Cytological and molecular evidence of deletion of ribosomal RNA genes in chromosome 6 of barley (Hordeum vulgare)

Mapping of unmethylated sites in rDNA repeats in barley NOR deletion line

Extensive cytosine methylation is characteristic of plant rDNA. Evidence exists, however, that the active rRNA genes are less methylated. In this work we report on the mapping of unmethylated CCGG sites in Hordeum vulgare rDNA repeats by digestion with methylation sensitive restriction enzyme HpaII and indirect end-labeling of the generated fragments. For mapping we used genomic DNA from barley deletion line with a single NOR on chromosome 5H. This NOR is more active in order to compensate for the missing NOR 6H. The enhanced NOR 5H activity in the deletion mutant is not due to higher multiplicity of the rRNA genes or, as sequencing showed, to changes in the subunit structure of the intergenic spacer. The HpaII sites in barley rDNA are heavily methylated. Nevertheless, a fraction of the rDNA repeats is hypomethylated with unmethylated CCGG sites at various positions. One unmethylated CCGG sequence is close to the transcription start site, downstream of the 135bp subrepeats. Unmethylated sites are also present in the external transcribed spacer and in the genes coding mature rRNAs. The patterns of unmethylated sites in the barley deletion line and in lines with two NORs were compared. It is hypothesized that the occurrence of unmethylated sites on a fixed subset of rDNA repeats correlates with their transcriptional activity.

Analyzing meiosis in barley

This chapter contains a detailed description of the immunological and cytological techniques developed to determine factors involved in crossover control during meiosis in barley. The immunological technique involves digesting fresh anthers followed by chromosome spreading to remove cytoplasm that causes unwanted background, whilst protecting the fragile chromosome structure from being compromised. Specific antibodies raised against meiotic proteins are then incubated with nuclei, detected with secondary antibodies conjugated to fluorescent dyes, and visualized with either wide-field or confocal microscopes. In the cytological technique, barley inflorescences are fixed, followed by dissecting out the anthers, digesting the cell walls and then spreading the meiotic chromosomes. Both techniques can be used in conjunction with specific DNA probes for fluorescent in situ hybridization (FISH) to label telomeres, centromeres, and ribosomal DNA; to identify DNA modifications such as 5-methylcytosine; and to detect the incorporation of DNA base analogues such as 5-bromo-2'-deoxyuridine (BrdU) or 5-ethynyl-2'-deoxyuridine (EdU) to be used for a meiotic time-course or assaying newly synthesized DNA. Although these techniques have been specifically developed for barley, they should be directly transferable to other cereal crop species such as wheat and rice.

The use of double fluorescence in situ hybridization to physically map the positions of 5S rDNA genes in relation to the chromosomal location of 18S-5.8S-26S rDNA and a C genome specific DNA sequence in the genus Avena

A physical map of the locations of the 5S rDNA genes and their relative positions with respect to 18S-5.8S-26S rDNA genes and a C genome specific repetitive DNA sequence was produced for the chromosomes of diploid, tetraploid, and hexaploid oat species using in situ hybridization. The A genome diploid species showed two pairs of rDNA loci and two pairs of 5S loci located on both arms of one pair of satellited chromosomes. The C genome diploid species showed two major pairs and one minor pair of rDNA loci. One pair of subtelocentric chromosomes carried rDNA and 5S loci physically separated on the long arm. The tetraploid species (AACC genomes) arising from these diploid ancestors showed two pairs of rDNA loci and three pairs of 5S loci. Two pairs of rDNA loci and 2 pairs of 5S loci were arranged as in the A genome diploid species. The third pair of 5S loci was located on one pair of A-C translocated chromosomes using simultaneous in situ hybridization with 5S rDNA genes and a C genome specific repetitive DNA sequence. The hexaploid species (AACCDD genomes) showed three pairs of rDNA loci and six pairs of 5S loci. One pair of 5S loci was located on each of two pairs of C-A/D translocated chromosomes. Comparative studies of the physical arrangement of rDNA and 5S loci in polyploid oats and the putative A and C genome progenitor species suggests that A genome diploid species could be the donor of both A and D genomes of polyploid oats. Key words : oats, 5S rDNA genes, 18S-5.8S-26S rDNA genes, C genome specific repetitive DNA sequence, in situ hybridization, genome evolution.

DNA methylation pattern in a barley reconstructed karyotype with deleted ribosomal gene cluster of chromosome 6H

A reconstructed barley karyotype (T-35) was utilised to study the influence of chromosomal rearrangements on the DNA methylation pattern at chromosome level. Data obtained were also compared with the distribution of Giemsa N-bands and high gene density regions along the individual chromosomes that have been previously described. In comparison to the control karyotype (T-1586), the DNA methylation pattern was found to vary not only in the reconstructed chromosomes but also in the other chromosomes of the complement. Significant remodelling process of methylation pattern was found also in the residual nucleolus organiser regions (NOR) on chromosome 5H as a consequence of deletion comprising the whole NOR of chromosome 6H in T-35. Moreover, differences between corresponding segments of the homologues with respect to some other chromosome locations were also observed. Repositioning of genomic DNA methylation along the metaphase chromosomes following chromosomal reconstruction in barley seems to be essential to ensure correct chromatin organisation and function.

DNA methylation and chromosomal rearrangements in reconstructed karyotypes of Hordeum vulgare L

One standard and two reconstructed barley karyotypes were used to study the influence of chromosomal rearrangements on the distribution pattern of DNA methylation detectable at the chromosome level. Data obtained were also compared with Giemsa N-bands and high gene density regions that had been previously described. The effect of chromosomal reconstruction in barley seems to be decidedly prominent in the repositioning of genomic DNA methylation along metaphase chromosomes. In comparison to the standard karyotype, the DNA methylation pattern was found to vary not only in the reconstructed chromosomes but also in the other chromosomes of the complements not subjected to structural alterations. Moreover, differences may occur between corresponding regions of homologues. Some specific chromosomal bands, including the nucleolus-organizing regions, showed a relative constancy in the methylation pattern, but this was not the case when the two satellites were combined by translocation in chromosome 6H(5H) of line T-30. Our results suggest that epigenetic changes like DNA methylation may play an important role in the overall genome reorganization following chromosome reconstruction.

Efficient repair of bleomycin-induced double-strand breaks in barley ribosomal genes

Ability of barley ribosomal genes to cope with damage produced in vivo by the radiomimetic agent bleomycin was investigated. Repair kinetics of bleomycin-induced double-strand breaks in ribosomal and total genomic DNA was compared. Induction and repair of double-strand breaks in defined regions of the ribosomal genes was also analyzed. Preferential sensitivity of barley linker DNA towards bleomycin treatment in vivo was established. Relatively higher yield of initially induced double-strand breaks in genomic DNA in comparison to ribosomal DNA was also found. Fragments containing intergenic spacers of barley rRNA genes displayed higher sensitivity to bleomycin than the coding sequences. No heterogeneity in the repair of DSB between transcribed and non-transcribed regions of ribosomal genes was detected. Data indicate that DSB repair in barley rDNA, although more efficient than in genomic DNA, does not correlate with the activity of nucleolus organizer regions.

Induction and recovery of double-strand breaks in barley ribosomal DNA

Barley nucleolus organizing regions (NORs) were previously found to behave as prominent aberration hot-spots after treatment with some restriction endonucleases. The ability of MspI for directed induction of double-strand breaks in barley ribosomal DNA was further analyzed. Ionizing radiation-produced strand breakage within the ribosomal gene clusters was also a subject of investigation. Reconstructed barley karyotypes T1586 and T35 with normal and increased expression of rRNA genes were utilized to evaluate the relationship between transcriptional activity and damage induction. Scanning densitometry of the hybridization profiles revealed that MspI is generating double-strand breaks in barley rDNA with efficiency being independent from the NOR activity. Damage induction observed after treatment with gamma-rays was also not influenced by the transcriptional status of the ribosomal genes. A tendency towards restoration of rDNA integrity after irradiation of both germinating and dry seeds was observed which is indicative for the efficient recovery of double-strand breaks in barley ribosomal DNA.

The 5S rDNA of mussels Mytilus galloprovincialis and M. edulis: sequence variation and chromosomal location

The 5S ribosomal DNA of the mussels Mytilus galloprovincialis and M. edulis was amplified by PCR using contiguous primers. The most general 5S rDNA amplification pattern consisted of several products in both mussels. Two main PCR products of about 250 bp and 760 bp were cloned and sequenced, revealing two classes of 5S rDNA units. These were characterized as containing an identical coding region of 119 bp but with highly divergent spacers. Clones of each unit type exhibited minimal differences except those of the large unit of M. edulis. The sequences analysed of the two mussels possess the same coding region and only six fixed base changes on the spacers. FISH, carried out with specific probes, consistently showed hybridization signals on the largest metacentric pair (two differentiated sites) and with variable frequency on two other metacentric pairs (one site on each pair). Differences in the 5S rDNA distribution between both mussels were not found. In M. edulis, chromosomes carrying 18S-28S rDNA were also identified by FISH. These correspond to two submetacentric-subtelocentric pairs, as was previously reported in M. galloprovincialis, demonstrating that the two rDNA multigene families are located on different chromosome pairs in these mussels.

Physical mapping of 45S and 5S rDNA on maize metaphase and sorted chromosomes by FISH

Physical locations of 45S and 5S rDNA were detected in maize by fluorescence in situ hybridization (FISH). The FISH results on metaphase chromosome spreads showed the 45S rDNA was located just at the nucleolus organizer region (NOR) on 6S (the short arm) of chromosome 6) as expected, and 5S rDNA at the distal region of 2L (the long arm of chromosome 2). No signals were detected on the other maize chromosomes for these two probes. The precision of the chromosomal position of a hybridization site is related to the number of measurements. We also mapped the location of 5S rDNA at the same sites on 2L by FISH on sorted chromosomes. We could calculate more precisely the percentage distance of hybridization signals since we had large numbers of target chromosomes on a small spot on the slide by flow sorting. The percentage distance from centromere to the hybridization site was 85% for 5S rDNA on 2L. The physical location of 5S rDNA was inconsistent with its genetic site, which was positioned in the middle of genetic linkage group 2. A FISH procedure for mapping genes on sorted plant chromosomes is described and occurrence of only one 45S or 5S rDNA site on maize genome is discussed.

Physical mapping and activity of ribosomal RNA genes in mussel Mytilus galloprovincialis

In bivalve molluscs, NOR analysis was carried out by silver staining, and extensive intra- and interindividual differences in the apparent number of NORs were reported. In this work, we determine the physical mapping of 18S and 28S ribosomal genes of the mussel M. galloprovincialis by fluorescence in situ hybridization (FISH). We also apply silver staining to the same individuals in order to determine if structural changes are involved in the heteromorphism detected by this technique. Our results show that rDNA loci map on the telomeric region of the long arm of two submetacentric-subtelocentric chromosome pairs. In addition to variations in NOR expression, we found some cases of structural variations that affect the number of rDNA loci between individuals and the location of the rDNA locus between the cells of the individual. We suggest that FISH should be applied to other bivalves to assess the variation of rDNA loci and undertake more accurate interspecific comparisons.