragments renatures within a very short time, a further lot takes somewhat longer, while a third fraction renatures pretty slowly. The ratio of these three fractions differs depending on plant (or animal) species. The three fractions of DNA are called highly repetitive, moderately repetitive, and nonrepetitive (nonrepeated) nucleotide sequences. The amount of repetitive DNA can exceed 90 percent of the total DNA in some species. These analyses reveal nothing of the information or the function of this type of DNA.

It is obvious that it was always tried to understand the biological significance of the single fractions. It showed that the coding genome sequences, the genes, are usually nonrepeated. This does not mean that the complete nonrepeated DNA are active genes. In the case of some few genes, like histones or the rRNA and tRNA genes, numerous copies are known to exist. Autoradiography showed that identical genes do usually follow one another, and that such clusters can be located on several chromosomes.

The majority of the highly repetitive DNA has no coding function and constitutes the main amount of the (constitutive) heterochromatin. The moderately repetitive and the only weakly repetitive sequences are evenly scattered over the whole genome (also called interspersed pattern). They seem to have an important function in the regulation of gene expression and for the frequency of recombination.

An overview of the size of the single fractions in as many species as possible is required in order to gain an insight into the plant genome’s organization and to estimate the ratio of coding to non-coding DNA. The establishing of the ratio of nonrepetitive to repetitive DNA alone is not sufficient for this purpose. Moreover, all products of transcription (RNA) have to be captured to understand their complexity and relate them to the complexity of the DNA. This topic has hardly been covered for plants up till now. W. WENZEL and V. HEIMLEBEN (Institute of Biology, University of Tübingen, Germany) collected the data published until 1982 and compiled them in a table.

A first important result of these data is the fact that the ratio of nonrepeated (nonrepetitive, singular) to repetitive DNA (S/R) differs significantly in monocots and dicots.

Furthermore, two additional observation can be made:

  1. In most dicots, the genome sizes (applied to 1C) are small and almost constant while at the same time the S/R ratio varies strongly.
  2. In monocots and few dicots (Ranunculaceae) the genomes are large and variable, but display a low S/R ratio.

These results mean, that the taxa of group 1 change mainly by selective down- or up-replication of nonrepetitive and/or repetitive DNA while the total size of the genome remains mostly unaltered. Group 2 in contrast, reduces or multiplies both nonrepetitive and repetitive DNA sequences simultaneously. As a consequence, the genome sizes vary. Plants belonging to the second group are obviously predestined to the accumulation of new (mutated) alleles, like the selective multiplication (also called amplification) of certain parts of the genome in order to keep genes with an adaptive value.

Monocots have often very large chromosomes with a lesser tendency towards polyploidization than displayed by small chromosomes. Monocots with the exceptions of Gramineae and Cyperaceae do therefore display far less polyploidy than dicots. In dicots with their relatively small genomes, enlargement by polyploidization and thus recombination between different, but related genomes is common.

The variation of the S/R ratio has an effect on gene expression and leads finally to a larger variability in phenotype. This strategy proved to be more successful than that of most monocots, that have far less wealth of forms than dicots and a limited ability for adaptive radiation, i.e. in the colonization of new habitats. 

On the whole, large amounts of highly repetitive DNA seem to reduce the ability of recombination and thus the restructuring of genomes drastically. 

The animal kingdom offers a parallel example. Anura (frogs) have large genomes with a lot of repetitive DNA and do all look pretty similar. Mamalia, in contrast, have very small genomes with chromosomal numbers varying from species to species, and they are characterized by a variety of shapes and performances. Just think about the differences between bat, whale, and human beings. The results reviewed thus far together with supplementing experiments, observations, and ideas led to the conclusion that moderately repetitive DNA plays a role in the DNA’s recombination. DNA, nevertheless, is unable to restructure itself. Enzymes and certain nucleotide sequences to be specifically recognized by these enzymes are required. Specific DNA sections can thus be removed and possibly be inserted again at another, likewise specific site. Such restructurings can cytologically be detected as chromosome mutations, on the level of the DNA, the restructuring may effect the S/R ratio. The molecular reasons are, as has just been indicated, the abilities of certain DNA sections to ‘jump’ with the aid of certain enzymes. These DNA sections are also called jumping genes.

In angiosperm genera, specialization goes along with a reduction of the genome’s size. The composite genus Microseris provides a good example for this. Specialization is not just linked to a reduction of size, a transition from a perennial to an annual lifestyle, and a change from allogamy to autogamy, but causes simultaneously also a reduction of the variability of each morphological feature. In the course of their specialization, Microseris-species lost DNA of all three fractions. An analysis of their rRNA genes showed, that the number of active genes has decreased during specialization, too.

© Peter v. Sengbusch - Impressum