A tissue-specific decrease in the pre-mRNA level of L1-and Alu-containing alleles of human genes

LINE1 and Alu retroelements occupy approximately 17 and 13% of the human genome, respectively. They include the evolutionarily youngest element groups Ta-L1, AluYa5, and AluYb8, many inserts of which are polymorphic in the Homo sapiens population. Despite the data on the ability of L1 and Alu elements to cause various modifications of the genome, the effects of these retroelements on gene expression have yet not been studied. Using the RT PCR method, we analyzed the pre-mRNA (heterogeneous nuclear RNA) content of allele pairs of four genes in five human cell lines, heterozygous with respect to intronic inserts of L1 and Alu elements. We showed for the first time a tissue-specific decrease in the pre-mRNA content of the gene allele bearing L1 or Alu inserts relative to the other allele of the same gene lacking the retroelement.     

Genome differentiation in Aegilops. 4. Evolution of the U-genome cluster

Phylogenetic relationships of polyploid Aegilops species sharing the U-genome were investigated by analyzing heterochromatin banding patterns of their somatic metaphase chromosomes as revealed by C-banding and fluorescence in situ hybridization (FISH) with the heterochromatin-limited repetitive DNA probes pSc119, pAs1, as well as the distribution of NOR and 5S DNA loci revealed by pTa71 (18S-26S rDNA), and pTa794 (5S rDNA) probes. Seven tetraploid (Ae. triuncialis, Ae. peregrina, Ae. kotschyi, Ae. geniculata, Ae. biuncialis, Ae. columnaris, and 4x Ae. neglecta) and one hexaploid (6x Ae. neglecta) Aegilops species of the U-genome cluster were studied. The U^t and C^t chromosomes of 4x Ae. triuncialis (U^tC^t) were similar to the diploid donors Ae. umbellulata (U) and Ae. caudata (C). However, the size of the NOR locus on chromosome 5U^t was reduced. Karyotypic analyses confirmed that 4x Ae. peregrina (S^pU^p) was derived from a hybridization of the diploid species Ae. umbellulata with Ae. longissima, whereas Ae. umbellulata and Ae. sharonensis (or an immediate precursor) were the diploid progenitor species of Ae. kotschyi (S^kU^k). In both 4x species, the NORs on S-genome chromosomes were inactivated and were accompanied with a decrease or loss of rDNA sequences. Karyotypes of the tetraploid species, Ae. geniculata (U^gM^g) and Ae. biuncialis (U^bM^b) differed from each other and from the putative diploid progenitors Ae. umbellulata and Ae. comosa indicating that various types of chromosomal alterations occurred during speciation. Inactivation of major NORs on the M-genome chromosomes, redistribution of 5S rDNA sites, and loss of some minor 18S-26S rDNA loci were observed in Ae. geniculata and Ae. biuncialis. Significant differences in the total amount and distribution of heterochromatin, the number and location of 5S and 18S-26S rDNA loci observed between Ae. columnaris (U^cX^c)/4x Ae. neglecta (UⁿXⁿ) and Ae. geniculata/Ae. biuncialis indicate that these species have different origins. Similarities in C-banding and FISH patterns of most Ae. columnaris and 4x Ae. neglecta chromosomes suggest that they were probably derived from a common ancestor, whereas distinct differences of three chromosome pairs may indicate that the divergence of these species was probably associated with chromosomal rearrangements and/or introgressive hybridization. Ae. umbellulata contributed the U genome, however, the source of their second genomes remains unknown. The formation of 6x Ae. neglecta (UⁿXⁿNⁿ) was not associated with large modifications of the parental genomes.     

Evolution of blue-flowered species of genus <Emphasis Type="Italic">Linum</Emphasis> based on high-throughput sequencing of ribosomal RNA genes

Background

The species relationships within the genus Linum have already been studied several times by means of different molecular and phylogenetic approaches. Nevertheless, a number of ambiguities in phylogeny of Linum still remain unresolved. In particular, the species relationships within the sections Stellerolinum and Dasylinum need further clarification. Also, the question of independence of the species of the section Adenolinum still remains unanswered. Moreover, the relationships of L. narbonense and other species of the section Linum require further clarification. Additionally, the origin of tetraploid species of the section Linum (2n?=?30) including the cultivated species L. usitatissimum has not been explored. The present study examines the phylogeny of blue-flowered species of Linum by comparisons of 5S rRNA gene sequences as well as ITS1 and ITS2 sequences of 35S rRNA genes.

Results

High-throughput sequencing has been used for analysis of multicopy rRNA gene families. In addition to the molecular phylogenetic analysis, the number and chromosomal localization of 5S and 35S rDNA sites has been determined by FISH.Our findings confirm that L. stelleroides forms a basal branch from the clade of blue-flowered flaxes which is independent of the branch formed by species of the sect. Dasylinum. The current molecular phylogenetic approaches, the cytogenetic analysis as well as different genomic DNA fingerprinting methods applied previously did not discriminate certain species within the sect. Adenolinum. The allotetraploid cultivated species L. usitatissimum and its wild ancestor L. angustifolium (2n?=?30) could originate either as the result of hybridization of two diploid species (2n?=?16) related to the modern L. gandiflorum and L. decumbens, or hybridization of a diploid species (2n?=?16) and a diploid ancestor of modern L. narbonense (2n?=?14).

Conclusions

High-throughput sequencing of multicopy rRNA gene families allowed us to make several adjustments to the phylogeny of blue-flowered flax species and also reveal intra- and interspecific divergence of the rRNA gene sequences.

     

Genome Comparisons with Chromosomal and Molecular Markers for Three Closely Related Flax Species and Their Hybrids

Chromosome C-banding patterns were analyzed in three closely related flax species (Linum usitatissimumL., 2n = 30; L. angustifolium Huds., 2n = 30; and L. bienneMill., 2n = 30) and their hybrids. In each case, the karyotype included metacentrics, submetacentrics, and one or two satellite chromosomes. Chromosomes of the three flax species were similar in morphology, size (1–3 m), and C-banding pattern and slightly differed in size of heterochromatic regions. In all accessions, a large major site of ribosomal genes was revealed by hybridization in the pericentric region of a large metacentric. A minor 45S rDNA site was observed on a small chromosome in L. usitatissimum and L. bienne and on a medium-sized chromosome in L. angustifolium. Upon silver staining, a nucleolus-organizing region (NOR) was detected on a large chromosome in all species. InL. angustifolium, an Ag-NOR band was sometimes seen on a medium-sized chromosome. In the karyotypes of interspecific hybrids, silver-stained rDNA loci were observed on satellite chromosomes of both parental species. RAPD analysis with 22 primers revealed a high similarity of the three species. The greatest difference was observed between L. angustifolium and the other two species. The RAPD patterns of L. bienne and L. usitatissimum differed in fewer fragments. A dendrogram of genetic similarity was constructed for the three flax species on the basis of their RAPD patterns. Genome analysis with chromosome and molecular markers showed thatL. bienne must be considered as a subspecies of L. usitatissimum rather than a separate species. The three species were assumed to originate from a common ancestor, L. angustifoliumbeing closest to it.     

Repairing the Sickle Cell mutation. II. Effect of psoralen linker length on specificity of formation and yield of third strand-directed photoproducts with the mutant target sequence

Three identical deoxyoligonucleotide third strands with a 3′-terminal psoralen moiety attached by linkers that differ in length (N = 16, 6 and 4 atoms) and structure were examined for their ability to form triplex-directed psoralen photoproducts with both the mutant T residue of the Sickle Cell β-globin gene and the comparable wild-type sequence in linear duplex targets. Specificity and yield of UVA (365 nm) and visible (419 nm) light-induced photoadducts were studied. The total photoproduct yield varies with the linker and includes both monoadducts and crosslinks at various available pyrimidine sites. The specificity of photoadduct formation at the desired mutant T residue site was greatly improved by shortening the psoralen linker. In particular, using the N-4 linker, psoralen interaction with the residues of the non-coding duplex strand was essentially eliminated, while modification of the Sickle Cell mutant T residue was maximized. At the same time, the proportion of crosslink formation at the mutant T residue upon UV irradiation was much greater for the N-4 linker. The photoproducts formed with the wild-type target were fully consistent with its single base pair difference. The third strand with the N-4 linker was also shown to bind to a supercoiled plasmid containing the Sickle Cell mutation site, giving photoproduct yields comparable with those observed in the linear mutant target.     

Chromosomal localization of 5S and 45S ribosomal DNA in species of Linum L. section Linum (syn=Protolinum and Adenolinum)

Fluorescence in situ hybridization (FISH) was for the first time used to study the chromosomal location of the 45S (18-2.5S-26S) and 5S ribosomal genes in the genomes of five flax species of the section Linum (syn. Protolinum and Adenolinum). In L. usitatissimum L. (2n = 30), L. angustifolium Huds. (2n = 30), and L. bienne Mill. (2n = 30), a major hybridization site of 45S rDNA was observed in the pericentric region of a large metacentric chromosome. A polymorphic minor locus of 45S rDNA was found on one of the small chromosomes. Sites of 5S rDNA colocalized with those of 45S rDNA, but direct correlation between signal intensities from the 45S and 5S rDNA sites was observed only in some cases. Other 5S rDNA sites mapped to two chromosomes in these flax species. In L. grandiflorum Desf. (2n = 16) and L. austriacum L. (2n = 18), large regions of 45S and 5S rDNA were similarly located on a pair of homologous satellite-bearing chromosomes. An additional large polymorphic site of 45S and 5S rDNA was found in the proximal region of one arm of a small chromosome in the L. usitatissimum. L. angustifolium, and L. bienne karyotypes. The other arm of this chromosome contained a large 5S rDNA cluster. A similar location of the ribosomal genes in the pericentric region of the pair of satellite-bearing metacentrics confirmed the close relationships of the species examined. The difference in chromosomal location of the ribosomal genes between flax species with 2n = 30 and those with 2n = 16 or 18 testified to their assignment to different sections. The use of ribosomal genes as chromosome markers was assumed to be of importance for comparative genomic studies in cultivated flax, a valuable crop species of Russia, and in its wild relatives.     

Polymorphism of heterochromatic regions of flax chromosomes

The C-banding technique was used to study flax chromosomes (Linum usitatissimum L., 2n = 30). Heterochromatin was located mainly in pericentromeric regions of chromosomes. In spite of small size (1.5-3.5 microm), all 15 pairs of homologous chromosomes were identified on the basis of the C-banding pattern and morphology. An idiogram of C-banded chromosomes of L usitatissimum L. is presented. Polymorphism of chromosomal heterochromatic regions was studied in karyotypes of three flax samples: L usitatissimum L., accession K-603 (L usitatissimum var. usitatissimum), and accession K-594 (L. usitatissimum var. humile (Mill.)). A common C-banding pattern was observed in all forms studied, although there were some distinctions in the individual band size. The fibre flax (accession K-603) karyotype had the C-banding pattern similar to that of L usitatissimum L., but some intercalary and telomeric C-bands were somewhat larger, and a satellite (NOR) was observed in the short arm of chromosome I. In crown flax, (K-594) chromosomal C-banding pattern exhibited smaller pericentromeric and larger intercalary bands; telomeric bands were present on almost all chromosomes. Thus, the intraspecies polymorphism revealed in the chromosomal C-banding pattern makes possible the use of C-bands as chromosome markers in the studies of genetic and genomic polymorphism of this species.     

Comparative cytogenetic study of the forms of <Emphasis Type="Italic">Macleaya cordata</Emphasis> (Willd.) R. Br. From different localities

A comparative cytogenetic study of two introduced forms of Makleaya cordata (Willd.) R. Br. = syn. Bocconia cordata Willd. grown in different ecological and geographical regions (Moscow and Donetsk areas) was carried out. In the study, a complex of methods utilizing various chromosomal markers, i.e., C- and DAPI-banding technique, fluorescence in situ hybridization (FISH) with probes of 26S and 5S rDNA, as well as estimation of the total area of C-positive regions (C-HCH) in prophase nucleoli and meiosis analysis, was used. In the karyotypes (2n = 20), each chromosome was identified on the basis of C-banding and FISH patterns and the chromosome ideograms were built. Pericentrometric and telomeric C-positive bands in chromosomes of the Moscow form karyotype were found to be smaller and intercalary bands, larger than the corresponding bands in the M. cordata form grown in Donetsk. It was found that the content of C-HCH in prophase nucleoli in the form of M. cordata grown in Donetsk was higher than in the form grown in Moscow. In both forms sites of 26S rDNA and 5s rDNA were localized on satellite chromosome 1 and on chromosome 4 respectively but the signals were more intensive in the plant form grown in Donetsk. The results of this study enable selecting M. cordata forms for use in pharmacology and recommending them for cultivation in various ecological and geographical regions.     

Termination of tyrphostin AG1478 application results in different recovery of EGF receptor tyrosine residues 1045 and 1173 phosphorylation in A431 cells

Tyrphostin AG1478 is known as a specific and reversible inhibitor of TK (tyrosine kinase) activity of the EGFR [EGF (epidermal growth factor) receptor]. It is attractive as an anticancer agent for cancers with elevated EGFR TK levels. However, post‐application effects of AG1478 are not well studied. We have analysed EGFR phosphorylation after termination of AG1478 application using human epidermoid carcinoma A431 cells. It was found that AG1478 inhibitory action is fast, but not fully reversible: removal of tyrphostin resulted in incomplete restoration of the overall EGFR phosphorylation. Analysing the state of two individual autophosphorylation sites of internalized EGFR, Tyr¹⁰⁴⁵ and Tyr¹¹⁷³, we demonstrated that phosphorylation of Tyr¹¹⁷³ involved in stimulation of the MAPK (mitogen‐activated protein kinase) cascade was restored much more efficiently than that in position 1045, which binds the ubiquitin ligase c‐Cbl and is necessary for targeting the receptor for lysosomal degradation. c‐Cbl association with EGFR abolished by AG1478 was not reestablished after tyrphostin cessation. As a consequence, ubiquitination‐dependent EGFR delivery to lysosomes was blocked, while phosphorylation of ERK1/2 (extracellular‐signal‐regulated kinase 1/2) was even increased. Thus, after termination of AG1478, the intracellular level of the inhibitor can be reached at which mitogenic signalling will be restored, whereas the EGFR negative regulation due to lysosomal degradation will not.     

Intraspecific divergence in wheats of the Emmer group using in situ hybridization with the Spelt-1 family of tandem repeats

Fluorescence in situ hybridization (FISH) was used to study the distribution of Spelt-1 repetitive DNA sequences on chromosomes of 37 accessions representing eight polyploidy wheat species of the Emmer evolutionary lineage: Triticum dicoccoides Körn, T. dicoccum (Schrank) Schuebel, T. durum Desf., T. polonicum L., T. carthlicum Nevski, T. aethiopicum Jakubz., T. aestivum L., and T. spelta L. Substantial polymorphism in the number, distribution, and the sizes of the Spelt-1 loci was revealed. On the chromosomes of the accessions examined, Spelt-1 tandem repeats were found in seven different positions (per haploid chromosome set). These were “potential hybridization sites”, including the subtelomeric regions of either short or long arms of chromosomes 2A and 6B, the short arm of chromosome 1B, and the long arms of chromosomes 2B and 3B. However, in individual genotypes, only from one to three Spelt-1 loci were revealed. Furthermore, no hybridization with Spelt-1 probe was detected on chromosomes from 12 accessions. Thus, the total number of Spelt-1 sites in karyotypes varied from zero to three, with the average number of 1.16. This was substantially lower than in the species of the Timopheevi section and diploid Aegilops speltoides Tausch, a putative donor of the B genome. The decrease of the content of Spelt-1 sequences in the genomes of the Emmer group wheats in comparison with the species of the Timopheevii group and diploid Ae. speltoides was assumed to result from the repetitive sequences reorganization during polyploidization and the repeat elimination during wheat evolution.