Genome size and chromatin condensation in vertebrates

Vinogradov, Alexander E.

doi:10.1007/s00412-004-0323-3

Cited by 36 publications

(26 citation statements)

References 74 publications

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“…The non-coding DNA was also supposed to play a 'buffering' role, damping the effect of solvent fluctuations on the nuclear machinery (Vinogradov 1998a). Recently, it was shown in comparison of two closely related amphibian species differing in genome size that chromatin condensation was steadier and its reaction to changes in solvent composition (caused by elevated extracellular salinity) was more inertial in species with the larger genome, which is in agreement with the buffering model (Vinogradov 2005a). The ability of DNA to act as 'buffer' to control the concentration of DNA-binding proteins and smaller solutes was even used for the development of experimental methods for investigation of histone-DNA interaction and DNA thermostability (Thastrom et al 2004;Volker & Breslauer 2005).…”

Section: K4supporting

confidence: 70%

“…The redundant non-coding DNA is supposed to serve for adjustment of metabolic rate mediated by a change in general cellular parameters (such as nuclear size, chromatin condensation, nucleocytoplasmic ratio), which in multicellulars can be independent of body size (Szarski 1983;Cavalier-Smith 1985;Vinogradov 1995Vinogradov , 1997Vinogradov , 1998aGregory 2002;Kozlowski et al 2003;Olmo 2003;Vinogradov & Anatskaya 2004;Vinogradov 2005a). The link between genome size and metabolic rate can be considered as an example of the symmorphosis, a general principle of evolutionary biology defined as a quantitative match of structural design and functional demand (Weibel et al 1991;Diamond & Hammond 1992;Weibel 2000).…”

Section: K4mentioning

confidence: 99%

“…The larger genome is associated with a number of phenotypic traits, the most prominent of which are the larger nuclear and cell sizes, longer cell cycle and development and lower metabolic rate (reviewed by Bennett 1998;Petrov 2001;Vinogradov 2004a). The latter trait is of special interest because it might have a clear adaptive significance: the more economical physiology should allow a species to occupy a niche with a low energy supply (Szarski 1983;Vinogradov 1998aVinogradov , 2005a. However, the link between metabolic rate and genome size was demonstrated only in amniotes (in reptiles, on a limited dataset; Vinogradov 1995Vinogradov , 1997Gregory 2002;Waltari & Edwards 2002;Olmo 2003;Vinogradov & Anatskaya 2004).…”

Section: Introductionmentioning

confidence: 99%

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

Vinogradov

Anatskaya

2005

Proc. R. Soc. B.

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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.

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Section: K4supporting

confidence: 70%

Section: K4mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Vinogradov

Anatskaya

2005

Proc. R. Soc. B.

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“…The size of the presumed loops depends on the distance of cohesion sites and determines the degree of compaction. If the degree of compaction increases with genome size (Vinogradov 2005), larger genomes might have fewer cohesion sites and larger loops between them, possibly yielding positional separation along sister chromatids with a higher probability than, for instance, in budding yeast . However, during prophase sister chromatids are continuously aligned and the distance between FISH signals on sister chromatids becomes very small or not resolvable by light microscopy.…”

Section: Discussionmentioning

confidence: 99%

Sister Chromatids Are Often Incompletely Aligned in Meristematic and Endopolyploid Interphase Nuclei of Arabidopsis thaliana

et al. 2006

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We analyzed whether sister chromatids are continuously aligned in meristematic and endopolyploid Arabidopsis interphase nuclei by studying sister-chromatid alignment at various chromosomal positions. FISH with individual BACs to flow-sorted 4C root and leaf nuclei frequently yielded more than two hybridization signals, indicating incomplete or absent sister-chromatid alignment. Up to 100% of 8C, 16C, and 32C nuclei showed no sister-chromatid alignment at defined positions. Simultaneous FISH with BACs from different chromosomal positions revealed more frequent sister-chromatid alignment in terminal than in midarm positions. Centromeric positions were mainly aligned up to a ploidy level of 16C but became separated or dispersed in 32C nuclei. DNA hypomethylation (of the whole genome) and transcriptional activity (at FWA gene position) did not impair sister-chromatid alignment. Only 6.1% of 4C leaf nuclei showed sister-chromatid separation of the entire chromosome 1 top arm territories. Homozygous transgenic tandem repeat (lac operator) arrays showing somatic homologous pairing more often than average euchromatic loci did not promote an increased frequency of sister-chromatid alignment. The high frequency of separated sister-chromatid arm positions in $4C nuclei suggests that sister-chromatid cohesion is variable, dynamic, and not obligatory along the entire chromosome arm in meristematic and differentiated Arabidopsis nuclei.T HE colinear alignment of sister chromatids is defined as ''cohesion'' (Maguire 1990;Miyazaki and Orr-Weaver 1994). It is widely assumed that sister chromatids are aligned from replication in S phase until the onset of anaphase to ensure postreplicational recombination repair as well as correct segregation of eukaryotic nuclear genomes from cell to cell and from generation to generation. A ring-shaped complex of cohesin proteins apparently mediates cohesion of newly replicated sister chromatids until complete bipolar orientation is achieved during metaphase (for recent reviews see

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“…

So far, investigation of the relationship between DNA content and different parameters, such as chromatin density, chromosome structure, chromosome size, nuclear size and cell size using different methods such as serial thin sectioning and three-dimensional reconstructing techniques (Bennett et al, 1983), microspectrofl uorometry, cytophotometry and confocal microscopy (Baluška and Kubica, 1992;Melaragno et al, 1993;Gray et al, 1999) has led to contradictory conclusions.For vertebrates, an increase in chromatin condensation with increasing genome size has been reported (Vinogradov, 2005). A comparison between DNA content per nucleus and the total volume of metaphase chromosomes in several plant species suggested that DNA density might vary even within a species (for review see Bennett and Leitch, 2005).

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mentioning

confidence: 99%

Nuclear DNA content and nuclear and cell volume are positively correlated in angiosperms

Jovtchev

Schubert

Meister

et al. 2006

Cytogenet Genome Res

134

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Volumes of flow sorted nuclei were analyzed from two highly endopolyploid (diploids with endopolyploid tissues) species (Arabidopsis thaliana and Barbarea stricta), from a less endopolyploid species (Allium cepa) and from two non-endopolyploid species (Chrysanthemum multicolor and Fritillaria uva-vulpis). Intraspecific as well as interspecific comparisons revealed a highly positive correlation (r >0.99) between DNA content and nuclear volume. No significant differences between expected and measured nuclear volumes were noted indicating that chromatin packing is not increased with increasing DNA content in the tested plant species. In epidermis cells of A. thaliana, A. cepa and Ch. multicolor, a lower (r between 0.6 and 0.7) but significant positive correlation between nuclear volume and cell volume was found. This correlation is compatible with the hypothesis that endopolyploidization (EP = consecutive replication cycles not separated by nuclear and cell divisions) might speed up the growth of endopolyploid species and compensate for small genome size.

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Genome size and chromatin condensation in vertebrates

Cited by 36 publications

References 74 publications

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

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

Sister Chromatids Are Often Incompletely Aligned in Meristematic and Endopolyploid Interphase Nuclei of Arabidopsis thaliana

Nuclear DNA content and nuclear and cell volume are positively correlated in angiosperms

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