C-value Paradox Research Articles

Junk DNA and sectorial gene repression

Transcriptional repression in eukaryotes often involves tens or hundreds of kilobase pairs, two to three orders of magnitude more than the bacterial operator/repressor model does. Classical repression, represented by this model, was maintained over the whole span of evolution under different guises, and consists of repressor factors interacting primarily with promoters and, in later evolution, also with enhancers. The use of much larger amounts of DNA in the other mode of repression, here called the sectorial mode (‘superrepression’), results in the conceptual transfer of so-called junk DNA to the domain of functional DNA. This contribution to the solution of the c-value paradox involves perhaps 15% of genomic ‘junk’, and encompasses the bulk of the introns, thought to fill a stabilizing role in sectorially repressed chromatin structures. In the case of developmental genes, such structures appear to be heterochromatoid in character. However, solid clues regarding general structural features of superrepressed terminal differentiation genes remain elusive. The competition among superrepressible DNA sectors for sectorially binding factors offers, in principle, a molecular mechanism for developmental switches. Position effect variegation may be considered an abnormal manifestation of normal processes that underly development and involve heterochromatoid sectorial repression, which is apparently required for local elimination or modulation of morphological features (morpholysis). Sectorial repression of genes participating either in development or in terminal differentiation is considered instrumental in establishing stable cell types, and provides a basis for the distinction between determination and cell type specification. The gamut of possible stable cell types may have been broadened by the appearance in evolution of heavy isochores. Additional types of relatively frequent GC-rich cis-acting DNA motifs may offer reiterated binding sites to factors endowed with a selective (though not individually strong) affinity for these motifs. The majority of sequence motifs thought to be used in superrepression need not be individually maintained by natural selection. It is re-emphasized that the dispensability of sequences is not an indicator of their nonfunctionality and that in many cases, along noncoding sequences, nucleotides tend to fill functions collectively, rather than individually.

High intrinsic rate of DNA loss in Drosophila.

Pseudogenes are common in mammals but virtually absent in Drosophila. All putative Drosophila pseudogenes show patterns of molecular evolution that are inconsistent with the lack of functional constraints. The absence of bona fide pseudogenes is not only puzzling, it also hampers attempts to estimate rates and patterns of neutral DNA change. The estimation problem is especially acute in the case of deletions and insertions, which are likely to have large effects when they occur in functional genes and are therefore subject to strong purifying selection. We propose a solution to this problem by taking advantage of the propensity of retrotransposable elements without long terminal repeats (non-LTR) to create non-functional, 'dead-on-arrival' copies of themselves as a common by-product of their transpositional cycle. Phylogenetic analysis of a non-LTR element, Helena, demonstrates that copies lose DNA at an unusually high rate, suggesting that lack of pseudogenes in Drosophila is the product of rampant deletion of DNA in unconstrained regions. This finding has important implications for the study of genome evolution in general and the 'C-value paradox' in particular.

Variations in genome mass

1. 1. Genome size varies considerably among vertebrates, ranging from less than 1 pg to more than 200 pg; the amount of DNA differing among individuals in a population can equal the amount in the entire structural gene complement. 2. 2. Recent technological advances permit evaluation of genome size variation at several levels including sub-chromosomal, chromosomal and cellular. 3. 3. Genome size variation may also be viewed from taxonomic levels, and across evolutionary time frames. 4. 4. As sources of genome size variation are identified and studied, the conundrum of the C-value paradox (lack of correlations among genome size, genomic complexity and phylogenetic status of organisms) may prove to be more apparent than real. 5. 5. For example, the limited and relatively constant genome size of avians may be related to the physiological constraints of flight.

A unified matrix hypothesis of DNA-directed morphogenesis, protodynamism and growth control.

A theoretical concept is proposed, in order to explain some enigmatic aspects of cellular and molecular biology of eukaryotic organisms. Among these are the C-value paradox of DNA redundancy, the correlation of DNA content and cell size, the disruption of genes at DNA level, the "Chromosome field" data of Lima de Faria (Hereditas 93:1, 1980), the "quantal mitosis" proposition of Holtzer et al. (Curr. Top. Dev. Biol. 7:229 1972), the inheritance of morphological patterns, the relations of DNA and chromosome organisation to cellular structure and function, the molecular basis of speciation, etc. The basic proposition of the "Unified Matrix Hypothesis" is that the nuclear DNA has a direct morphogenic function, in addition to its coding function in protein synthesis. This additional genetic information is thought to be largely contained in the non-protein coding transcribed DNA, and in the untranscribed part of the genome.

Gene regulation and DNA C-value paradox: A model based on diffusion of regulatory molecules

The general idea of the model is that regulatory molecules can move stochastically from site to site along DNA and that according to their chromosomal position, genes should have a more or less high probability to be activated (or repressed) during differentiation. In this model the role of non coding DNA is to maintain genes in a relative position that determines what is usually called the “differentiation programme”.

A Unified Matrix Hypothesis of DNA-directed morphogenesis, protodynamism and growth control

A theoretical concept is proposed, in order to explain some enigmatic aspects of cellular and molecular biology of eukaryotic organisms. Among these are the C-value paradox of DNA redundancy, the correlation of DNA content and cell size, the disruption of genes at DNA level, the “Chromosome field” data of Lima de Faria (Hereditas93:1, 1980), the “quantal mitosis proposition” of Holtzer et al. (Curr. Top. Dev. Biol.7:229, 1972), the inheritance of morphological patterns, the relations of DNA and chromosome organisation to cellular structure and function, the molecular basis of speciation, etc. The basic proposition of the “Unified Matrix Hypothesis” is that the nuclear DNA has a direct morphogenic function, in addition to its coding function in protein synthesis. This additional genetic information is thought to be largely contained in the non-protein coding transcribed DNA, and in the untranscribed part of the genome.

The C-value paradox: The paradox that never was the evolution of genome size. Edited by T. Cavalier-Smith. John Wiley & Sons, 1985. Pp. 523, �38.50

The C-value paradox: The paradox that never was the evolution of genome size. Edited by T. Cavalier-Smith. John Wiley & Sons, 1985. Pp. 523, �38.50

The C‐value paradox: The paradox that never was the evolution of genome size. Edited by T. Cavalier‐Smith. John Wiley & Sons, 1985. Pp. 523, £38.50

BioEssaysVolume 4, Issue 5 p. 234-236 Book Review The C-value paradox: The paradox that never was the evolution of genome size. Edited by T. Cavalier-Smith. John Wiley & Sons, 1985. Pp. 523, £38.50 Gabriel A. Dover, Gabriel A. Dover Department of Genetics, University of Cambridge, Downing St, Cambridge CB2 3EH, UKSearch for more papers by this author Gabriel A. Dover, Gabriel A. Dover Department of Genetics, University of Cambridge, Downing St, Cambridge CB2 3EH, UKSearch for more papers by this author First published: May 1986 https://doi.org/10.1002/bies.950040515AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Volume4, Issue5May 1986Pages 234-236 RelatedInformation

Structure and function of repetitive DNA in eukaryotes

Prokaryotes possess relatively small genomes consisting predominantly oflow-copy numberDNA sequences. The genome sizes ofdifferent species vary by less than an order of magnitude (Kingsbury, 1969). In contrast, eukaryotic genomes are generally much larger than their prokaryotic counterparts, and a far greater proportion of this DNA (about 30-40%) is repeated (Britten & Kohne, 1968; Laird, 1971). This repetitive component takes on several guises, and for the purpose of previous discussions it has often been useful to classify these sequences according to their various characteristic properties: structure, distribution and reiteration frequency (Jelinek & Schmid, 1982). Recent applications ofDNA cloning methods and more powerful analytical techniques to study specific sequence families has provided a different perspective on the apparent diversity of structure and organization of eukaryotic repetitive DNA. Does this new information provide us with clues as to what the functions of these sequences might be? An unresolved, and possibly related, question centres on the considerable variation seen in the haploid nuclear DNA contents, or 'C-values', of eukaryotes (Britten & Davidson, 1969). These differences are found in many different phyla encompassing amphibians (Straus, 1971), plants (Rothfels et al., 1966; Rees & Jones, 1967), insects (Keyl, 1965) and rodents (Mazrimas & Hatch, 1972). C-value variation can, on occasion, be especially dramatic; it is sometimes observed in organisms of the same genus that have virtually identical morphology and karyotype. This is the essential element of the so-called 'C-value paradox'; nearly identical species must express about the same number of genes despite significant differences in their C-values. What is the nature of all this extra non-coding DNA? It does not, as one might have anticipated, all correspond to additional repetitive elements; it also includes a considerable increase in the amount of 'single-copy' DNA. Such considerations led some to conceive radical theories of genetic organization in eukaryotes to provide a function for this extra DNA (Callan, 1967; Britten & Davidson, 1969; Thomas, 1971) which, in their simplest forms, have proved to be incorrect. A more recent theory, based on the involvement of dispersed repetitive sequences, envisages that some of these elements may have a nuclear role in selecting which mRNA molecules enter the cell cytoplasm (Davidson & Britten, 1979). A recent study may offer some support for such an idea (Sutcliffe et al., 1984), but others disagree with the interpretation of these data (Owens et al., 1985). In any event, such proposals may provide a function for a minority of the non-coding sequences in eukaryotic genomes, but what of the remainder? Attention has periodically focused on -the persuasively presented alternative argument that the bulk of the 'extra' DNA in eukaryotes might be 'selfish' and have no function (Doolittle & Sapienza, 1980; Orgel & Crick, 1980). This Review will re-examine the idea in the light of recent studies of the structure of specific eukaryotic repetitive DNA elements.

The C-Value Paradox

The C-value paradox concerns apparent incongruities in the relationship between genome size, number of proteins synthesized, and organismal complexity. Particularly puzzling has been the large size of eukaryotic genomes relative to the amount of information needed to code for all synthesized proteins. Advances in molecular biology are described that clarify some aspects of the paradox. (Accepted for publication 21 March 1984)

Skeletal DNA and the evolution of genome size.

The mass of DNA in a haploid nucleus is usually constant in any one species and is known as its C-value (134) or genome size. Just as atomic theory explains the different masses and properties of atoms, so genetics ought to be able to explain the different masses and properties of genomes. But despite elegant physical explanations for qualitative genetic variation and inheritance, in terms of how nucleotide sequences code for proteins, we lack a generally accepted theory of what determines genome sizes. Particularly puzzling has been the almost 105-fold variation in C-value among different eukaryote species (Figure 1). Often dubbed the C-value paradox (21,27, 137), it appears inexplicable in terms of qualita­ tive differences between organisms. The purpose of this review is to discuss recent ideas and evidence concerning the C-value paradox; these suggest that DNA may have quantitative noncoding functions (10, 11,27, 35) in addition to its better established qualitative coding ones. The problem is distinctly biophysical, involving the approaches and ideas of both Galileo and Darwin; i.e. Galileo's principle of scaling and Darwin's principle of selection. Galileo (54) first showed that mere

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.

Chromosome structure and the C-value paradox.

Chromosome structure and the C-value paradox.

A general function of noncoding polynucleotide sequences. Mass binding of transconformational proteins.

It is proposed that a general function of noncoding DNA and RNA sequences in higher organisms (intergenic and intervening sequences) is to provide multiple binding sites over long stretches of polynucleotide for certain types of regulatory proteins. Through the building up or abolishing of high-order structures, these proteins either sequester sites for the control of, e.g., transcription or make the sites available to local molecular signals. If this is to take place, the existence of a 'c-value paradox' becomes a requirement. Multiple binding sites for a given protein may recur in the form of a sequence 'motif' that is variable within certain limits. Noncoding sequences of the chickens ovalbumin gene furnish an appropriate example of a sequence motif. GAAAATT. Its improbably high frequency and significant periodicity are both absent from the coding sequences of the same gene and from the noncoding sequences of a differently controlled gene in the same organisms, the preproinsulin gene. This distribution of a sequence motif is in keeping with the concepts outlined. Low specificity of sequences that bind protein is likely to be compatible with highly specific conformational changes.

Nuclear volume control by nucleoskeletal DNA, selection for cell volume and cell growth rate, and the solution of the DNA C-value paradox

The 40,000-fold variation in eukaryote haploid DNA content is unrelated to organismic complexity or to the numbers of protein-coding genes. In eukaryote microorganisms, as well as in animals and plants, DNA content is strongly correlated with cell volume and nuclear volume, and with cell cycle length and minimum generation time. These correlations are simply explained by postulating that DNA has 2 major functions unrelated to its protein-coding capacity: (1) the control of cell volume by the number of replicon origins, and (2) the determination of nuclear volume by the overall bulk of the DNA: cell growth rates are determined by the cell volume and by the area of the nuclear envelope available for nucleocytoplasmic transport of RNA, which in turn depends on the nuclear volume and therefore on the DNA content. During evolution nuclear volume, and therefore DNA content, has to be adjusted to the cell volume to allow reasonable growth rates. The great diversity of cell volumes and growth rates, and therefore of DNA contents, among eukaryotes results from a varying balance in different species between r-selection, which favours small cells and rapid growth rates and therefore low DNA C-values, and K-selection which favours large cells and slow growth rates and therefore high DNA C-values. In multicellular organisms cell size needs to vary in different tissues: size differences between somatic cells result from polyteny, endopolyploidy, or the synthesis of nucleoskeletal RNA. Conflict between the need for large ova and small somatic cells explains why lampbrush chromosomes, nurse cells, chromatin diminution and chromosome elimination evolved. Similar evolutionary considerations clarify the nature of polygenes, the significance of the distribution of haploidy, diploidy and dikaryosis in life cycles and of double fertilization in angiosperms, and of heteroploidy despite DNA constancy in cultured cells, and other puzzles in eukaryote chromosome biology. Eukaryote DNA can be divided into genic DNA (G-DNA), which codes for proteins (or serves as recognition sites for proteins involved in transcription, replication and recombination), and nucleoskeletal DNA (S-DNA) which exists only because of its nucleoskeletal role in determining the nuclear volume (which it shares with G-DNA, and performs not only directly, but also indirectly by coding for nucleoskeletal RNA). Mechanistic and evolutionary implications of this are discussed.

Gene control in eukaryotes and thec-value paradox “Excess” DNA as an impediment to transcription of coding sequences

Ways in which control of gene activity may lead to the observed high DNA content per haploid eukaryote genome are examined. It is proposed that deoxyribonucleoprotein (DNP) acts as a barrier to transcription at two distinct structural levels. At the lower level, melting of the nucleosome supercoil (quaternary structure) and of the nucleosomes (tertiary structure) might be brought about by the process of transcription itself. After unwinding the barrier section, the polymerase would eventually reach the structural gene. The transcripts of noncoding sequences, at least as far as their "unique" sequence components are concerned, may thus have filled their main function through the very process of transcription. The possibility of an inverse relationship between the length of the DNP barrier and the rates of transcription of the coding sequences is to some extent supported by available data. Different modes of coordination between the transcription of mRNA and of hnRNA from a single functional unit of gene action (funga) are considered. An analysis of gene control at high structural levels of DNP is made on the basis of other data, in relation to the concepts of eurygenic and stenogenic control. The concept of a euryon is introduced, namely of a set of linked fugas under common eurygenic control. Structure of order higher than quaternary can be inferred to exist in larger chromomeres of polytene chromosomes and in corresponding sections of ordinary chromosomes. Only moderate amounts of highest order interphase euchromatic structure are likely to be able to be accomodated in average chromomeres and none in very thin chromomeres. Puffs are interpreted as the melting of highest order interphase structure, and the absence of puffs during transcription as the absence of this highest order structure in the resting state of the chromomeres. Genes that are constantly active in all tissues may dispense with highest order interphase structure and with the corresponding control mechanism, and the fugas involved thus may not puff. Puffs, large chromomeres and highest order interphase euchromatic DNP structure seem to be correlated with genes that need to be transcribed only under certain developmental conditions. It is proposed that the function of high order structure is to sequester genetic material, namely mainly controller sequences. Since such high order structure, in most cases, would be built up to house the controller dependencies of just one structural gene, the amount of DNA per structural gene needed for gene control would be considerable, and the concept, if correct, would go a long way towards explaining the c-value paradox ("excess" DNA in eukaryotes). In eurygenic determination, the high order structure is thought to be conditioned for melting or to actually melt to an intermediate level of structure. From there, stenogenic control, leading to transcription, is considered to carry the melting process further to yet lower structural levels...

Analysis of the C-value paradox by molecular hybridization.

Poly(A)-containing RNA was isolated from ovaries of Xenopus laevis laevis and Triturus cristatus carnifex and used as a template for the synthesis of radioactive complementary DNA with RNA-dependent DNA polymerase. When annealed with an excess of homologous DNA, the complementary DNA is rendered double-stranded with kinetics that suggest that the coding sequences are single-copy in both these organisms. In Triturus, these sequences are distinct from the majority of the genome, which consists of repeated sequences, and distinct from the ribosomal cistrons, which are present in proportion to the increase in C-value relative to the Xenopus genome. Moreover, the number of different poly(A)-containing molecules in the ovary (sequence complexity) is the same in Xenopus and in Triturus.