Genetic Redundancy in Rye Shows in a Variety of Ways.

Fifty years ago Susumu Ohno formulated the famous C-value paradox, which states that there is no correlation between the physical sizes of the genome, i.e., the amount of DNA, and the complexity of the organism, and highlighted the problem of genome redundancy.

The origin and evolution of a two-component system of paralogous genes encoding the centromeric histone CENH3 in cereals.

Background: The cereal family Poaceae is one of the largest and most diverse angiosperm families. The central component of centromere specification and function is the centromere-specific histone H3 (CENH3). Some cereal species (maize, rice) have one copy of the gene encoding this protein, while some (wheat, barley, rye) have two.

Expression of Two Rye CENH3 Variants and Their Loading into Centromeres.

Gene duplication and the preservation of both copies during evolution is an intriguing evolutionary phenomenon. Their preservation is related to the function they perform. The central component of centromere specification and function is the centromere-specific histone H3 (CENH3).

Chromosomal assignment of centromere-specific histone CENH3 genes in rye ( L.) and their phylogeny.

Centromeres are essential for correct chromosome segregation during cell division and are determined by the presence of centromere-specific histone 3 (CENH3). Most of the diploid plant species, in which the structure and copy number of genes have been determined, have this gene as a singleton; however, some cereal species in the tribe Triticeae have been found to have CENH3 in two variants. In this work, using the set of the wheat-rye addition lines we wanted to establish the chromosomal assignment of the genes in the cultivated rye, (Linnaeus, 1753), in order to expand our knowledge about synteny conservation in the most important cereal species and about their chromosome evolution.

Conserved molecular structure of the centromeric histone CENH3 in Secale and its phylogenetic relationships.

It has been repeatedly demonstrated that the centromere-specific histone H3 (CENH3), a key component of the centromere, shows considerable variability between species within taxa. We determined the molecular structure and phylogenetic relationships of CENH3 in 11 Secale species and subspecies that possess distinct pollination systems and are adapted to a wide range of abiotic and biotic stresses. The rye (Secale cereale) genome encodes two paralogous CENH3 genes, which differ in intron-exon structure and are transcribed into two main forms of the protein, αCENH3 and βCENH3.

The expansion of heterochromatin blocks in rye reflects the co-amplification of tandem repeats and adjacent transposable elements.

Background: A prominent and distinctive feature of the rye (Secale cereale) chromosomes is the presence of massive blocks of subtelomeric heterochromatin, the size of which is correlated with the copy number of tandem arrays. The rapidity with which these regions have formed over the period of speciation remains unexplained.

Results: Using a BAC library created from the short arm telosome of rye chromosome 1R we uncovered numerous arrays of the pSc200 and pSc250 tandem repeat families which are concentrated in subtelomeric heterochromatin and identified the adjacent DNA sequences.

[Organization and evolution of the subtelomeric regions of the rye chromosomes].

Subtelomeric regions of chromosomes are particularly dynamic and variable parts in the evolution of the eukaryotic genomes. A specific feature of the rye (Secale) chromosomes is large heterochromatin blocks at the arms of all seven pairs of chromosomes. Within the genus Secale, an interspecific variation in the genome size reaches nearly 15% between Secale cereale (cultivated rye) and the ancient species S.

[Functional analysis of the Xist promoter region in mouse Mus musculus].

X-chromosome inactivation which takes place in early embryogenesis of all higher mammals is largely determined by the Xist gene activity. This gene encodes long untranslated RNA, which provides transcriptional silencing of the genes on chromosome. In the present study, three enhancer and three silencing transcriptional elements were identified in the Xist promoter region.

[Comparative analysis of the DXPas34 regulatory region in rodents].

Mouse X chromosome inactivation center contains the DXPas34 minisatellite locus which plays an important role in expression regulation of the Tsix and Xist genes, involved into female dosage compensation. Comparative analysis of the DXPas34 locus from mouse, rat, and four common vole species revealed similar organization of this region in the form of tandem repeat blocks. A search for functionally important elements in this locus showed that all the species examined carried the conservative motif monomers, which could be involved in regulation of X inactivation.

[Role of G(-43)A polymorphism in the promoter region of the Xist gene in non-random X-chromosome inactivation in intraspecific hybrid voles].

Interaction of transcription factor CTCF with the minimal promoter of Xist gene was investigated in intraspecific hybrids ofcommon voles. CTCF was shown to bind with the minimal promoter region in vivo. However, the experiments of the delay in gel resulted in the absence of interaction between the CTCF factor and its potential binding site.

[Investigation of the Tsix gene regulatory region in vole Microtus rossiaemeridionalis].

The Tsix regulatory region was examined in vole Microtus rossiaemeridionalis. The minimal promoter region, three potential enhancer regulatory elements and one transcription suppressor element were identified. The enhancer regions contained potential binding sites of transcription activators, while in the region of putative silencer contained potential binding site of the ARP1 (NR2F2) protein.

[Comparative organization and the origin of noncoding regulatory RNA genes from X-chromosome inactivation center of human and mouse].

After the radiation of primates and rodents, the evolution of X-chromosome inactivation centers in human and mouse (XIC/Xic) followed two different directions. Human XIC followed the pathway towards transposon accumulation (the repeat proportion in the center constitutes 72%), especially LINEs, which prevail in the center. On the contrary, mouse Xic eliminated long repeats and accumulated species-specific SIN Es (the repeat proportion in the center constitutes 35%).

[Exon-intron structure of the Xist gene in elephant, armadillo, and the ancestor of placental mammals].

The Xist gene belongs to the class of long noncoding regulatory RNA genes which play a key role in the process of inactivation of one of the X chromosomes in females of placental mammals. Based on interspecific comparative sequence analysis performed using a set ofbioinformatic programs and approaches, the exon-intron gene structure was first described in two species, elephant and armadillo, belonging to the most primitive placental mammal groups, Afrotheria and Xenarthra. Using multiple sequence alignment of the species representing all main groups of placental mammals (12 species), consensus sequence of the ancestral gene was reconstructed.

[Molecular composition of the chromosome 2 pericentric heterochromatin in malarial mosquitoes (Diptera, Culicidae)].

Rich in repeated DNA sequences and poor in genes, the heterochromatin is an important functional part of the eukaryotic genome. Heterochromatin exhibits high evolutionary variability, which was revealed on the cytological and molecular levels in malarial mosquito species from the Anopheles maculipennis complex. In this connection, investigation of the heterochromatin molecular composition in species of this complex is of interest.

[Relationship between two distinct families of tandem repeats in rye heterochromatin].

BAC library constructed from the short arm of the first rye (Secale cereale L.) chromosome 1R was screened extensively in order to identify clones containing the copies of a tandemly organized repetitive DNA family, pSc200, which is the most abundant in the rye subtelomeric heterochromatin. Molecular organization of the monomers array and adjacent sequences have been studied in BAC 126/C20.

[Molecular genetic characterization of the regulatory region of the Xist gene in the common vole Microtus rossiaemeridionalis].

Two conserved regions were discovered as a result of interspecific comparison of the 5'-region of the Xist gene, which is the key gene in the process of X-chromosome inactivation in mammalian females. The first region corresponds to the minimal promoter, and the second spans between -480 bp and -400 bp from the start of Xist transcription. Footprinting experiments revealed protected regions corresponding to the potential binding sites for TBP, SP1, API, SRY, ER, and some other transcription factors.

[The structure and evolution of the MaSMC4 gene of common vole Microtus arvalis (Arvicolidae, Rodentia)].

In eukaryotes, the SMC (Structural Maintenance of Chromosomes) gene family is represented by at least six genes. Some of these genes have tissue-specific homologs. Eukaryotic SMC structural proteins are the members of biochemical complexes responsible for cohesion of sister chromatids, recombination, repair, regulation of gene expression, and formation of mitotic chromosomes.

Novel genes identified by manual annotation and microarray expression analysis in the pancreas.

The mouse PancChip, a microarray developed for studying endocrine pancreatic development and diabetes, represents over 13,000 cDNAs. After computationally assigning the cDNAs on the array to known genes, manual curation of the remaining sequences identified 211 novel transcripts. In microarray experiments, we found that 196 of these transcripts were expressed in total pancreas and/or pancreatic islets.

[Structure and expression of the F6.2 gene in Chironomus thummi and other Chironomus species].

A full-length copy of the F6.2 gene from the tissue-specific BRa locus of the Chironomus thummi chromosome IV was isolated and analyzed. The gene contains two exons (715 and 644 bp, respectively) and one 172-bp intron.

[Genomic organization and chromosomal localization of a new repeat MS7, specific for heterochromatin of sex chromosomes in Microtus species voles of the arvalis group].

The tandemly arranged MS4 repeat with monomeric units of 4.1 kb is species-specifically distributed in heterochromatin of sex chromosomes of four common vole species of genus Microtus, group arvalis [1, 2]. In this work, we studied the genomic organization of the MS4 homolog in euchromatin of the X chromosome of M.

[Organization of extended repeats in heterochromatin in sex chromosomes in the common vole species Microtus group "arvalis"].

Two long repeats, MS3 and MS4, are predominantly located in sex-chromosomal heterochromatin in common vole species. Their tandem arrangement was revealed by means of the PCR analysis of genomic DNAs of four Microtus species and by restriction mapping of clones selected from a M. rossiaemeridionalis genomic library.