Alexander E. Vinogradov

Genome size and GC‐percent in vertebrates as determined by flow cytometry: The triangular relationship

Genome size and GC-percent were determined by means of a special method of DNA flow cytometry in 154 vertebrate species. For the total dataset, a highly significant positive correlation was found between both parameters. The overall distribution of points is not linear but triangular: a wide range of GC-percent values is observed at the lower end of genome size range, whereas with an increase in genome size the lower limit for GC-percent is elevated, gradually approaching the upper limit (about 46%). In teleost fishes, which occupy the lower part of genome size range, the negative relationship between both parameters was observed. Two positive linear relationships were found between mean genome size and GC-percent of the main vertebrate groups (one includes fishes, amphibians, and mammals, the other consists of reptiles and birds, which show the higher GC-percent for their genome sizes). Distribution of variance between taxonomic levels indicates that GC-percent is more evolutionarily conservative than genome size in anamniotes. Anuran amphibians show the greatest part of genome size variability at the lower taxonomic levels as compared to other vertebrates (with no additional variance already above the genus level). The data obtained with different methods are compared. It is shown that the proposed method can provide useful data for studies on genome evolution and biodiversity.

Intron–Genome Size Relationship on a Large Evolutionary Scale

Abstract. The intron–genome size relationship was studied across a wide evolutionary range (from slime mold and yeast to human and maize), as well as the relationship between genome size and the ratio of intervening/coding sequence size. The average intron size is scaled to genome size with a slope of about one-fourth for the log-transformed values; i.e., on the global scale its increase in evolution is lower than the increase in genome size by four orders of magnitude. There are exceptions to the general trend. In bakers yeast introns are extraordinarily long for its genome size. Tetrapods also have longer introns than expected for their genome sizes. In teleost fish the mean intron size does not differ significantly, notwithstanding the differences in genome size. In contrast to previous reports, avian introns were not found to be significantly shorter than introns of mammals, although avian genomes are smaller than genomes of mammals on average by about a factor of 2.5. The extra-/intragenic ratio of noncoding DNA can be higher in fungi than in animals, notwithstanding the smaller fungal genomes. In vertebrates and invertebrates taken separately, this ratio is increasing as the increase in genome size. Two hypotheses are proposed to explain the variation in the extra-/intragenic ratio of noncoding DNA in organisms with similar numbers of genes: transition (dynamic) and equilibrium (static). According to the transition model, this variation arises with the rapid shift of genome size because the bulk of extragenic DNA can be changed more rapidly than the finely interspersed intron sequences. The equilibrium model assumes that this variation is a result of selective adjustment of genome size with constraints imposed on the intron size due to its putative link to chromatin structure (and constraints of the splicing machinery).

Noncoding DNA, isochores and gene expression: nucleosome formation potential

The nucleosome formation potential of introns, intergenic spacers and exons of human genes is shown here to negatively correlate with among-tissues breadth of gene expression. The nucleosome formation potential is also found to negatively correlate with the GC content of genomic sequences; the slope of regression line is steeper in exons compared with noncoding DNA (introns and intergenic spacers). The correlation with GC content is independent of sequence length; in turn, the nucleosome formation potential of introns and intergenic spacers positively (albeit weakly) correlates with sequence length independently of GC content. These findings help explain the functional significance of the isochores (regions differing in GC content) in the human genome as a result of optimization of genomic structure for epigenetic complexity and support the notion that noncoding DNA is important for orderly chromatin condensation and chromatin-mediated suppression of tissue-specific genes.

Intron Length and Codon Usage

Saccharomyces cerevisiae 224 39.0 0.61 0.69 −0.59 −0.72 (baker’s yeast) 17.1 (<10 ) (<10) (<10) (<10) Schizosaccharomyces 2,309 30.8 — — −0.13 −0.10 pombe(fission yeast) 14.9 (<10 ) (<10) Emericella nidulans(mold) 203 59.9 0.18 0.44 −0.09 −0.30 12.6 (<0.02) (<10) (<0.3) (<10) Neurospora crassa(fungus) 133 70.6 0.15 0.36 −0.14 −0.35 12.0 (<0.1) (<10) (<0.2) (<10) Candida albicans 34 26.1 — — −0.77 −0.60 (pathogenic yeast) 31.7 (<10 ) (<10) Dictyostelium discoideum 138 15.7 0.35 0.15 −0.01 −0.27 (cellular slime mold) 44.5 (<10 ) (<0.1) (<0.7) (<10) Tetrahymena thermophila 22 40.0 — — −0.62 −0.59 (ciliate) 39.7 (<0.01) (<0.01) Chlamydomonas reinhardtii 83 86.2 −0.16 0.06 (unicellular plant) 5.0 (<0.2) (<0.6) Caenorhabditis elegans 14,673 37.6 −0.03 −0.07 0.12 0.14 (nematode) 23.0 (<10 ) (<10) (<10) (<10) Xenopus laevis 54 50.3 0.23 0.11 (clawed frog) 16.1 (<0.1) (<0.5) Gallus gallus 158 67.5 — — 0.34 0.30 (chicken) 24.6 (<10 ) (<10) Mus musculus 981 62.2 — — 0.07 0.15 (mouse) 17.2 (<0.03) (<10 ) Rattus norvegicus 348 62.7 0.17 0.26 (rat) 17.9 (<0.01) (<10 ) Homo sapiens 2,543 64.0 — — 0.25 0.27 (human) 24.7 (<10 ) (<10) Arabidopsis thaliana 21,238 40.0 — — 0.16 0.05 (thale cress) 15.3 (<10 ) (<0.12) Zea mays 91 76.6 — — 0.26 0.55 (corn) 23.4 (<0.02) (<10 )

Genome size and metabolic intensity in tetrapods : a tale of two lines

We show the negative link between genome size and metabolic intensity in tetrapods, using the heart index (relative heart mass) as a unified indicator of metabolic intensity in poikilothermal and homeothermal animals. We found two separate regression lines of heart index on genome size for reptiles–birds and amphibians–mammals (the slope of regression is steeper in reptiles–birds). We also show a negative correlation between GC content and nucleosome formation potential in vertebrate DNA, and, consistent with this relationship, a positive correlation between genome GC content and nuclear size (independent of genome size). It is known that there are two separate regression lines of genome GC content on genome size for reptiles–birds and amphibians–mammals: reptiles–birds have the relatively higher GC content (for their genome sizes) compared to amphibians–mammals. Our results suggest uniting all these data into one concept. The slope of negative regression between GC content and nucleosome formation potential is steeper in exons than in non-coding DNA (where nucleosome formation potential is generally higher), which indicates a special role of non-coding DNA for orderly chromatin organization. The chromatin condensation and nuclear size are supposed to be key parameters that accommodate the effects of both genome size and GC content and connect them with metabolic intensity. Our data suggest that the reptilian–birds clade evolved special relationships among these parameters, whereas mammals preserved the amphibian-like relationships. Surprisingly, mammals, although acquiring a more complex general organization, seem to retain certain genome-related properties that are similar to amphibians. At the same time, the slope of regression between nucleosome formation potential and GC content is steeper in poikilothermal than in homeothermal genomes, which suggests that mammals and birds acquired certain common features of genomic organization.

‘Genome design’ model and multicellular complexity: golden middle

Human tissue-specific genes were reported to be longer than housekeeping genes (both in coding and intronic parts). The competing neutralist and adaptationist models were proposed to explain this observation. Here I show that in human genome the longest are genes with the intermediate expression pattern. From the standpoint of information theory, the regulation of such genes should be most complex. In the genomewide context, they are found here to have the higher informational load on all available levels: from participation in protein interaction networks, pathways and modules reflected in Gene Ontology categories through transcription factor regulatory sets and protein functional domains to amino acid tuples (words) in encoded proteins and nucleotide tuples in introns and promoter regions. Thus, the intermediately expressed genes have the higher functional and regulatory complexity that is reflected in their greater length (which is consistent with the ‘genome design’ model). The dichotomy of housekeeping versus tissue-specific entities is more pronounced on the modular level than on the molecular level. There are much lesser intermediate-specific modules (modules overrepresented in the intermediately expressed genes) than housekeeping or tissue-specific modules (normalized to gene number). The dichotomy of housekeeping versus tissue-specific genes and modules in multicellular organisms is probably caused by the burden of regulatory complexity acted on the intermediately expressed genes.

Organismal complexity, cell differentiation and gene expression: human over mouse

We present a molecular and cellular phenomenon underlying the intriguing increase in phenotypic organizational complexity. For the same set of human–mouse orthologous genes (11 534 gene pairs) and homologous tissues (32 tissue pairs), human shows a greater fraction of tissue-specific genes and a greater ratio of the total expression of tissue-specific genes to housekeeping genes in each studied tissue, which suggests a generally higher level of evolutionary cell differentiation (specialization). This phenomenon is spectacularly more pronounced in those human tissues that are more directly involved in the increase of complexity, longevity and body size (i.e. it is reflected on the organismal level as well). Genes with a change in expression breadth show a greater human–mouse divergence of promoter regions and encoded proteins (i.e. the functional genomics data are supported by the structural analysis). Human also shows the higher expression of translation machinery. The upstream untranslated regions (5′UTRs) of human mRNAs are longer than mouse 5′UTRs (even after correction for the difference in genome sizes) and contain more uAUG codons, which suggest a more complex regulation at the translational level in human cells (and agrees well with the augmented cell specialization).

Somatic polyploidy promotes cell function under stress and energy depletion: evidence from tissue-specific mammal transcriptome

Polyploid cells show great among-species and among-tissues diversity and relation to developmental mode, suggesting their importance in adaptive evolution and developmental programming. At the same time, excessive polyploidization is a hallmark of functional impairment, aging, growth disorders, and numerous pathologies including cancer and cardiac diseases. To shed light on this paradox and to find out how polyploidy contributes to organ functions, we review here the ploidy-associated shifts in activity of narrowly expressed (tissue specific) genes in human and mouse heart and liver, which have the reciprocal pattern of polyploidization. For this purpose, we use the modular biology approach and genome-scale cross-species comparison. It is evident from this review that heart and liver show similar traits in response to polyploidization. In both organs, polyploidy protects vitality (mainly due to the activation of sirtuin-mediated pathways), triggers the reserve adenosine-5′-triphosphate (ATP) production, and sustains tissue-specific functions by switching them to energy saving mode. In heart, the strongest effects consisted in the concerted up-regulation of contractile proteins and substitution of energy intensive proteins with energy economic ones. As a striking example, the energy intensive alpha myosin heavy chain (providing fast contraction) decreased its expression by a factor of 10, allowing a 270-fold increase of expression of beta myosin heavy chain (providing slow contraction), which has approximately threefold lower ATP-hydrolyzing activity. The liver showed the enhancement of immunity, reactive oxygen species and xenobiotic detoxication, and numerous metabolic adaptations to long-term energy depletion. Thus, somatic polyploidy may be an ingenious evolutionary instrument for fast adaptation to stress and new environments allowing trade-offs between high functional demand, stress, and energy depletion.

Genome size and chromatin condensation in vertebrates

Cell membrane-dependent chromatin condensation was studied by flow cytometry in erythrocytes of 36 species from six classes of vertebrates. A positive relationship was found between the degree of condensation and genome size. The distribution of variances among taxonomic levels is similar for both parameters. However, chromatin condensation varied relatively more at the lower taxonomic levels, which suggests that the degree of DNA packaging might serve for fine-tuning the ‘skeletal’ and/or ‘buffering’ function of noncoding DNA (although the range of this fine-tuning is smaller than the range of genome size changes). For two closely related amphibian species differing in genome size, change in chromatin condensation under the action of elevated extracellular salinity was investigated. Condensation was steadier and its reaction to changes in solvent composition was more inertial in the species with a larger genome, which is in agreement with the buffering function postulated for redundant DNA. The uppermost genome size in vertebrates (and in living beings in general) was updated using flow cytometry and was found to be about 80 pg (78,400 Mb). The widespread opinion that the largest genome occurs in unicellular organisms is rejected as being based on artifacts.

Mirrored genome size distributions in monocot and dicot plants.

The variation in genome size and basic chromosome number was analyzed in the wide range of angiosperm plants. A divergence of monocots vs. dicots (eudicots) genome size distributions was revealed. A similar divergence was found for annual vs. perennial dicots. The divergence of monocots vs. dicots genome size distributions holds at different taxonomic levels and is more pronounced for species with larger genomes. Using nested analysis of variance, it was shown that putative constraints on genome size variation are not only stronger in dicots as compared to monocots but in the former they start to operate already at the family level, whereas in the latter they do so only at the order level. At the same time, variation in basic chromosome number is constrained at the order level in both groups. Higher basic chromosome numbers were found in perennial plants as compared to the annual ones, which can be explained by their need for a higher genetic recombination as compensation for the longer life-cycles. A negative correlation was found between genome size and basic chromosome number, which can be explained as a trade-off between different recombination mechanisms.