Junk DNA and sectorial gene repression

Clusters of lineage-specific genes are anchored by ZNF274 in repressive perinucleolar compartments

Long known as the site of ribosome biogenesis, the nucleolus is increasingly recognized for its role in shaping three-dimensional (3D) genome organization. Still, the mechanisms governing the targeting of selected regions of the genome to nucleolus-associated domains (NADs) remain enigmatic. Here, we reveal the essential role of ZNF274, a SCAN-bearing member of the Krüppel-associated box (KRAB)-containing zinc finger protein (KZFP) family, in sequestering lineage-specific gene clusters within NADs. Ablation of ZNF274 triggers transcriptional activation across entire genomic neighborhoods-encompassing, among others, protocadherin and KZFP-encoding genes-with loss of repressive chromatin marks, altered the 3D genome architecture and de novo CTCF binding. Mechanistically, ZNF274 anchors target DNA sequences at the nucleolus and facilitates their compartmentalization via a previously uncharted function of the SCAN domain. Our findings illuminate the mechanisms underlying NAD organization and suggest that perinucleolar entrapment into repressive hubs constrains the activation of tandemly arrayed genes to enable selective expression and modulate cell differentiation programs during development.

Chromatin diminution as a tool to study some biological problems

This work reveals the opportunities to obtain additional information about some biological problems through studying species that possess chromatin diminution. A brief review of the hypothesized biological significance of chromatin diminution is discussed. This article analyzes the biological role of chromatin diminution as it relates to the C-value enigma. It is proposed to consider chromatin diminution as a universal mechanism of genome reduction, reducing the frequency of recombination events in the genome, which leads to specialization and adaptation of the species to more narrow environmental conditions. A hypothesis suggesting the role of non-coding DNA in homologous recombination in eukaryotes is proposed. Cyclopskolensis Lilljeborg, 1901 (Copepoda, Crustacea) is proposed as a model species for studying the mechanisms of transformation of the chromosomes and interphase nuclei structure of somatic line cells due to chromatin diminution. Chromatin diminution in copepods is considered as a stage of irreversible differentiation of embryonic cells during ontogenesis. The process of speciation in cyclopoids with chromatin diminution is considered.

Evolution of complex genome architecture in gymnosperms

Gymnosperms represent an ancient lineage that diverged from early spermatophytes during the Devonian. The long fossil records and low diversity in living species prove their complex evolutionary history, which included ancient radiations and massive extinctions. Due to their ultra-large genome size, the whole-genome assembly of gymnosperms has only generated in the past 10 years and is now being further expanded into more taxonomic representations. Here, we provide an overview of the publicly available gymnosperm genome resources and discuss their assembly quality and recent findings in large genome architectures. In particular, we describe the genomic features most related to changes affecting the whole genome. We also highlight new realizations relative to repetitive sequence dynamics, paleopolyploidy, and long introns. Based on the results of relevant genomic studies of gymnosperms, we suggest additional efforts should be made toward exploring the genomes of medium-sized (5–15 gigabases) species. Lastly, more comparative analyses among high-quality assemblies are needed to understand the genomic shifts and the early species diversification of seed plants.

Molecular characteristics of S-RNase alleles as the determinant of self-incompatibility in the style of Fragaria viridis

Strawberry (Fragaria spp.) is a member of the Rosoideae subfamily in the family Rosaceae. The self-incompatibility (SI) of some diploid species is a key agronomic trait that acts as a basic pollination barrier; however, the genetic mechanism underlying SI control in strawberry remains unclear. Two candidate S-RNases (S_a- and S_b-RNase) identified in the transcriptome of the styles of the self-incompatible Fragaria viridis 42 were confirmed to be SI determinants at the S locus following genotype identification and intraspecific hybridization using selfing progenies. Whole-genome collinearity and RNase T2 family analysis revealed that only an S locus exists in Fragaria; however, none of the compatible species contained S-RNase. Although the results of interspecific hybridization experiments showed that F. viridis (SI) styles could accept pollen from F. mandshurica (self-compatible), the reciprocal cross was incompatible. S_a and S_b-RNase contain large introns, and their noncoding sequences (promotors and introns) can be transcribed into long noncoding RNAs (lncRNAs). Overall, the genus Fragaria exhibits S-RNase-based gametophytic SI, and S-RNase loss occurs at the S locus of compatible germplasms. In addition, a type of SI-independent unilateral incompatibility exists between compatible and incompatible Fragaria species. Furthermore, the large introns and neighboring lncRNAs in S-RNase in Fragaria could offer clues about S-RNase expression strategies.

MicroRNAs and thyroid hormone action

MicroRNAs (miRNAs) are small noncoding RNAs that post-transcriptionally repress gene expression by binding generally to the 3'-untranslated regions of their target mRNAs. miRNAs regulate a large fraction of the genome, playing a key role in most physiological and pathological processes. The thyroid hormones (T4 and T3) are major regulators of development, metabolism and cell growth. The thyroid hormones (THs) are synthetized in the thyroid gland and enter the cells through transporter proteins. In the cells, T4 and T3 are metabolized by deiodinase enzymes and bind to nuclear receptors (TRs), which have a higher affinity by T3. TRs act as hormone dependent transcription factors by binding to thyroid hormone response elements (TREs) in the target genes and recruiting transcriptional coregulators. There is increasing evidence that a variety of miRNAs target deiodinases and the receptor, thus regulating TH signaling is different tissues. In turn, the THs have been shown to modulate the expression of specific miRNAs and their mRNA targets in different cell types and organs. In many cases, the existence of TREs in the regulatory regions of these miRNAs has been identified, and the hormone bound receptors transcriptionally regulate expression of these molecules. Changes in the levels of miRNAs have been demonstrated to mediate some of the important actions of the THs in processes such as muscle and heart function, lipid liver metabolism or skin physiology. In addition, miRNA regulation is involved in the effects of TRs on cell proliferation and cancer.

Non-coding RNAs and the mineralocorticoid receptor in the kidney

The final steps in the Renin-Angiotensin-Aldosterone signaling System (RAAS) involve binding of the corticosteroid hormone, aldosterone to its mineralocorticoid receptor (MR). The bound MR interacts with response elements to induce or repress the transcription of aldosterone-regulated genes. Along with the classic genomic targets of aldosterone that alter mRNA and protein expression, aldosterone also regulates the expression of non-coding RNAs (ncRNAs). Short ncRNAs termed microRNAs (miRs) have been shown to play a role in transducing aldosterone's actions via MR signaling. The role of miRs in homeostatic regulation of aldosterone signaling, and the potential for aldosterone-regulated miRs to act as feedback regulators of MR have been recently reported. In this review, the role of miRs in RAAS signaling and feedback regulation of MR in kidney epithelial cells will be discussed.

Regulation of Aldosterone Signaling by MicroRNAs

The mineralocorticoid hormone aldosterone is released by the adrenal glands in a homeostatic mechanism to regulate blood volume. Several cues elicit aldosterone release, and the long-term action of the hormone is to restore blood pressure and/or increase the retrieval of sodium from filtered plasma in the kidney. While the signaling cascade that results in aldosterone release is well studied, the impact of this hormone on tissues and cells in various organ systems is pleotropic. Emerging evidence indicates aldosterone may alter non-coding RNAs (ncRNAs) to integrate the hormonal response, and these ncRNAs may contribute to the heterogeneity of signaling outcomes in aldosterone target tissues. The best studied of the ncRNAs in aldosterone action are the small ncRNAs, microRNAs. MicroRNA expression is regulated by aldosterone stimulation, and microRNAs are able to modulate protein expression at all steps in the renin-angiotensin-aldosterone-signaling system. The discovery and synthesis of microRNAs will be briefly covered followed by a discussion of the reciprocal role of aldosterone/microRNA regulation, including misregulation of microRNA signaling in aldosterone-linked disease states.

That 70s show: regulation, evolution and development beyond molecular genetics

This paper argues that the "long 1970s" (1969-1983) is an important though often overlooked period in the development of a rich landscape in the research of metabolism, development, and evolution. The period is marked by: shrinking public funding of basic science, shifting research agendas in molecular biology, the incorporation of new phenomena and experimental tools from previous biological research at the molecular level, and the development of recombinant DNA techniques. Research was reoriented towards eukaryotic cells and development, and in particular towards "giant" RNA processing and transcription. We will here focus on three different models of developmental regulation published in that period: the two models of eukaryotic genetic regulation at the transcriptional level that were developed by Georgii P. Georgiev on the one hand, and by Roy Britten and Eric Davidson on the other; and the model of genetic sufficiency and evolution of regulatory genes proposed by Emile Zuckerkandl. These three bases illustrate the range of exploratory hypotheses that characterised the challenging landscape of gene regulation in the 1970s, a period that in hindsight can be labelled as transitional, between the biology at the laboratory bench of the preceding period, and the biology of genetic engineering and intensive data-driven research that followed.

Relationship between gene compactness and base composition in rice and human genome

In human, highly expressed genes contain shorter and fewer introns and these have been attributed to selection for economy in transcription and translation. On the other hand, in plants, it has been shown that highly expressed genes tend to be longer than lowly expressed genes. Here, in this study, we analyzed compositional influence on genome organization in both rice and human. We demonstrated that, in GC rich rice genes, highly expressed genes are less compact than lowly expressed genes. In GC-poor class, there is no difference in gene compactness between highly and lowly expressed genes. However, the scenario is different for human as there is no influence of GC composition on gene compactness due to their expression levels. We also reported that, highly expressed rice GC-rich pre-mRNA tend to form less stable secondary structure than that of lowly expressed genes. However, on removing intronic sequences, highly expressed mRNA form a stable secondary structure as compared to lowly expressed GC-rich genes. We suggest that in GC-rich rice genes long introns are under selection for enhancing transcriptional efficiency by modulating pre-mRNA secondary structural stability. Thus evolutionary mechanisms behind genome organization are different between these two genomes (human and rice).

Characterization and chromosomal organization of satellite DNA sequences in Picea abies

Three clones containing satellite DNA sequences were selected from a randomly sheared genomic DNA library of Picea abies (clones PAF1, PAG004P22F (2F), and PAG004E03C (3C)). PAF1 contained 7 repeats that were 37-55 bp in length and had 68.9%-91.9% nucleotide sequence similarity. Two 2F repeats were 305-306 bp in length and had 83% sequence similarity. Two 3C repeats were 193-226 bp in length and had a sequence similarity of 78.6%. The copy number per 1C DNA of PAF1, 2F, and 3C repeats was 2.7 x 10(6), 2.9 x 10(5), and 2.9 x 10(4), respectively. In situ hybridization showed centromeric localization of these sequences in two chromosome pairs with PAF1, all pairs but one with 2F, and three pairs with 3C. Moreover, PAF1 sequences hybridized at secondary constrictions in six pairs, while 2F-related sequences were found at these chromosome regions only in four pairs. These hybridization patterns allow all chromosome pairs to be distinguished. PAF1-related repeats were contained in the intergenic spacer (IGS) of ribosomal cistrons in all six nucleolar organizers of the complement, while sequences related to 2F were found on only one side of the rDNA arrays in four pairs, showing structural diversity between rDNA regions of different chromosomes.

‘Junk’ DNA and phenotypic evolution inSilenesectionSiphonomorpha

One of the long-standing mysteries in genomic evolution is the observation that much of the genome is composed of repetitive DNA, resulting in inter- and intraspecific variation in nuclear DNA content. Our discovery of a negative correlation between nuclear DNA content and flower size inSilene latifoliahas been supported by our subsequent investigation of changes in DNA content as a correlated response to selection on flower size. Moreover, we have observed a similar trend across a range of related dioecious species inSilenesect.Elisanthe. Given the presence of sex chromosomes in dioeciousSilenespecies, and the tendency of sex chromosomes to accumulate repetitive DNA, it seems plausible that dioecious species undergo genomic evolution in ways that differ from what one might expect in hermaphroditic species. Specifically, we query whether the observed relationship between nuclear DNA content and flower size observed in dioeciousSileneis a peculiarity of sex chromosome evolution. In the present study we investigated nuclear DNA content and flower size variation in hermaphroditic species ofSilenesect.Siphonomorpha, as close relatives of the dioecious species studied previously. Although the nuclear DNA contents of these species were lower than those for species in sect.Elisanthe, there was still significant intra- as well as interspecific variation in nuclear DNA content. Flower size variation was found among species of sect.Siphonomorphafor petal claw and petal limb lengths, but not for calyx diameter. This last trait varies extensively in sect.Elisanthe, in part due to sex-specific selection. A negative correlation with nuclear DNA content was found across populations for petal limb length, but not for other floral dimensions. We conclude that impacts of nuclear DNA content on phenotypic evolution do manifest themselves in hermaphroditic species, so that the effects observed in sect.Elisanthe, and particularly inS. latifolia, while perhaps amplified by the genomic impacts of sex chromosomes, are not limited to dioecious taxa.

Combinatorial epigenetics, “junk DNA”, and the evolution of complex organisms

At certain evolutionary junctures, two or more mutations participating in the build-up of a new complex function may be required to become available simultaneously in the same individuals. How could this happen in higher organisms whose populations are small compared to those of microbes, and in which chances of combined nearly simultaneous highly specific favorable mutations are correspondingly low? The question can in principle be answered for regulatory evolution, one of the basic processes of evolutionary change. A combined resetting of transcription rates in several genes could occur in the same individual. It is proposed that, in eukaryotes, changes in epigenetic trends and epigenetically transforming encounters between alternative chromatin structures could arise frequently enough so as to render probable particular conjunctions of changed transcription rates. Such conjunctions could involve mutational changes with low specificity requirements in gene-associated regions of non-protein-coding sequences. The effects of such mutations, notably when they determine the use of histone variants and covalent modifications of histones, can be among those that migrate along chromatin. Changes in chromatin structure are often cellularly inheritable over at least a limited number of generations of cells, and of individuals when the germ line is involved. SINEs and LINEs, which have been considered "junk DNA", are among the repeat sequences that would appear liable to have teleregulatory effects on the function of a nearby promoter, through changes in their numbers and distribution. There may also be present preexisting unstably inheritable epigenetic trends leading to cellular variegation, trends endemic in a cell population based on DNA sequences previously established in the neighborhood. Either way, epigenetically conditioned teleregulatory trends may display only limited penetrance. The imposition at a distance of new chromatin structures with regulatory impact can occur in cis as well as in trans, and is examined as intrachromosomally spreading teleregulation and interchromosomal "gene kissing". The chances for two or more particular epigenetically determined regulatory trends to occur together in a cell are increased thanks to the proposed low specificity requirements for most of the pertinent sequence changes in intergenic and intronic DNA or in the distribution of middle repetitive sequences that have teleregulatory impact. Inheritable epigenetic changes ("epimutations") with effects at a distance would then perdure over the number of generations required for "assimilation" of the several regulatory novelties through the occurrence and selection, gene by gene, of specific classical mutations. These mutations would have effects similar to the epigenetic effects, yet would provide stability and penetrance. The described epigenetic/genetic partnership may well at times have opened the way toward certain complex new functions. Thus, the presence of "junk DNA", through co-determining the (higher or lower) order and the variants of chromatin structure with regulatory effects at a distance, might make an important contribution to the evolution of complex organisms.

Expression dynamics and functional implications of DNA topoisomerase II beta in the brain

Mammalian DNA topoisomerase II beta is a type II DNA topoisomerase that catalyses topological transformations of genomic DNA by the transport of one DNA double helix through another. The II beta enzyme is highly expressed in cells that have undergone the final cell division and committed to differentiate into neuronal cells. The II beta enzyme in the differentiating neuronal cells is located in the nucleoplasm and is actively engaged in its catalytic reaction in vivo. When enzyme action is interfered with a specific inhibitor in vitro, transcriptional induction of a subset of genes fails to occur during neuronal differentiation. Detailed analyses of developing rat cerebellum and the cerebrum of mice with disrupted II beta genes have revealed that DNA topoisomerase II beta is necessary for the developmentally regulated expression of certain genes in cells committed to a neuronal fate after the final division. Herein, we review a dynamic aspect of DNA topoisomerase II beta in the brain with special emphasis on developing cerebellar neurons.

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: evidence from conserved intronic sequence in human-mouse comparison

Introns are shorter in housekeeping genes than in tissue- or development-specific genes. Differing explanations have been offered for this phenomenon: selection for economy (in housekeeping genes), mutation bias or "genomic design." The large-scale implementation in this present paper of a rigorous local sequence alignment algorithm revealed an unprecedented fraction of evolutionarily conserved DNA in human-mouse introns ( approximately 60% of human and approximately 70% of mouse intron length remained after masking for lineage-specific repeats). The length distributions of both conserved and nonconserved regions are very broad but show peaks close to nucleosomal and di-nucleosomal DNA. Both the fraction of conserved sequence and its absolute length were higher in introns of tissue-specific genes than housekeeping genes. This difference remained after control for between-species identity of the conserved fraction, mutation rate, and GC content. In a more direct control, the product of the conserved sequence fraction and the between-species identity of this fraction (which can be considered to be the fraction of conserved nucleotides) was greater in introns of tissue-specific genes than housekeeping genes. Neither the fraction of intron length covered by repeats nor the balance of small insertions and deletions (indels) can explain the greater length of introns in tissue-specific genes. The length of the conserved intronic DNA in a gene is correlated with the number of functional domains in the protein encoded by that gene. These results suggest that the greater length of introns in tissue-specific genes is not due to selection for economy or mutation bias but instead is related to functional complexity (probably mediated by chromatin condensation), and that the evolution of the bulk of noncoding DNA is not completely neutral.

Phenotypic impacts of repetitive DNA in flowering plants

The discovery that nuclear DNA content varies widely among species, and even within species, was unexpected because it was thought that the number of genes required for an organism should be common across taxa. We now know that the bulk of nuclear DNA content variation is caused by repetitive DNA sequences characterized according to the nature of repeat (tandem vs dispersed) or chromosomal location/mechanism of replication (pericentromeric, telomeric or subtelomeric, microsatellites, minisatellites, satellites, transposable elements, retroelements). Variation in repetitive DNA, manifested as variation in nuclear DNA content, has been shown to have broad ecological and life-history consequences. For example, large genome size appears to limit fitness in extreme environmental conditions. Within species, variation in DNA content has been coupled to growth and development, such as maturation time in crop species. In Silene latifolia, DNA content is negatively correlated with flower size, a character that, in turn, has well documented ecological significance. These intraspecific studies suggest a connection between repetitive DNA and quantitative genetic determination of continuous characters. Novel insights into mechanisms by which repetitive DNA influences phenotype will lead to models of evolutionary change that extend well beyond the conventional view of evolution by allelic substitution.

'Junk' DNA and long-term phenotypic evolution in Silene section Elisanthe (Caryophyllaceae)

Nuclear DNA content variation over orders of magnitude across species has been attributed to 'junk' repetitive DNA with limited adaptive significance. By contrast, our previous work on Silene latifolia showed that DNA content is negatively correlated with flower size, a character of clear adaptive relevance. The present paper explores this relationship in a broader phylogenetic context to investigate the long-term evolutionary impacts of DNA content variation. The relationship between nuclear DNA content and phenotype variation was determined for four closely related species of Silene section Elisanthe (Caryophyllaceae). In addition to a consistent sexual dimorphism in DNA content across all of the species, we found DNA content variation among populations within, as well as among, species. We also found a general trend towards a negative correlation between DNA content and flower and leaf size over all four species, within males and females as well as overall. These results indicate that repetitive DNA may play a role in long-term phenotypic evolution.

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.

Growth and decline of introns

To gauge the processes that might direct the length of introns, I studied the balance of indels (insertions or deletions, determined using Alu and LINE1 retroposon repeats) and the density of these repeats in the introns of the human genome. The indel balance is biased in favour of deletions and correlated with the divergence of repeats. At fixed repeat divergence, the indel bias correlated with the intron size: the shorter the intron, the more deletions were favoured over insertions. This correlation with the intron size was stronger than with the gene-wide or isochore-wide parameters. The density of repeats (the number of repeats in a unit of intron length) correlated positively with the intron size. Thus, quite different mechanisms, the indel bias and the integration and/or persistence of retroposons, act in the same direction in regards to intron size, which suggests selection for the size of individual introns.

Transcriptional induction of MKP-1 in response to stress is associated with histone H3 phosphorylation-acetylation

Mitogen-activated protein (MAP) kinase phosphatase 1 (MKP-1) has been shown to play a critical role in mediating the feedback control of MAP kinase cascades in a variety of cellular processes, including proliferation and stress responsiveness. Although MKP-1 expression is induced by a broad array of extracellular stimuli, the mechanisms mediating its induction remain poorly understood. Here we show that MKP-1 mRNA was potently induced by arsenite and ultraviolet light and modestly increased by heat shock and hydrogen peroxide. Interestingly, arsenite also dramatically induces phosphorylation-acetylation of histone H3 at a global level which precedes the induction of MKP-1 mRNA. The transcriptional induction of MKP-1, histone H3 modification, and elevation in MKP-1 mRNA in response to arsenite are all partially prevented by the p38 MAP kinase inhibitor SB203580, suggesting that the p38 pathway is involved in these processes. Finally, analysis of the DNA brought down by chromatin immunoprecipitation (ChIP) reveals that arsenite induces phosphorylation-acetylation of histone H3 associated with the MKP-1 gene and enhances binding of RNA polymerase II to MKP-1 chromatin. ChIP assays following exposure to other stress agents reveal various degrees of histone H3 modification at the MKP-1 chromatin. The differential contribution of p38 and ERK MAP kinases in mediating MKP-1 induction by different stress agents further illustrates the complexity and versatility of stress-induced MKP-1 expression. Our results strongly suggest that chromatin remodeling after stress contributes to the transcriptional induction of MKP-1.

Within-intron correlation with base composition of adjacent exons in different genomes

Within-intron difference of correlation with base composition of the adjacent exons was studied in the genomes of 34 species. For this purpose, GC-percent was determined for segments of 50 bp in length taken at both intron margins and in the internal part of the intron. It was found that in certain genomes the coefficient of correlation with GC-percent of the adjacent exon was significantly higher for the intron margin than for the internal part of the intron (homeotherms, cereals). Only part of this difference can be explained by unequal probability of insertion of transposable elements. Those multicellular organisms which have a low or no within-intron difference in correlation with the adjacent exons (anamniotes, invertebrates, dicots) show a higher local compositional heterogeneity (a greater exon/intron contrast in the GC-content). These results are evidence against the mutational bias being a possible explanation for the compositional genome heterogeneity. Thus, in the genomes with a high global heterogeneity there seems to be a selective force for compliance of intron base composition with the adjacent exons. This force is stronger in those parts of the intron that are closer to exons. In addition, the previously found positive general correlation between the genome size and average intron length was confirmed with a much larger dataset. However, within separate phylogenetic groups this rule can be broken, as it occurs in the cereals (family Poaceae), where a negative correlation was found.

Involvement of DNA topoisomerase IIbeta in neuronal differentiation

Two isoforms of DNA topoisomerase II (topo II) have been identified in mammalian cells. While topo IIalpha is essential for chromosome segregation in mitotic cells, in vivo function of topo IIbeta remains to be clarified. Here we demonstrate that the nucleoplasmic topo IIbeta, highly expressed in differentiating cerebellar neurons, is the catalytically competent entity operating directly on chromatin DNA in vivo. When the cells reached terminal differentiation, this in vivo activity decreased to a negligible level with concomitant loss of the nucleoplasmic enzyme. Effects of topo II-specific inhibitors were analyzed in a primary culture of cerebellar granule neurons that can mimic the in vivo situation. Only the beta isoform was expressed in granule cells differentiating in vitro. ICRF-193, a catalytic topo II inhibitor, suppressed the transcriptional induction of amphiphysin I which is essential for mature neuronal activity. The effect decreased significantly as the cells differentiate. Expression profiling with a cDNA macroarray showed that 18% of detectable transcripts were up-regulated during the differentiation and one-third of them were susceptible to ICRF-193. The results suggest that topo IIbeta is involved in an early stage of granule cell differentiation by potentiating inducible neuronal genes to become transcribable probably through alterations in higher order chromatin structure.

Genomes and form. The case for teleomorphic recursivity

The genotype-phenotype (genome-form) distinction is considered by many to be fundamental to modern evolutionary thinking. Indeed, the premises that: DNA solely constitutes the genotype; that the phenotype is a transient product of the genotype, with the latter not only describing, but also implementing the construction of the former; and that the constructed materials and systems of the cell have no impact on the genotype, have become dogmas. Yet a vast body of data from molecular genetics reveals that cellular systems, directly and indirectly, alter the genome. Some of these data are reviewed. Proteins can influence mutations along the chromosomes, heritably modify the information content of DNA sequences, and, in some instances, reorganize the germline or somatic genome via DNA engineering pathways. These data suggest that the constructed (proteins, chromatin arrays, and metabolic pathways) has an important role in shaping the descriptor. Insofar as it is biochemically possible for states adopted by cellular structures to be stabilized and eventually memorized by engineering chromosomes, semantic closure can be transcended--meaning can be transferred from the domain of form to the genome, and this presumably ongoing process is termed teleomorphic recursivity. Throughout the paper, I implicitly argue that the genome-form partition is strictly a formal one, with no deeply material basis.

Sectorial gene repression in the control of development

Some evidence suggests that a number of regulator genes and gene clusters will likely be found to share with HOX complexes the property of being repressible ('superrepressible') through factor-driven conformational changes over whole sectors of chromatin, and of being assigned body locations in which they are either stably superrepressed or poised for transcription, according to determinants that act vectorially across a morphological zone. Such a subpopulation of regulator genes is expected to include, notably, genes governing developmental processes and might be thought to number, in mammals, between one hundred and several hundreds. When superrepressed, regulator genes are anticipated either to block programs of gene action or to permit these programs to unfold. To a significant extent, development would be determined by successive intersections of the paths of gene action deployment with superrepressed genes. These intersections, in cell lines advancing toward terminal differentiation, would be responsible for the progressive narrowing of the range of gene action programs potentially still available for later development. One implication of this model is that mosaic and regulative embryos are distinct merely by virtue of the time of onset of superrepression in their different cell lineages. Determination and transdetermination are considered to express the differential distribution over the genome of bound regulatory factors that function as molecular tools of superrepression, notably polycomb-group-like proteins. In turn, superrepressed genes are anticipated to be differentially distributed over cell types and thus to furnish a major framework for progressive differentiation and for the progressive limitation of the developmental potential of cells.