DNase I sensitivity of ribosomal RNA genes in chromatin and nucleolar dominance in wheat

Integrating Wheat Nucleolus Structure and Function: Variation in the Wheat Ribosomal RNA and Protein Genes

We review the coordinated production and integration of the RNA (ribosomal RNA, rRNA) and protein (ribosomal protein, RP) components of wheat cytoplasmic ribosomes in response to changes in genetic constitution, biotic and abiotic stresses. The components examined are highly conserved and identified with reference to model systems such as human, Arabidopsis, and rice, but have sufficient levels of differences in their DNA and amino acid sequences to form fingerprints or gene haplotypes that provide new markers to associate with phenotype variation. Specifically, it is argued that populations of ribosomes within a cell can comprise distinct complements of rRNA and RPs to form units with unique functionalities. The unique functionalities of ribosome populations within a cell can become central in situations of stress where they may preferentially translate mRNAs coding for proteins better suited to contributing to survival of the cell. In model systems where this concept has been developed, the engagement of initiation factors and elongation factors to account for variation in the translation machinery of the cell in response to stresses provided the precedents. The polyploid nature of wheat adds extra variation at each step of the synthesis and assembly of the rRNAs and RPs which can, as a result, potentially enhance its response to changing environments and disease threats.

Personal Perspectives on Plant Ribosomal RNA Genes Research: From Precursor-rRNA to Molecular Evolution

The history of rDNA research started almost 90 years ago when the geneticist, Barbara McClintock observed that in interphase nuclei of maize the nucleolus was formed in association with a specific region normally located near the end of a chromosome, which she called the nucleolar organizer region (NOR). Cytologists in the twentieth century recognized the nucleolus as a common structure in all eukaryotic cells, using both light and electron microscopy and biochemical and genetic studies identified ribosomes as the subcellular sites of protein synthesis. In the mid- to late 1960s, the synthesis of nuclear-encoded rRNA was the only system in multicellular organisms where transcripts of known function could be isolated, and their synthesis and processing could be studied. Cytogenetic observations of NOR regions with altered structure in plant interspecific hybrids and detailed knowledge of structure and function of rDNA were prerequisites for studies of nucleolar dominance, epistatic interactions of rDNA loci, and epigenetic silencing. In this article, we focus on the early rDNA research in plants, performed mainly at the dawn of molecular biology in the 60 to 80-ties of the last century which presented a prequel to the modern genomic era. We discuss - from a personal view - the topics such as synthesis of rRNA precursor (35S pre-rRNA in plants), processing, and the organization of 35S and 5S rDNA. Cloning and sequencing led to the observation that the transcribed and processed regions of the rRNA genes vary enormously, even between populations and species, in comparison with the more conserved regions coding for the mature rRNAs. Epigenetic phenomena and the impact of hybridization and allopolyploidy on rDNA expression and homogenization are discussed. This historical view of scientific progress and achievements sets the scene for the other articles highlighting the immense progress in rDNA research published in this special issue of Frontiers in Plant Science on "Molecular organization, evolution, and function of ribosomal DNA."

Perspective: 50 years of plant chromosome biology

The past 50 years has been the greatest era of plant science discovery, and most of the discoveries have emerged from or been facilitated by our knowledge of plant chromosomes. At last we have descriptive and mechanistic outlines of the information in chromosomes that programs plant life. We had almost no such information 50 years ago when few had isolated DNA from any plant species. The important features of genes have been revealed through whole genome comparative genomics and testing of variants using transgenesis. Progress has been enabled by the development of technologies that had to be invented and then become widely available. Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) have played extraordinary roles as model species. Unexpected evolutionary dramas were uncovered when learning that chromosomes have to manage constantly the vast numbers of potentially mutagenic families of transposons and other repeated sequences. The chromatin-based transcriptional and epigenetic mechanisms that co-evolved to manage the evolutionary drama as well as gene expression and 3-D nuclear architecture have been elucidated these past 20 years. This perspective traces some of the major developments with which I have become particularly familiar while seeking ways to improve crop plants. I draw some conclusions from this look-back over 50 years during which the scientific community has (i) exposed how chromosomes guard, readout, control, recombine, and transmit information that programs plant species, large and small, weed and crop, and (ii) modified the information in chromosomes for the purposes of genetic, physiological, and developmental analyses and plant improvement.

The Hordeum bulbosum 25S-18S rDNA region: comparison with Hordeum vulgare and other Triticeae

Hordeum vulgare and Hordeum bulbosum are two closely related barley species, which share a common H genome. H. vulgare has two nucleolar organizer regions (NORs), while the NOR of H. bulbosum is only one. We sequenced the 2.5 kb 25S-18S region in the rDNA of H. bulbosum and compared it to the same region in H. vulgare as well as to the other Triticeae. The region includes an intergenic spacer (IGS) with a number of subrepeats, a promoter, and an external transcribed spacer (5'ETS). The IGS of H. bulbosum downstream of 25S rRNA contains two 143-bp repeats and six 128-bp repeats. In contrast, the IGS in H. vulgare contains an array of seven 79-bp repeats and a varying number of 135-bp repeats. The 135-bp repeats in H. vulgare and the 128-bp repeats in H. bulbosum show similarity. Compared to H. vulgare, the 5'ETS of H. bulbosum is shorter. Additionally, the 5'ETS regions in H. bulbosum and H. vulgare diverged faster than in other Triticeae genera. Alignment of the Triticeae promoter sequences suggests that in Hordeum, as in diploid Triticum, transcription starts with guanine and not with adenine as it is in many other plants.

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.

Chromatin: linking structure and function in the nucleolus

The nucleolus is an informative model structure for studying how chromatin-regulated transcription relates to nuclear organisation. In this review, we describe how chromatin controls nucleolar structure through both the modulation of rDNA activity by convergently-evolved remodelling complexes and by direct effects upon rDNA packaging. This packaging not only regulates transcription but may also be important for suppressing internal recombination between tandem rDNA repeats. The identification of nucleolar histone chaperones and novel chromatin proteins by mass spectrometry suggests that structure-specific chromatin components remain to be characterised and may regulate the nucleolus in novel ways. However, it also suggests that there is considerable overlap between nucleolar and non-nucleolar-chromatin components. We conclude that a fuller understanding of nucleolar chromatin will be essential for understanding how gene organisation is linked with nuclear architecture.

Sterility and gene expression in hybrid males of Xenopus laevis and X. muelleri

BACKGROUND

Reproductive isolation is a defining characteristic of populations that represent unique biological species, yet we know very little about the gene expression basis for reproductive isolation. The advent of powerful molecular biology tools provides the ability to identify genes involved in reproductive isolation and focuses attention on the molecular mechanisms that separate biological species. Herein we quantify the sterility pattern of hybrid males in African Clawed Frogs (Xenopus) and apply microarray analysis of the expression pattern found in testes to identify genes that are misexpressed in hybrid males relative to their two parental species (Xenopus laevis and X. muelleri).

METHODOLOGY/PRINCIPAL FINDINGS

Phenotypic characteristics of spermatogenesis in sterile male hybrids (X. laevis x X. muelleri) were examined using a novel sperm assay that allowed quantification of live, dead, and undifferentiated sperm cells, the number of motile vs. immotile sperm, and sperm morphology. Hybrids exhibited a dramatically lower abundance of mature sperm relative to the parental species. Hybrid spermatozoa were larger in size and accompanied by numerous undifferentiated sperm cells. Microarray analysis of gene expression in testes was combined with a correction for sequence divergence derived from genomic hybridizations to identify candidate genes involved in the sterility phenotype. Analysis of the transcriptome revealed a striking asymmetric pattern of misexpression. There were only about 140 genes misexpressed in hybrids compared to X. laevis but nearly 4,000 genes misexpressed in hybrids compared to X. muelleri.

CONCLUSIONS/SIGNIFICANCE

Our results provide an important correlation between phenotypic characteristics of sperm and gene expression in sterile hybrid males. The broad pattern of gene misexpression suggests intriguing mechanisms creating the dominance pattern of the X. laevis genome in hybrids. These findings significantly contribute to growing evidence for allelic dominance in hybrids and have implications for the mechanism of species differentiation at the transcriptome level.

Epigenetic disruption of ribosomal RNA genes and nucleolar architecture in DNA methyltransferase 1 (Dnmt1) deficient cells

The nucleolus is the site of ribosome synthesis in the nucleus, whose integrity is essential. Epigenetic mechanisms are thought to regulate the activity of the ribosomal RNA (rRNA) gene copies, which are part of the nucleolus. Here we show that human cells lacking DNA methyltransferase 1 (Dnmt1), but not Dnmt33b, have a loss of DNA methylation and an increase in the acetylation level of lysine 16 histone H4 at the rRNA genes. Interestingly, we observed that SirT1, a NAD+-dependent histone deacetylase with a preference for lysine 16 H4, interacts with Dnmt1; and SirT1 recruitment to the rRNA genes is abrogated in Dnmt1 knockout cells. The DNA methylation and chromatin changes at ribosomal DNA observed are associated with a structurally disorganized nucleolus, which is fragmented into small nuclear masses. Prominent nucleolar proteins, such as Fibrillarin and Ki-67, and the rRNA genes are scattered throughout the nucleus in Dnmt1 deficient cells. These findings suggest a role for Dnmt1 as an epigenetic caretaker for the maintenance of nucleolar structure.

rRNA gene silencing and nucleolar dominance: insights into a chromosome-scale epigenetic on/off switch

Ribosomal RNA (rRNA) gene transcription accounts for most of the RNA in prokaryotic and eukaryotic cells. In eukaryotes, there are hundreds (to thousands) of rRNA genes tandemly repeated head-to-tail within nucleolus organizer regions (NORs) that span millions of basepairs. These nucleolar rRNA genes are transcribed by RNA Polymerase I (Pol I) and their expression is regulated according to the physiological need for ribosomes. Regulation occurs at several levels, one of which is an epigenetic on/off switch that controls the number of active rRNA genes. Additional mechanisms then fine-tune transcription initiation and elongation rates to dictate the total amount of rRNA produced per gene. In this review, we focus on the DNA and histone modifications that comprise the epigenetic on/off switch. In both plants and animals, this system is important for controlling the dosage of active rRNA genes. The dosage control system is also responsible for the chromatin-mediated silencing of one parental set of rRNA genes in genetic hybrids, a large-scale epigenetic phenomenon known as nucleolar dominance.

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.

Agrobacterium T-DNA integration in Arabidopsis is correlated with DNA sequence compositions that occur frequently in gene promoter regions

Mobile insertion elements such as transposons and T-DNA generate useful genetic variation and are important tools for functional genomics studies in plants and animals. The spectrum of mutations obtained in different systems can be highly influenced by target site preferences inherent in the mechanism of DNA integration. We investigated the target site preferences of Agrobacterium T-DNA insertions in the chromosomes of the model plant Arabidopsis thaliana. The relative frequencies of insertions in genic and intergenic regions of the genome were calculated and DNA composition features associated with the insertion site flanking sequences were identified. Insertion frequencies across the genome indicate that T-strand integration is suppressed near centromeres and rDNA loci, progressively increases towards telomeres, and is highly correlated with gene density. At the gene level, T-DNA integration events show a statistically significant preference for insertion in the 5' and 3' flanking regions of protein coding sequences as well as the promoter region of RNA polymerase I transcribed rRNA gene repeats. The increased insertion frequencies in 5' upstream regions compared to coding sequences are positively correlated with gene expression activity and DNA sequence composition. Analysis of the relationship between DNA sequence composition and gene activity further demonstrates that DNA sequences with high CG-skew ratios are consistently correlated with T-DNA insertion site preference and high gene expression. The results demonstrate genomic and gene-specific preferences for T-strand integration and suggest that DNA sequences with a pronounced transition in CG- and AT-skew ratios are preferred targets for T-DNA integration.

Epigenetic silencing of RNA polymerase I transcription

The genes that encode ribosomal RNA exist in two distinct types of chromatin--an 'open' conformation that is permissive to transcription and a 'closed' conformation that is transcriptionally refractive. Recent studies have provided insights into the molecular mechanisms that silence either entire nucleolus organizer regions (NORs) in genetic hybrids or individual rRNA genes within a NOR. An emerging theme from these studies is that epigenetic mechanisms operating at the level of DNA methylation and histone modifications alter the chromatin structure and control the ratio of active and inactive rRNA genes.

Structure, molecular evolution, and phylogenetic utility of the 5(') region of the external transcribed spacer of 18S-26S rDNA in Lessingia (Compositae, Astereae)

The 18S-26S nuclear rDNA external transcribed spacer (ETS) has recently gained attention as a region that is valuable in phylogenetic analyses of angiosperms primarily because it can supplement nucleotide variation from the widely used and generally shorter internal transcribed spacers (ITS-1 and ITS-2) and thereby improve phylogenetic resolution and clade support in rDNA trees. Subrepeated ETS sequences (often occurring in the 5(') region) can, however, create a challenge for systematists interested in using ETS sequence data for phylogeny reconstruction. We sequenced the 5(')ETS for members of Lessingia (Compositae, Astereae) and close relatives (26 taxa total) to characterize the subrepeat variation across a group of closely related plant lineages and to gain improved understanding of the structure, molecular evolution, and phylogenetic utility of the region. The 5(')ETS region of Lessingia and relatives varied in length from approximately 245 to 1009 bp due to the presence of a variable number of subrepeats (one to eight). We assessed homology of the subrepeats using phylogenetic analysis and concluded that only two of the subrepeats and a portion of a third ( approximately 282 bp in total) were orthologous across Lessingia and could be aligned with confidence and included in further analyses. When the partial 5(')ETS data were combined with 3(')ETS and ITS data in phylogenetic analyses, no additional resolution of relationships among taxa was obtained beyond that found from analysis of 3(')ETS + ITS sequences. Inferred patterns of concerted evolution indicate that homogenization is occurring at a faster rate in the 3(')ETS and ITS regions than in the 5(')ETS region. Additionally, homogenization appears to be acting within but not among subrepeats of the same rDNA array. We conclude that challenges in assessing subrepeat orthology across taxa greatly limit the utility of the 5(')ETS region for phylogenetic analyses among species of Lessingia.

Restricted chromosomal silencing in nucleolar dominance

Failure of one parent's chromosomes to organize nucleoli in an interspecific hybrid is an epigenetic phenomenon known as nucleolar dominance. Selective gene silencing on a scale of millions of bp is known to be involved, but the full extent to which nucleolus organizer region (NOR)-bearing chromosomes are inactivated beyond the NORs is unknown. Aided by genome sequence data for Arabidopsis thaliana, we have mapped the extent of nucleolar dominance-induced silencing in Arabidopsis suecica, the allotetraploid hybrid of A. thaliana and Arabidopsis arenosa. Using a sensitive reverse transcription PCR assay, we show that the four A. thaliana NORs, each approximately 4 Mbp in size, are approximately 99.5% silenced in A. suecica vegetative leaves, whereas the NORs inherited from A. arenosa remain fully active. The two A. thaliana NORs, NOR2 and NOR4, abut the telomeres on chromosomes 2 and 4, thus there are no genes distal to the NORs. The three protein-coding genes nearest NOR4 on its centromere-proximal side, the closest of which is only 3.1 kb from rRNA gene sequences, are shown to be transcribed in the hybrid despite the silencing of the adjacent approximately 4-Mbp NOR. These data argue against hypotheses in which NOR inactivation is attributed to the spread of silencing from adjacent chromosomal regions, but favor models in which NORs or rRNA genes are the targets of regulation.

Nucleolar dominance and silencing of transcription

Nucleolar dominance is a phenomenon in plant and animal hybrids whereby one parental set of ribosomal RNA (rRNA) genes is transcribed, but the hundreds of rRNA genes inherited from the other parent are silent. The phenomenon gets it name because only transcriptionally active rRNA genes give rise to a nucleolus, the site of ribosome assembly. Nucleolar dominance provided the first clear example of DNA methylation and histone deacetylation acting in partnership in a gene-silencing pathway. However, the sites of chromatin modification and the ways in which one set of rRNA genes are targeted for repression remain unclear. Another unresolved question is whether the units of regulation are the individual rRNA genes or the multi-megabase chromosomal domains that encompass the rRNA gene clusters.

Tandem duplication of nucleolus organizer region (NOR) in the Japanese macaque, Macaca fuscata fuscata

During exploration of chromosome polymorphisms in Japanese macaques, a heteromorphic polymorphism was found in a population in the Zigokudani monkey park. The population consisted of three troops (social units). Of 36 monkeys examined, five females showed heterozygotic 'marker' chromosome (chromosome 9). The polymorphism was a tandem duplication of the nucleolus organizer region (NOR) of the short arm of chromosome 9, which was found for the first time in the genus Macaca. FISH and fibre-FISH using human 18S rDNA and sequential silver nitrate staining revealed that the duplicated region included a part of the euchromatic satellite and the stalk and that the euchromatic block (intercalary satellite) divided the NOR into two parts (distal and proximal). Furthermore, it showed that the distal region possessed much more rDNA than the proximal region, and that the duplications might have been introduced via a mechanism of gene amplification (inverted duplications associated with over-replication and recombination events). As the tandem duplication was observed sporadically in four maternal pedigrees in two troops and the mothers of the variants all had normal chromosomes, the variation might have been introduced from another population's gene pool by a solitary male immigrant.

Patterns of DNase I sensitivity in the holocentric chromosomes of the aphid Megoura viciae

Using the in situ nick translation technique, we looked for the presence of DNase I sensitive sites in Megoura viciae chromosomes, to study the distribution of active or potentially active genes in aphids, a group of insects possessing holocentric chromosomes. Cytological preparations obtained by the spreading of embryo cells were treated in situ with increasing concentrations (ranging from 5 to 200 ng/mL) of DNase I. At DNase I concentrations below 50 ng/mL, only one hypersensitive site was observed, and this was located on a telomeric region of the X chromosome that contains transcriptionally active nucleolar organizing regions, as assayed by silver staining. Interestingly, at intermediate concentrations of DNase, the incorporation of biotinylated nucleotide occurred uniformly throughout all chromosomes, whereas at concentrations above 100 ng/mL, a C-like banding pattern was produced. Our data differ from results obtained with mammalian, frog, and grasshopper chromosomes, where it was found that DNase I nicking is concentrated at the distal regions of all chromosomes.Key words: aphids, holocentric chromosomes, DNase I sensitivity, nick translation.

Variability in CpNpG methylation in higher plant genomes

The methylation status of ribosomal gene (rRNA) clusters have been investigated in a large variety of angiosperm species. Here we have analysed methylation in ribosomal gene (rRNA) clusters using MspI, HpaII, BstNI, EcoRII and CfoI restriction enzymes in combination with Southern hybridization to the 25S rDNA probe. It was shown that cytosine methylation at CpG dinucleotides and CpNpG trinucleotides occurred in all plant genomes examined. Methylation of rDNA units at CpG dinucleotides (studied with CfoI) was high in all species tested with approx. 40-70% of units being completely or nearly completely methylated. In contrast, the extent of the CpNpG methylation (studied with MspI and EcoRII) varied significantly between species; the percentage of the rDNA fraction entirely methylated at CpNpG trinucleotides ranged from less than 1% to almost 90% depending on the genome studied. Larger interspecies than within species variation was also observed among several non-transcribing repetitive sequences. In a small genome of A. thaliana, the CpNpG methylation appeared to be highly compartmentalized into the repetitive fraction. The methylation of trinucleotides was abundant in large A+T-rich genomes and it is proposed that the CpA(T)pG trinucleotides may help to maintain a high density of methylatable targets in plant repeated sequences.

Transcriptional analysis of nucleolar dominance in polyploid plants: biased expression/silencing of progenitor rRNA genes is developmentally regulated in Brassica

Nucleolar dominance is an epigenetic phenomenon that describes the formation of nucleoli around rRNA genes inherited from only one parent in the progeny of an interspecific hybrid. Despite numerous cytogenetic studies, little is known about nucleolar dominance at the level of rRNA gene expression in plants. We used S1 nuclease protection and primer extension assays to define nucleolar dominance at a molecular level in the plant genus Brassica. rRNA transcription start sites were mapped in three diploids and in three allotetraploids (amphidiploids) and one allohexaploid species derived from these diploid progenitors. rRNA transcripts of only one progenitor were detected in vegetative tissues of each polyploid. Dominance was independent of maternal effect, ploidy, or rRNA gene dosage. Natural and newly synthesized amphidiploids yielded the same results, arguing against substantial evolutionary effects. The hypothesis that nucleolar dominance in plants is correlated with physical characteristics of rRNA gene intergenic spacers is not supported in Brassica. Furthermore, in Brassica napus, rRNA genes silenced in vegetative tissues were found to be expressed in all floral organs, including sepals and petals, arguing against the hypothesis that passage through meiosis is needed to reactivate suppressed genes. Instead, the transition of inflorescence to floral meristem appears to be a developmental stage when silenced genes can be derepressed.

Reprogramming of rye rDNA in triticale during microsporogenesis

To test the hypothesis that interspecific genomic and chromosome interactions leading to nucleolar dominance could be reprogrammed in meiosis, we compared the expression of distinct nucleolar organizing region (NOR) loci in hexaploid triticale root tip meristematic cells, pollen mother cells and young pollen grains. Interphase and metaphase cells were silver stained to quantify nucleoli and active NOR loci respectively. A marked difference in the ribosomal RNA gene activity of each locus was observed when different types of cells were compared: in somatic and pollen mother cells, rRNA gene activity was mainly restricted to major wheat NORs (1B and 6B) with only a small contribution from rye NORs (1R). In contrast, in young pollen grains, all NORs present, including the 1R NORs, were consistently active. The expression of all NORs just after meiosis is considered to be a consequence of meiotic reprogramming of rye origin rDNA. Gene reprogramming mediated by the resetting of methylation patterns established early in embryogenesis is suggested to be responsible for the differential expression of the NORs of rye origin in distinct developmental stages of triticale.

Methylation-dependent binding of wheat nuclear proteins to the promoter region of ribosomal RNA genes

Here, we report data on the binding of wheat nuclear proteins (NP) to the promoter region of the rDNA intergenic spacer (IGS), with emphasis on the possible effects of methylation with M-HpaII on this binding. We have found that a number of NP specifically bind to the rDNA promoter, and to upstream and downstream IGS sequences. A 240-kDa NP binds specifically to a 174-bp fragment located downstream from the transcription start point (tsp), and this fragment competes with a 135-bp subrepeat element fragment for specific binding to this 240-kDa NP. Specific binding of the 240-kDa NP to the 174-bp fragment is greatly inhibited by methylation of internal cytosine residues in its two CCGG sites, whereas NP binding to the 135-bp subrepeat element is not affected by M-HpaII methylation. A 202-bp fragment containing the tsp is partially homologous to the 174-bp downstream region fragment. Nevertheless, it neither binds the 240-kDa NP nor is its binding to NP affected by methylation of CCGG sites. Thus, multiple specific NP may be involved in rDNA transcription initiation. Methylation-dependent inhibition of rDNA transcription initiation appears to be mediated by direct interference with the binding of some of these transcription factors to their respective regulatory elements.

Structure and comparative analysis of the rDNA intergenic spacer of Brassica rapa. Implications for the function and evolution of the Cruciferae spacer

The sequence of the intergenic spacer (IGS) of the Brassica rapa rDNA was determined and compared with those of other Cruciferae species. In the 3012-bp IGS, two segments of mostly unique sequence flank a 1.5-kb region consisting of two tandem arrays of repeats. A putative transcription initiation site (TIS) was identified by sequence comparison, 395 bp downstream from the repeat region. The intercalating segment displays unusual sequence patterns, and modelling of its topology predicts intrinsically bent DNA, with two elements of bending centered at positions -118 and -288 relative to the TIS. Comparative analysis of spacers from Cruciferae, revealed a common organization and high sequence similarity in their 5' and, particularly, 3' regions, whereas the repeat region upstream of TIS diverges rapidly. The conservation of structural elements, including the bent DNA upstream from the TIS, is discussed in light of their possible involvement in the IGS functions and structure of spacers in common ancestors. Examination of the Cruciferae spacers shows that, in addition to unequal crossover and gene conversion, insertional mutagenesis and replication slippage are molecular mechanisms significantly contributing to their evolution.

Pattern and degree of methylation in ribosomal RNA genes of Cucurbita pepo L

Methylation with respect to its degree and distribution throughout the 18S, 5.8S and 25S rRNA gene clusters (rDNA) and within single rDNA repeats in seedlings of the higher plant Cucurbita pepo L. (zucchini) was investigated. In this plant, which is characterized by several thousand repeats, at least 70% are completely or nearly completely methylated in CpGs and to a lower degree in CpNpGs. Detailed methylation analysis revealed that a fraction of about 3-4% of all repeats is hypomethylated near the transcription initiation site (TIS) which may indicate the fraction of active repeats in C. pepo. However, a different fraction (3-4% of all repeats) which is not methylated in all sites tested (including those at the TIS) is present in C. pepo and may thus represent active but differentially methylated rDNA. The results are discussed in context of recent models on methylation and gene activity.

The influence of the rye genome on the accumulation of HSP18 and HSP70 transcripts in a wheat genetic background

The influence of the rye genome on the accumulation of HSP18 and HSP70 transcripts in a wheat genetic background was examined in the wheat/rye hybrid triticale (Triticum aestivum cv Chinese Spring x Secale cereale cv Imperial). To quantify the amount of transcript accumulation in wheat, rye, triticale, and in the disomic and the ditelosomic rye addition lines to wheat, we used two independant methods, namely (1) Northern dot-blot hybridizations and (2) an exami-nation of the in-vitro translation products. Both the HSP18 and HSP70 transcripts were expressed at similar levels in Chinese Spring wheat, Imperial rye, and triticale. The HSP18 and HSP70 transcript levels of the disomic and the ditelosomic addition lines to wheat were compared to the transcript levels in wheat. With the exception of 5R, increased levels of HSP18 and/or HSP70 transcripts were expressed in all six of the remaining disomic addition lines. A neutral or suppressed level of HSP18 and HSP70 transcripts accumulated in addition lines 5R, 5RL, 5RS and 6RL. Wheat/rye genomic interactions influenced the level of heat-shock gene transcript accumulation in triticale. Rye chromosome 5R, and in particular both arms of rye chromosome 5R (5RL and 5RS), had a strong suppressive influence on the accumulation of wheat HSP18 and HSP70 transcripts. The genes controlling rye HSP expression appeared to be widely distributed throughout the rye genome.

Ethylene is a selective ribosomal cistron regulator in Allium cepa epidermal cells

In Allium cepa L. (onion) the number, size, and morphology of visible nucleoli per nucleus varies during cell division, growth, differentiation, storage, activation of quiescent tissue, senescence, wounding, and disease (host-pathogen interactions). Since there are two types (differentiated visually by size) of ribosomal cistrons in onion (major and minor nucleoli differ in the external spacer nucleotide sequences), we inferred that they function separately. In controls, major nucleolar organizer regions (NORs) were visible in epidermal cell nuclei as nucleoli. After exposure of the tissue to ambient conditions, these nucleoli enlarged and changed morphology. Minor NORs (when in the genome) required more than 6 h to become developed as visible nucleoli. In the ethylene treatments, the major NORs (visible nucleoli in quiescent epidermal cells) increased in size a (activation of a greater number of tandem rRNA genes) as in the controls. The minor, quiescent NORs became active and visible (activation of quiescent, inactive NORs) within 3 h. Actinomycin D, and cycloheximide, with or without ethylene, inhibited the increase in size of the major NORs, and prevented activation of the minor NORs (i.e. they did not become visible). Silver nitrate and cobalt chloride had no effect on major NORs but inhibited the appearance of minor nucleoli when combined with ethylene treatments. We infer: ethylene acts to regulate the expression of the minor NORs (selective ribosomal cistron regulation); and, other hormone(s) are involved in the regulation of the major NORs. Yellow and white sweet Spanish onions we studied had two major NORs and two minor NORs. Red sweet Spanish onions we studied had only the two major NORs.

DNaseI-sensitive and undermethylated rDNA is preferentially expressed in a maize hybrid

An Eco RI polymorphism, present in the 26S ribosomal RNA gene (rDNA) of the maize hybrid Sx19 (B73 x Mo17), was utilized to correlate DNaseI sensitivity, undermethylation and expression in rDNA. We have previously shown that in double digest experiments with methylation-sensitive restriction enzymes and Eco RI, Sx19 rDNA fragments originating from repeat units with two Eco RI sites (8.0 kb) are undermethylated, whereas the fragments originating from repeat units with a single Eco RI site (9.1 kb) are completely methylated. In the present study, Sx19 rDNA chromatin structure was examined by purifying intact nuclei and digesting them briefly with increasing amounts of DNaseI. Analysis of this DNA with Eco RI showed that the 8.0 kb rDNA fragments are extremely sensitive to DNaseI digestion, while the 9.1 kb rDNA fragments are relatively resistant to digestion even at high levels of DNaseI. Specific sites hypersensitive to DNaseI cleavage were mapped to a region in the intergenic spacer (IGS) near the major undermethylated site. Analysis of polymerase chain reaction (PCR) products synthesized using Sx19, B73, and Mo17 DNAs as templates indicated that the Eco RI polymorphism is due to a base change in the recognition site. Direct rRNA sequencing identified a single-base change in Mo17 rRNA relative to B73 rRNA. Allele-specific oligonucleotide probes containing the region surrounding and including the Eco RI polymorphic site were utilized to detect a nucleolar dominance effect by quantitating levels of rRNA transcripts in Sx19 and the reciprocal cross. Results from these single-base-pair mismatch hybridization experiments indicate that the majority of the rRNA transcripts in Sx19 originate from the DNaseI-sensitive, undermethylated, Eco RI-polymorphic rDNA repeat units.

Different patterns of rDNA distribution in Pisum sativum nucleoli correlate with different levels of nucleolar activity

We have used in situ hybridization with probes to rDNA, labelled either with digoxygenin or directly with fluorescein, to determine the arrangement of these genes within the nucleoli of Pisum sativum L. root cells. Confocal laser scanning microscopy was used to image the three-dimensional structures revealed, but we have also compared this technique with deconvolution of conventional (wide-field) fluorescence images measured with a cooled CCD camera, and have shown that the results are remarkably similar. When the deconvolution technique was applied to the confocal data it gave clearer images than could be achieved by confocal microscopy alone. We have analysed the distribution of rDNA in the different cell types observable in root tips: the quiescent centre; active meristematic cells; and relatively differentiated root cap, epidermal and cortical cells. In addition to four perinucleolar knobs of condensed, inactive rDNA genes, corresponding to the four nucleolar organizers in P. sativum, which were the most brightly labelled structures, several characteristic patterns of intranucleolar labelling were apparent, including bright foci, large central chromatin masses, and fine, decondensed interconnecting fibres. The larger and more active the nucleolus, the smaller the proportion of condensed perinucleolar rDNA. In some large and active meristematic nucleoli, all the internal rDNA is decondensed, showing that transcription cannot be restricted to the bright foci, and is most likely to occur on the decondensed fibres.

Correlation between the size of the intergenic regulatory region, the status of cytosine methylation of rRNA genes and nucleolar expression in wheat

A large number of wheat rRNA genes are methylated at all the CCGG sites that are present in the intergenic regions. A smaller number of rRNA genes are not methylated at one or more CCGG sites. A subset of genes was found unmethylated at a specific CCGG site just downstream of the array of 135 bp A repeats in the intergenic region. In all the genotypes studied, the rDNA loci with larger intergenic regions between their genes also possess a greater number of rRNA genes that are unmethylated at one or more CCGG sites in the intergenic regions than do the loci with shorter intergenic regions. In four genotypes (for which data were available), rDNA loci with longer intergenic regions had larger secondary constrictions on metaphase chromosomes, a measure of relative locus activity, than the loci with shorter intergenic regions. The results have been integrated into a model for the control of rDNA expression based on correlations between cytosine methylation patterns and the number of upstream 135 bp repeats in intergenic regions. According to this model the 135 bp repeats play a part in the control of gene activity by binding a protein(s) that is in limiting supply, thereby predisposing the neighbouring gene to become active preferentially.

Ribosomal gene clusters are uniquely proportioned between open and closed chromatin structures in both tomato leaf cells and exponentially growing suspension cultures

The accessibility of regulatory molecules to specific DNA sequences and chromatin regions in the nucleus is crucial to gene expression. In this study, we examined the chromatin structure in tomato leaf cells and in exponentially growing tomato cell suspension cultures. The structure of ribosomal chromatin was investigated by micrococcal nuclease and psoralen photocrosslinking. We showed that ribosomal genes in tomato are folded into two distinct types of chromatin: an open chromatin conformation and a closed nucleosomecontaining chromatin. In contrast to previous findings in Friend cells, where half of the ribosomal genes were found to be complexed within an inactive chromatin structure, we demonstrated that the canonical nucleosome-containing chromatin is present in the majority (approximately 80%) of the tomato rRNA-encoding DNA clusters. The minor open chromatin population (approximately 20% of the ribosomal genes) could be detected only after analysis following psoralen crosslinking. The relative amounts of the two ribosomal chromatin structures are similar in stationary and exponentially growing cells. This suggests that the proportions of open and closed chromatin structures present in either stationary or exponentially growing tomato cells are not dependent on the transcriptional process.

Compensatory changes in silver-stainability of nucleolar organizer regions in mice

Silver-stainability of nucleolar organizer regions (NORs) that contain genes for ribosomal RNA (rDNA) was investigated using two mouse strains, BALB/cCrSlc and MOA, and their hybrid progeny. The patterns of segregation of the rDNA clusters were analyzed in terms of chromosomal C-banding and by use of a polymorphic probe for the variable region in backcrossed N2 and N3 individuals. The results indicate that the intensity of Ag-NOR staining is stably inherited in most of the rDNA clusters, irrespective of different genetic backgrounds. In some clusters, such as those on chromosome 12 of BALB/cCrSlc, a modulation of the intensity is observed. This modulation seems to be due to compensatory activation via a change in the number of actively transcribed genes. The change from silver-negative to silver-positive staining of the NOR of chromosome 12 of BALB/cCrSlc was correlated with demethylation of the genes.

Expression of Thinopyrum distichum NORs in wheat×Thinopyrum amphiploids and their backcross generations

The C-banding pattern of the satellited chromosomes in Thinopyrum distichum and Triticum durum was established. Both T. durum and Th. distichum contained two pairs of satellited chromosomes, which could be distinguished from one another. In the amphiploids [T. durum×Th. distichum (2x=56)] and in the backcross T. durum/(T. durum×Th. distichum)(2), BC1F3, and BC1F5 (2n = 42) the satellite was visible on only 1B and 6B of T. durum. The vector pTa 71 containing the rRNA gene from wheat hybridized to two pairs of chromosomes (four hybridization sites) in T. durum and Th. distichum, to eight sites in the amphiploid hybrid (2n=56), and to six sites in the backcross populations BC1F1. BC1F3, and BC1F5 (2n=42). The two satellite pairs in Th. distichum could be distinguished by the chromosomal location of the rRNA site (median or subterminal) and by the centromere position. One copy of each pair was present in the BC1F1, but in the BC1F3 and BC1F5 populations the pair with the subterminal location of rRNA genes was absent. Silver nitrate staining indicated that the rRNA genes of T. durum did not completely suppress those of Th. distichum. The octoploid amphiploid (2n = 56) contained a maximum of four large and four small nucleoli and the hexaploid BC1s (2n=42), four large and two small nucleoli.

rRNA synthesis in the nucleolus

The past year has seen advances in our understanding of three broad areas that concern ribosomal RNA production. It is becoming apparent that for a large number of eukaryotes, sequence elements that regulate ribosomal RNA transcription are arranged in a similar pattern. This conservation of arrangement implies conservation of regulatory mechanisms. Better understanding of the ribosomal gene transcription factors has emerged, and one factor has been purified and cloned. In vitro systems for processing ribosomal RNA are beginning to be developed, allowing the first direct proof that a small nuclear ribonucleoprotein (U3) is involved in ribosomal RNA processing.

Increased rRNA gene activity during a specific window of early pea leaf development

rRNA gene transcription rates were determined during light-mediated leaf development in Pisum sativum. The rate of transcription was observed to increase within 1 day of exposure to light and return to control levels 4 days after exposure. A striking similarity was observed between periods of elevated rRNA gene transcription and increased mitotic activity, suggesting a possible link between the two events.

Increased rRNA gene activity during a specific window of early pea leaf development

rRNA gene transcription rates were determined during light-mediated leaf development in Pisum sativum. The rate of transcription was observed to increase within 1 day of exposure to light and return to control levels 4 days after exposure. A striking similarity was observed between periods of elevated rRNA gene transcription and increased mitotic activity, suggesting a possible link between the two events.

Regulation of cytosine methylation in ribosomal DNA and nucleolus organizer expression in wheat

Cytosine methylation has been studied in wheat rRNA genes at nucleolar organizers displaying different activities. The methylation pattern within a specific multigene locus is influenced by the number and type of rRNA genes in other rDNA loci in the cell. One CCGG site 164 base-pairs upstream from the start of transcription is preferentially unmethylated in some genes. Dominant, very active loci have a higher proportion of rRNA genes with unmethylated cytosine residues in comparison with recessive and inactive loci. It is concluded that cytosine methylation in rDNA is regulated and that the methylation pattern correlates with the transcription potential of an rRNA gene.