Nonfunctional DNA Research Articles

The regulatory content of intergenic DNA shapes genome architecture.

Factors affecting the organization and spacing of functionally unrelated genes in metazoan genomes are not well understood. Because of the vast size of a typical metazoan genome compared to known regulatory and protein-coding regions, functional DNA is generally considered to have a negligible impact on gene spacing and genome organization. In particular, it has been impossible to estimate the global impact, if any, of regulatory elements on genome architecture. To investigate this, we examined the relationship between regulatory complexity and gene spacing in Caenorhabditis elegans and Drosophila melanogaster. We found that gene density directly reflects local regulatory complexity, such that the amount of noncoding DNA between a gene and its nearest neighbors correlates positively with that gene's regulatory complexity. Genes with complex functions are flanked by significantly more noncoding DNA than genes with simple or housekeeping functions. Genes of low regulatory complexity are associated with approximately the same amount of noncoding DNA in D. melanogaster and C. elegans, while loci of high regulatory complexity are significantly larger in the more complex animal. Complex genes in C. elegans have larger 5' than 3' noncoding intervals, whereas those in D. melanogaster have roughly equivalent 5' and 3' noncoding intervals. Intergenic distance, and hence genome architecture, is highly nonrandom. Rather, it is shaped by regulatory information contained in noncoding DNA. Our findings suggest that in compact genomes, the species-specific loss of nonfunctional DNA reveals a landscape of regulatory information by leaving a profile of functional DNA in its wake.

Surveying phylogenetic footprints in large gene clusters: applications to Hox cluster duplications

Evolutionarily conserved non-coding genomic sequences represent a potentially rich source for the discovery of gene regulatory regions. Since these elements are subject to stabilizing selection they evolve much more slowly than adjacent non-functional DNA. These so-called phylogenetic footprints can be detected by comparison of the sequences surrounding orthologous genes in different species. Therefore the loss of phylogenetic footprints as well as the acquisition of conserved non-coding sequences in some lineages, but not in others, can provide evidence for the evolutionary modification of cis-regulatory elements. We introduce here a statistical model of footprint evolution that allows us to estimate the loss of sequence conservation that can be attributed to gene loss and other structural reasons. This approach to studying the pattern of cis-regulatory element evolution, however, requires the comparison of relatively long sequences from many species. We have therefore developed an efficient software tool for the identification of corresponding footprints in long sequences from multiple species. We apply this novel method to the published sequences of HoxA clusters of shark, human, and the duplicated zebrafish and Takifugu clusters as well as the published HoxB cluster sequences. We find that there is a massive loss of sequence conservation in the intergenic region of the HoxA clusters, consistent with the finding in [Chiu et al., PNAS 99 (2002) 5492]. The loss of conservation after cluster duplication is more extensive than expected from structural reasons. This suggests that binding site turnover and/or adaptive modification may also contribute to the loss of sequence conservation.

Design considerations and effects of LNA in PCR primers

The effects of comprehensive LNA substitution in PCR primers for amplification of human genomic DNA targets are presented in this report. Previous research with LNA in other applications has shown interesting properties for molecular hybridization including enhanced specificity in allele-specific PCR. Here we systematically modified PCR primers and conditions for the human genomic DNA targets APOB and PAH, along with a β-globin amplification control, to study whether the number and position of LNA residues improves or diminishes amplification sensitivity and specificity. It was observed that the design rules for LNA substitution in PCR primers are complex and depend upon number, position and sequence context. Technical advantages were seen when compared to DNA controls for the best LNA primer designs, which were typically one to a few centrally located LNA residues. LNA advantages include increased maximum annealing temperature ( T max) and increased signal with limiting primer or Taq DNA polymerase. Several well-characterized designs exhibited different efficiencies with different brands of hot-start enzymes. Many shorter LNA primers were found to be functional compared to same-length non-functional native DNA controls. These results show that LNA-substituted PCR primers have potential for use in difficult PCR techniques, such as multiplex amplification at higher T max, once firm LNA primer design rules are established.

Congruent evolution of different classes of non-coding DNA in prokaryotic genomes.

Prokaryotic genomes are considered to be 'wall-to-wall' genomes, which consist largely of genes for proteins and structural RNAs, with only a small fraction of the genomic DNA allotted to intergenic regions, which are thought to typically contain regulatory signals. The majority of bacterial and archaeal genomes contain 6-14% non-coding DNA. Significant positive correlations were detected between the fraction of non-coding DNA and inter- and intra-operonic distances, suggesting that different classes of non-coding DNA evolve congruently. In contrast, no correlation was found between any of these characteristics of non-coding sequences and the number of genes or genome size. Thus, the non-coding regions and the gene sets in prokaryotes seem to evolve in different regimes. The evolution of non-coding regions appears to be determined primarily by the selective pressure to minimize the amount of non-functional DNA, while maintaining essential regulatory signals, because of which the content of non-coding DNA in different genomes is relatively uniform and intra- and inter-operonic non-coding regions evolve congruently. In contrast, the gene set is optimized for the particular environmental niche of the given microbe, which results in the lack of correlation between the gene number and the characteristics of non-coding regions.

A family of selfish minicircular chromosomes with jumbled chloroplast gene fragments from a dinoflagellate.

Chloroplast genes of several dinoflagellate species are located on unigenic DNA minicircular chromosomes. We have now completely sequenced five aberrant minicircular chromosomes from the dinoflagellate Heterocapsa triquetra. These probably nonfunctional DNA circles lack complete genes, with each being composed of several short fragments of two or three different chloroplast genes and a common conserved region with a tripartite 9G-9A-9G core like the putative replicon origin of functional single-gene circular chloroplast chromosomes. Their sequences imply that all five circles evolved by differential deletions and duplications from common ancestral circles bearing fragments of four genes: psbA, psbC, 16S rRNA, and 23S rRNA. It appears that recombination between separate unigenic chromosomes initially gave intermediate heterodimers, which were subsequently stabilized by deletions that included part or all of one putative replicon origin. We suggest that homologous recombination at the 9G-9A-9G core regions produced a psbA/psbC heterodimer which generated two distinct chimeric circles by differential deletions and duplications. A 23S/16S rRNA heterodimer more likely formed by illegitimate recombination between 16S and 23S rRNA genes. Homologous recombination between the 9G-9A-9G core regions of both heterodimers and additional differential deletions and duplications could then have yielded the other three circles. Near identity of the gene fragments and 9G-9A-9G cores, despite diverging adjacent regions, may be maintained by gene conversion. The conserved organization of the 9G-9A-9G cores alone favors the idea that they are replicon origins and suggests that they may enable the aberrant minicircles to parasitize the chloroplast's replication machinery as selfish circles.

M. leprae genome sequence

The completion of the Mycobacterium leprae genome sequence, which has now been published in Nature 1xMassive gene decay in the leprosy bacillus. Cole, S.T et al. Nature. 2001; 409: 1007–1011Crossref | PubMed | Scopus (1048)See all References1, is a landmark event, as this bacterium, discovered by Armauer G. Hansen as the causative organism for leprosy in 1873, was the first bacterial pathogen to be identified as the cause of a human infectious disease.Leprosy is a chronic infectious disease that has existed since the dawn of civilization and is still a major public health problem. Clinically, severe peripheral neuropathies underlie the sensorimotor loss that accounts for most of the deformities and disabilities associated with leprosy. Although WHO-introduced multidrug therapy has dramatically reduced the number of leprosy patients worldwide, the detection of new cases in endemic areas has not been reduced. Lack of understanding of the basic biology of M. leprae has thus far been the key to the failure of leprosy research to advance. Now, the completion of the genome sequence will enable testing of hypotheses that have immediate practical applications, such as drug discovery, diagnostic tools and vaccines.The M. leprae genome is 3.3 Mb, circular and has an average G+C content of 57.8%. Comparison with its close relative, Mycobacterium tuberculosis reveals that M. leprae might have lost ∼2000 genes from its common mycobacterial ancestor. Only 49.5% of the M. leprae genome contains functional genes and 27% are translationally inert psuedogenes with inactive reading frames. The remaining 23.5% do not seem to be coding, probably because of mutation. This raises questions as to why and how a bacterial chromosome retains non-functional DNA. Hopefully, future comparative genomic studies will provide clues.In spite of this reductive evolution, M. leprae appears to have preserved the most vital genes among the active 1604 genes that are required for its obligatory parasitism. Compared with M. tuberculosis, M. leprae has lost crucial metabolic activities and their regulatory pathways, which probably explains why attempts to culture it in vitro have failed. The genome sequence also sheds new light on its extensive capabilities for lipid metabolism and fatty acid degradation. Several genes that encode key enzymes for the synthesis of structural components of the mycobacterial cell wall and fatty acid degradation, which are functional in M. tuberculosis, are missing or inactive in M. leprae. However, M. leprae has several enzymes that have no counterparts in M. tuberculosis, and there are unique genes with no orthologue in M. tuberculosis. Considering the entirely different pathology and tissue specificity of these two mycobacterial species, the differences in their genomes were not unexpected; however, the role of these differences in the pathogenesis of leprosy is presently unknown.The complete sequence of the M. leprae genome will provide the foundation of future research and will be invaluable in understanding the molecular basis for the complicated pathogenic mechanisms of leprosy. Moreover, the use of comparative genomics of mycobacterial species will reveal the history of molecular evolution and enable us to understand how the genes of M. leprae and M. tuberculosis function in completely different pathological settings.

HTLV-1 proviruses encoding non-functional TAX in adult T-cell leukemia.

Adult T-cell leukemia (ATL) is associated with prior infection with human T-cell leukemia virus type 1 (HTLV-1). TAX, the major transactivator of HTLV-1, has been implicated in the immortalization of infected T-cells, but molecular mechanisms of in vivo malignant cell transformation induced by HTLV-1 remain unclear. To investigate the role of TAX in the monoclonal proliferation of ATL cells, we determined the nucleotide sequence of tax DNA clones obtained from 6 ATL patients and analysed the biological function of their products. We found that ATL cells from 2 of these patients possessed tax with a nonsense or frame-shift mutation resulting in the premature termination of its protein product, which was no longer functional. This strongly argued against an indispensable role of TAX for the maintenance of ATL cells in vivo. On the other hand, the frequency of nucleotide substitutions found in non-functional tax DNA clones from these patients was significantly lower than those in functional tax DNA clones from the others, suggesting a role for TAX in the genome instability of infected cells. Although mismatch repair defects in the microsatellite markers, including those in hMSH3, hMSH6, BAX, TGF-beta RII, and E2F4 genes, were infrequent, we found an increase in the number of CAG repeats of the E2F4 microsatellite marker in 1 patient. These findings indicate that while TAX may be a necessary prerequisite for malignant transformation of infected cells, it is not essential for the maintenance of ATL cells in vivo.

Sex identification in birds

Visually identifying the sex of a bird can be difficult. It cannot be done in half the world's species when they are adults, and virtually none can be sexed as chicks. Despite this, the sex of a bird is vital for aviculture, scientific research, and conservation. Over the years, surgery and chromosome inspection have been used for sex identification. At present, these techniques are being eclipsed by the use of DNA. DNA can be used because a male bird has two Z sex chromosomes, whereas the female has a Z and a W. Consequently, the presence of a W unique DNA sequence will identify a bird as female. However, the isolation of a W-linked marker can be laborious. This is being remedied through the use of two DNA amplification reactions, known as random amplification of polymorphic DNA (RAPD) and amplified fragment length polymorphs (AFLP). Unfortunately, the markers they yield are often nonfunctional DNA. This type of DNA is a mild parasite and makes up about 95% of the genome. It also evolves rapidly so that a test based on such a sequence will only work in a single species or a few close relatives. More recently, a W-linked gene has been found. This is named CHD1-W, and it evolves far more slowly than nonfunctional DNA. It can be used to sex all birds, barring ratites such as the ostrich. The technique is simple, cheap, and effective. To conclude, DNA sex identification is demonstrated in three situations: an experiment that has shown that birds can control the sex of their offspring; a race to identify the sex of the last wild Spix's Macaw from moulted feathers; and as a valuable aid to breeding in zoos.

The skeletal function of non-genic nuclear DNA: new evidence from ancient cell chimaeras.

DNA can be divided functionally into three categories: (1) genes--which code for proteins or specify non-messenger RNAs; (2) semons--short specific sequences involved in the replication, segregation, recombination or specific attachments of chromosomes, or chromosome regions (e.g. loops or domains) or selfish genetic elements; (3) secondary DNA--which does not function by means of specific sequences. Probably more than 90% of DNA in the biosphere is secondary DNA present in the nuclei of plants and phytoplankton. The amount of genic DNA is related to the complexity of the organism, whereas the amount of secondary DNA increases proportionally with cell volume, and not with complexity. This correlation is most simply explained by the skeletal DNA hypothesis, according to which nuclear DNA functions as the basic framework for the assembly of the nucleus and the total genomic DNA content functions (together with relatively invariant folding rules) in determining nuclear volumes. Balanced growth during the cell cycle requires the cytonuclear ratio to be basically constant, irrespective of cell volume; thus nuclear volumes, and therefore the overall genome size, have to be evolutionarily adjusted to changing cell volumes for optimal function. Bacteria, mitochondria, chloroplasts and viruses have no nuclear envelope; and the skeletal DNA hypothesis simply explains why secondary DNA is essentially absent from them but present in large cell nuclei. Hitherto it has been difficult to refute the alternative hypothesis that nuclear secondary DNA (whether 'junk' or selfish DNA) accumulates merely by mutation pressure, and that selection for economy is not strong enough to eliminate it, whereas accumulation in mitochondria and plastids is prevented by intracellular replicative competition between their multiple genomes. New data that discriminate clearly between these explanations for secondary DNA come from cryptomonads and chlorarachneans, two groups of algae that originated independently by secondary symbiogenesis (i.e., the merger of two radically different eukaryote cells) several hundred million years ago. In both groups the nucleus and plasma membrane of the former algal symbiont persist as the nucleomorphs and periplastid membrane, respectively. The fact that nucleomorphs have undergone a 200- to 1000-fold reduction in genome size and have virtually no secondary DNA shows that selection against non-functional nuclear DNA is strong enough to eliminate it very efficiently; therefore, the large amounts of secondary DNA in the former host nuclei of these chimaeras, and in nuclei generally, must be being maintained by positive selection. The divergent selection for secondary DNA in the nucleus and against it in nucleomorphs is readily explicable by the skeletal DNA hypothesis, given the different spectrum of gene functions that it encodes.

A Statistical Feature of Genetic Sequences

We consider the available genomes (total DNA content) of autonomous organisms as strings of symbols from a four-letter alphabet corresponding to their molecular components (or bases), and define words as continuous sequences of letters with a given length. With the aim of distinguishing between genomes and non-functional DNA chains, we devise a description of random letter substitutions along a genetic string, and show each of the extant genomes to be more robust against point mutations than chains obtained by randomly reordering its word frequencies.

Specific DNA Binding of Stat5, but Not of Glucocorticoid Receptor, Is Required for Their Functional Cooperation in the Regulation of Gene Transcription

Prolactin and glucocorticoid hormone are signals which regulate the transcription of milk protein genes in mammary epithelial cells. We have investigated the molecular mechanisms by which these hormones cooperate in the induction of transcription. Both hormones activate latent transcription factors in the cytoplasm of mammary epithelial cells. Prolactin exerts its effect through binding to the extracellular domain of the prolactin receptor and through receptor dimerization. This leads to the activation of a protein tyrosine kinase (Jak2), which is noncovalently associated with the cytoplasmic domain of the prolactin receptor. Jak2 phosphorylates the signal transducer and transcription activator (Stat5) which causes its dimerization and nuclear translocation where Stat5 specifically binds to sequence elements in the promoter regions of milk protein genes. In comparison, the glucocorticoid receptor is activated by a lipophilic steroid ligand in the cytoplasm which causes allosteric changes in the molecule, dimerization, and nuclear localization. It has been demonstrated that Stat5 and the glucocorticoid receptor form a molecular complex which cooperates in the induction of transcription of the beta-casein gene. We have defined the DNA sequence requirements for this cooperative mechanism and have delimited the functional domains in Stat5 and the glucocorticoid receptor that are necessary for the functional interaction. We find that the Stat5 response element (Stat5RE) within the beta-casein gene promoter is sufficient to elicit the cooperative action of Stat5 and the glucocorticoid receptor on transcription. Activation of Stat5 through phosphorylation of tyrosine 694 is an absolute prerequisite for transcription. Deletion of the transactivation domain of Stat5 results in a molecule which cannot mediate transactivation by itself but can still cooperate with the glucocorticoid receptor. Mutated variants of the glucocorticoid receptor with a nonfunctional DNA binding domain or a DNA binding domain contributed by the estrogen receptor are still able to cooperate with Stat5 in transcriptional induction. Deletion of the ligand binding domain of the glucocorticoid receptor does not impede cooperation with Stat5, whereas deletion of the AF-1 transactivation domain does prevent cooperation. Our results indicate that the glucocorticoid receptor acts as a ligand-dependent coactivator of Stat5 independently of its DNA binding function.

Chlorella virus SC-1A encodes at least five functional and one nonfunctional DNA methyltransferases.

Chlorella virus SC-1A encodes at least six DNA methyltransferases (MTases): four N6-methyldeoxyadenine (m6A) MTases, M x CviSI (TGCmA), M x CviSII (CmATG), M x CviSIII (TCGmA) and M x CviSIV (GmATC), one 5-methyldeoxycytosine (m5C) MTase, M x CviSV (approximately RCmCG), and one nonfunctional m5C MTase, M x CviSVI, which is homologous to the MTase M x CviJI [RGmC(T/C/G)] produced by another chlorella virus IL-3A. Genes encoding three of the SC-1A m6A MTases (M x CviSI, M x CviSII, and M x CviSIII) and the nonfunctional m5C MTase were cloned and sequenced. Neither M x CviSI nor M x CviSIII genes hybridized to genes for their respective isomethylomers, M x CviRI and M x CviBIII, from other chlorella viruses. However, the M x CviSII gene hybridized strongly to its M x CviAII isomethylomer gene from virus PBCV-1. Like the prototype chlorella virus PBCV-1, the SC-1A genome contains inverted terminal repeats, one of which is adjacent to the nonfunctional m5C MTase. The three cloned m6A MTase genes are distributed throughout the approx. 345 kb SC-1A genome.

Sensitivity of selected bacterial species to UV radiation.

The effect of exposure of bacterial suspensions to UV radiation by means of the dose-response curves was assessed. The D37 and D10 values were used for subsequent statistical analysis of the results. The aim of this article is to evaluate the sensitivity to UV radiation of several microorganisms of different habitats (Rhizobium meliloti, Rhodobacter sphaeroides, Escherichia coli, and Deinococcus radiodurans), two mutants with nonfunctional SOS DNA repair system (R. meliloti recA- and E. coli recA-), and a mutant in the synthesis of carotenoids (R. sphaeroides crtD). The results reveal that D. radiodurans was an extremely resistant bacterium, R. meliloti was more resistant than R. sphaeroides, and E. coli was the most sensitive bacterium tested. The high sensitivity of recA- mutants was also verify. Moreover, it seems that the possession of pigments had no important effect in the sensitivity of R. sphaeroides to UV radiation.

Inheritance of a co-transferred foreign gene in the progenies of transgenic rice plants

The integration pattern and the inheritance of exogenous DNA in transgenic rice plants were analysed. Plasmid pCH (4.8 kb), that contains chimaeric cauliflower mosaic virus 35S promoter-hygromycin phosphotransferase structural gene, and plasmid pGP400 (7.2 kb), possessing oat phytochrome promoter and structural gene of bacterial β-glucuronidase, were co-transferred into protoplasts of rice (Oryza sativa L.) plants via electroporation. Primary transformants (T0 generation) and their progenies (T1, T2 and T3) were selected by hygromycin B. Southern blot analysis of inserted genes in transgenic rice plants suggests the integration of an intact hygromycin phosphotransferase gene and non-functional DNA fragments into host genome. Co-inheritance of the hygromycin phosphotransferase gene and β-glucuronidase gene was also observed. There were no significant differences in terms of the morphology and size of seeds between untransformed and transgenic plants (T3 generation).

MOLECULAR GENETICS OF ADAPTATION IN AN EXPERIMENTAL MODEL OF COOPERATION.

The evolution of cooperation was studied in an empirical system utilizing a parasitic bacteriophage (f1) and a bacterial host. Infected cells were propagated by serial passage so that a phage could increase its representation among infected hosts only by enhancing the rate of growth of its host. Loss of infectivity was therefore without selective penalty, and phage benevolence could potentially evolve through a variety of genetic changes. The infected hosts evolved to grow faster over the course of the study, but the genetic bases of this phenotypic change were more difficult to anticipate. Two fundamentally different types of genetic changes in the phage were revealed. One involved the loss of some phage genes, resulting in a noninfectious plasmid that continued to replicate via the parental phage replicon. The second change involved integration of the phage genome into host DNA by a process that, at low frequency, could be reversed to produce infectious phage particles. Integration is a previously unknown property of wild-type f1, and in the system studied, may have resulted from the use of a phage bearing an insert containing nonfunctional DNA. The evolution of this novel function apparently depended only on the presence of a small region in the phage genome that provided some homology to the host DNA, with the host providing all necessary functions. Although f1 is one of the simplest phages known, these observations suggest that host-parasite interactions of the filamentous phages are more complicated than previously thought. More generally, the f1 system offers a useful model for many problems concerning the genetic basis of adaptation.

A 240 kd multisubunit protein complex, CBF3, is a major component of the budding yeast centromere

A key protein component (CBF3) of the budding yeast (S. cerevisiae) centromere/kinetochore has been purified and characterized. CBF3 is a 240 kd multisubunit protein complex that binds specifically to the yeast wild-type centromere DNA ( CEN), but not to nonfunctional CEN DNA containing a single base substitution in the critical CDEIII consensus sequence. When purified by affinity chromatography, CBF3 contains three protein components: CBF3A (110 kd), CBF3B (64 kd), and CBF3C (58 kd). Highly purified CBF3 requires the presence of a separate assembly factor or chaperone activity to bind to CEN DNA. Treatment with phosphatase inactivates CBF3, indicating that at least one of the CBF3 subunits must be phosphorylated for DNA binding to occur. A 56 bp region including the 26 bp CDEIII consensus is protected from DNAase I cleavage in the CBF3- CEN DNA complex.

Heterogeneity of the ARV-2 strain and natural isolates of the human immunodeficiency virus.

To study heterogeneity of HIV isolates ARV-2 and strains isolated from lymphocytes of asymptomatic carriers were cloned using limiting dilutions of virus and infected CEM cells. All viral stocks turned out to be biologically heterogeneous giving clones with cytotoxic and noncytotoxic type of infection. Coinfection of CEM cells with cytotoxic and noncytotoxic variants resulted in interference of their biological effects. This interference ended with distinct cytotoxicity. No correlation between the production of virus and the amount of HIV DNA was found pointing out that nonfunctional DNA copies exist.

Transient expression of the plasmid pCaMVCAT in plant protoplasts following transformation with polyethyleneglycol

Petunia and carrot protoplasts have been transformed with the plasmid pCaMVCAT by the use of polyethyleneglycol (PEG) as a facilitator. Transformation was revealed by the appearance of the chloramphenicol-acetyl transferase (CAT) enzyme within the tranformed cells. Maximal activity of the CAT enzyme was detected within 15 h following transformation, while after 60 h, its activity was significantly reduced, indicating transient expression of the CAT gene. The efficiency of transformation was highly dependent on the presence of CaCl 2 in the transformation system, was stimulated by non-functional carrier DNA and was independent on the molecular weight (MW) of PEG used.

The effects of mispair and nonpair correction in hybrid DNA on base ratios (G + C content) and total amounts of DNA.

Base ratios and total DNA amounts can vary substantially between and within higher taxa and genera, and even within species. Gene conversion is one of several mechanisms that could cause such changes. For base substitutions, disparity in conversion direction is accompanied by an equivalent disparity in base ratio at the heterozygous site. Disparity in the direction of gene conversion at meiosis is common and can be extreme. For transitions (which give purine [R]/pyrimidine [Y] mispairs) and for transversions giving unlike R/R and Y/Y mispairs in hybrid DNA, this disparity could give slow but systematic changes in G + C percentage. For transversions giving like R/R and Y/Y mispairs, it could change AT/TA and CG/GC ratios. From the extent of correction direction disparity, one can deduce properties of repair enzymes, such as the ability (1) to excise preferentially the purine from one mispair and the pyrimidine from the other for two different R/Y mispairs from a single heterozygous site and (2) to excise one base preferentially from unlike R/R or Y/Y mispairs. Frame-shifts usually show strong disparity in conversion direction, with preferential cutting of the nonlooped or the looped-out strand of the nonpair in heterozygous h-DNA. The opposite directions of disparity for frame-shifts and their intragenic suppressors as Ascobolus suggest that repair enzymes have a strong, systematic bias as to which strand is cut. The conversion spectra of mutations induced with different mutagens suggest that the nonlooped strand is preferentially cut, so that base additions generally convert to mutant and deletions generally convert to wild-type forms. Especially in nonfunctional or noncoding DNA, this could cause a general increase in DNA amounts. Conversion disparity, selection, mutation, and other processes interact, affecting rates of change in base ratios and total DNA.

Gene conversion: a possible mechanism for eliminating selfish DNA.

A strong case has recently been made for the existence of selfish DNA in higher organisms (Doolittle and Sapienza, 1980; Orgel and Crick, 1980). Given that genetic elements exist which have the means of reproducing themselves by transposition to new locations, they would be expected to gradually accumulate in the genome, especially in diploid organisms. The essence of the argument is that each insertion of a nonfunctional DNA sequence, which only very slightly increases the size of the genome, would have a neglible phenotypic effect on the individual and therefore would not be selected against. For the amount of DNA to increase, all that is required is that the probability of a DNA sequence being added to the genome is greater than the probability of it being eliminated by natural selection or by random deletion. There will also be positive selection for genetic elements which increase by mutation their efficiency of transposition. Not only will genomes increase in size, but also most of the DNA will become “junk,” with no function for the organism. This conclusion may help solve the C-value paradox, namely, that higher organisms appear to have much more DNA than is required for the synthesis and control of gene products, and that there is enormous variation of DNA content between different taxonomic groups or even between quite closely related species of higher organisms.