The control of nucleolus volume in wheat, a genetic study at three developmental stages

Fine structure and transcription dynamics of bread wheat ribosomal DNA loci deciphered by a multi-omics approach

Three out of four RNA components of ribosomes are encoded by 45S ribosomal DNA (rDNA) loci, which are organized as long head-to-tail tandem arrays of nearly identical units, spanning several megabases of sequence. Due to this structure, the rDNA loci are the major sources of gaps in genome assemblies, and gene copy number, sequence composition, and expression status of particular arrays remain elusive, especially in complex genomes harboring multiple loci. Here we conducted a multi-omics study to decipher the 45S rDNA loci in hexaploid bread wheat. Coupling chromosomal genomics with optical mapping, we reconstructed individual rDNA arrays, enabling locus-specific analyses of transcription activity and methylation status from RNA- and bisulfite-sequencing data. We estimated a total of 6,650 rDNA units in the bread wheat genome, with approximately 2,321, 3,910, 253, and 50 gene copies located in short arms of chromosomes 1B, 6B, 5D, and 1A, respectively. Only 1B and 6B loci contributed substantially to rRNA transcription at a roughly 2:1 ratio. The ratio varied among five tissues analyzed (embryo, coleoptile, root tip, primary leaf, mature leaf), being the highest (2.64:1) in mature leaf and lowest (1.72:1) in coleoptile. Cytosine methylation was considerably higher in CHG context in the silenced 5D locus as compared with the active 1B and 6B loci. In conclusion, a fine genomic organization and tissue-specific expression of rDNA loci were deciphered, for the first time, in a complex polyploid species. The results are discussed in the context of wheat evolution and transcription regulation.

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.

Genomic asymmetry in allopolyploid plants: wheat as a model

The evolvement of duplicated gene loci in allopolyploid plants has become the subject of intensive studies. Most duplicated genes remain active in neoallopolyploids contributing either to a favourable effect of an extra gene dosage or to the build-up of positive inter-genomic interactions when genes or regulation factors on homoeologous chromosomes are divergent. However, in a small number of loci (about 10%), genes of only one genome are active, while the homoeoalleles on the other genome(s) are either eliminated or partially or completely suppressed by genetic or epigenetic means. For several traits, the retention of controlling genes is not random, favouring one genome over the other(s). Such genomic asymmetry is manifested in allopolyploid wheat by the control of various morphological and agronomical traits, in the production of rRNA and storage proteins, and in interaction with pathogens. It is suggested that the process of cytological diploidization leading to exclusive intra-genomic meiotic pairing and, consequently, to complete avoidance of inter-genomic recombination, has two contrasting effects. Firstly, it provides a means for the fixation of positive heterotic inter-genomic interactions and also maintains genomic asymmetry resulting from loss or silencing of genes. The possible mechanisms and evolutionary advantages of genomic asymmetry are discussed.

Ribosomal DNA heterochromatin in plants

The aim of this review is to integrate earlier results and recent findings to present the current state-of-the-art vision concerning the dynamic behavior of the ribosomal DNA (rDNA) fraction in plants. The global organization and behavioral features of rDNA make it a most useful system to analyse the relationship between chromatin topology and gene expression patterns. Correlations between several heterochromatin fractions and rDNA arrays demonstrate the heterochromatic nature of the rDNA and reveal the importance of the genomic environment and of developmental controls in modulating its dynamics.

Genome restructuring in rye affects the expression, organization and disposition of homologous rDNA loci

The standard rye cultivar `Imperial' and a structural variant carrying an intact 1R chromosome and two telocentric 1R chromosomes (short and long arms)were used to investigate expression patterns of homologous rDNA loci, and the influence of chromosome structural change on their interphase organisation and relative disposition. Sequential silver staining and in situ hybridization with the rDNA probe pTa71, established a correspondence between the expression and organization patterns of rDNA domains in metaphase and interphase cells. In most cells of the cultivar Imperial, nucleolar organizer region (NOR)silver staining on metaphase chromosomes with equivalent numbers of rDNA genes revealed a size heteromorphism between homologous rDNA loci, resulting from their differential expression. NOR heteromorphism in the structural variant line was significantly reduced. The preferential activity of one NOR over its homologue was found to be random within cells and independent of parental origin. Nucleotypic modifications mediated by changes in the 1R chromosome structure include increased proximity between homologous rDNA loci in interphase, and an increase in the frequency of cells with intra-nucleolar ribosomal condensed chromatin. These results seem to indicate a `sequence recognition' process for the regulation of homologous loci.

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.

Nucleolar dominance does not occur in root tip cells of allotetraploid Brassica species

Using in situ hybridization and silver staining methods, the numbers of active and inactive rDNA loci have been established for three allotetraploid species of Brassica (B. napus, B. carinata, and B. juncea) and their diploid ancestors (B. campestris, B. nigra, and B. oleracea). The allotetraploid species have chromosome numbers equal to the sum of the numbers in their diploid relatives, but have fewer rDNA loci. All species investigated have lower numbers of active NORs (AgNORs, nucleolar organizer regions) compared with the numbers of rDNA sites revealed by in situ hybridization. The number of active rDNA loci of the allotetraploid species is equal to the number of AgNORs in their diploid ancestors, indicating the absence of nucleolar dominance in amphidiploid Brassica species, at least in root meristematic cells.Key words: AgNOR, Brassica, FISH, nucleolar dominance, rDNA.

The differential expression of ribosomal RNA genes

Ribosomal RNA genes are localized at chromosomal sites termed nucleolus organizers because nucleoli form around transcribed ribosomal RNA genes. The relative activities of arrays of ribosomal RNA genes can be estimated cytologically by comparing the sizes of nucleoli in the same cell. Also, active nucleolus organizers give rise to visible constrictions in metaphase chromosomes whereas inactive nucleolus organizers do not. With these assays the differential expression of nucleolus organizers and ribosomal RNA genes has been observed frequently, especially in interspecies hybrids. Studies on wheat have revealed that differences in gene expression are associated with differences in chromatin structure and cytosine methylation. Active loci have higher proportions of their genes decondensed and accessible to proteins and also higher proportions with a non-methylated cytosine residue at a CCGG site in the region of the promoter. Short, related sequences with dyad symmetry have been noted between —140 and —70 base pairs from where transcription is initiated in a wheat ribosomal RNA gene. Similar sequences are reiterated upstream of the promoter over 2000 base pairs. From comparison of this gene structure with that ofXenopusribosomal RNA genes it can be concluded that these short sequences are likely to act as enhancers of transcription by binding to specific regulatory proteins that function to stimulate the attachment of polymerase I complexes. Differential expression of arrays of ribosomal RNA genes results when genes have different numbers of enhancer repeats or a higher affinity for the regulatory protein(s). This model to explain differential gene expression and the origins of genetic variation affecting ribosomal RNA gene expression are discussed.

Detection of a variable number of ribosomal DNA loci by fluorescent in situ hybridization inPopulusspecies

Fluorescent in situ hybridization (FISH) was applied to related Populus species (2n = 19) in order to detect rDNA loci. An interspecific variability in the number of hybridization sites was revealed using as probe an homologous 25S clone from Populus deltoides. The application of image analysis methods to measure fluorescence intensity of the hybridization signals has enabled us to characterize major and minor loci in the 18S–5.8S–25S rDNA. We identified one pair of such rDNA clusters in Populus alba; two pairs, one major and one minor, in both Populus nigra and P. deltoides; and three pairs in Populus balsamifera, (two major and one minor) and Populus euroamericana (one major and two minor). FISH results are in agreement with those based on RFLP analysis. The pBG13 probe containing 5S sequence from flax detected two separate clusters corresponding to the two size classes of units that coexist within 5S rDNA of most Populus species. Key words : Populus spp., fluorescent in situ hybridization, FISH, rDNA variability, image analysis.

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.

The developmental stage of inactivation of rye origin rRNA genes in the embryo and endosperm of wheat x rye F1 hybrids

To identify the developmental stage during which the preferential inactivation of rRNA genes from the rye parent occurs in wheat x rye hybrids, nucleolar activity was evaluated in the embryo and endosperm of developing seeds of the hybrids. The hybrids were obtained from crosses of euploid and aneuploid lines of hexaploid wheat, Triticum aestivum cv. Chinese Spring, with rye, Secale cereale cv. Centeio do Alto. The number of nucleolar organizing regions (NORs) and nucleoli present in the embryo and endosperm cells of wheat, and wheat x rye F1 hybrids, at different times after fertilization was scored by silver staining. The inactivation of rDNA of rye origin in F1 hybrids occurs simultaneously in the embryo and in the endosperm between 4 and 5 days after fertilization, when these have been through six and 10 cell cycles respectively. We conclude that the genomic interactions leading to the inactivation of the rye origin rDNA is a time-dependent process, related to the developmental stage and independent of the number of cell cycles (DNA replication rounds) they have been through.

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.

Cytological events induced by arachidonic acid in potato tubers

Necrosis of potato tuber cells is enhanced, after 24 h incubation, by arachidonic acid (AA), an elicitor of the hypersensitive response in Solarium tuberosum L. and also by Fenton's reagents (a hydroxyl radical-generating system) either alone or in association with AA. The phenomenon is independent of tuber age. In aged tubers, phenylthiourea (PTU) causes a significant reduction of AA-induced cell necrosis. Necrosis observed in the presence of PTU alone is lower than in other treatments, and neither different from the controls nor affected by-tuber age. Cell size is not affected by treatments or ageing. Nuclear hypertrophy occurs independently of tuber ape, with the highest values after treatment with AA and Fenton's reagents. Nucleolar extrusion is observed in all treatments but earliest in the presence of AA. AA also enhances the number of lignified parenchymal cells and, to a lesser extent, the number of traeheary elements.

Cytochemistry and immunocytochemistry of nucleolar chromatin in plants

This review attempts to document the most relevant data currently available on the in situ localization of nucleolar chromatin on plant cells. The data provided by the most powerful and recent in situ techniques, such as DNA specific ultrastructural staining, immunogold labelling, in situ molecular cytochemistry, in situ hybridization or confocal microscopy, are summarized and discussed in the light of the potential and limitations of each individual methodology. The presence of DNA in both fibrillar centres and regions of the dense fibrillar component is extensively documented. Data on the nucleolar distribution of other important macromolecules involved in ribosomal transcription are also shown and referred to with regard to the location of DNA. The comparison with the available data on the animal cell nucleolus points towards models of similar functional organization in both plant and animal nucleoli.

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.

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.

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.

Cytological characterization, powdery mildew resistance and storage protein composition of tetraploid and hexaploid 1BL/1RS wheat-rye translocation lines

Progenies of a tetraploid 1BL/1RS wheat-rye translocation line, CV 256, selected from the cross 'Cando' x 'Veery', were analyzed by means of Giemsa C-banding. CV 256 is cytologically stable for the presence of the 1BL/1RS translocation but still segregating for A- and B-genome chromosomes of 'Cando' and 'Veery'. In CV 256, nucleolar activity of the 1RS NOR locus is suppressed, as judged by the absence of a secondary constriction in that rye segment and the capability of organizing nucleoli. PAGE analysis of prolamins confirmed the presence of two 1RS secalins in all single seeds analyzed. SDS-PAGE analysis of reduced glutenins of single seeds indicated that some seeds contained the 'Cando' Glu-B1 locus (subunits 6+8), some contained the 'Veery' Glu-B1 locus (subunits 7+9) while others contained all four subunits, indicating that the material was heterozygous. Pm8 resistance is expressed in the tetraploid 1BL/1RS translocation line based on the reactions of six well-defined powdery mildew isolates. However, Pm8 resistance is not expressed in the hexaploid wheat cultivars 'Olymp', 'Heinrich' and 'Florida', which also contain the 1BL/1RS translocation. Obviously, the existence of the 1BL/1RS translocation is not a proof for the expression of the associated genes. PAGE results did not show a clear linkage between powdery mildew resistance and the presence of 1RS secalins.

Termination of transcription of ribosomal RNA genes of mung bean occurs within a 175 bp repetitive element of the spacer region

In mung bean (Vigna radiata, formerly Phaseolus aureus) one length heterogeneity in the intergenic spacer (IGS) of the ribosomal DNA (rDNA) is due to a variable number of 175-bp subrepeats. This spacer region downstream of the 25S rRNA coding region was characterized by sequencing the 2.4 kb EcoRI/HindIII fragment of a 10.5 kb mung bean rDNA repeat. Within the 175-bp repetitive elements a sequence was detected showing strong similarity to the T2/T3-box (GACTTGC) found in Xenopus rDNA and involved in termination and enhancing transcription. In mung bean this sequence partly forms the stem of a possible stem-loop structure at the 3'end of each subrepeat. Nuclease mapping of transcription termination sites (TTS) results in two signals, 65 bp and 315 bp downstream of the 3'end of the 25S rRNA coding region. The longer transcript terminates 20 bp downstream of the stem-loop structure at the end of the first 175-bp subrepeat. A spacer model is proposed which allows "readthrough enhancement". No cross-hybridization was observed between the 180-bp subrepeats in pea (Pisum sativum) rDNA and the mung bean 175-bp subrepeat.

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.

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

Ribosomal RNA genes at different nucleolar organizer (NOR) loci in hexaploid wheat are expressed at different levels. The degree of expression of a particular organizer depends on the genetic background, especially on the presence of other NOR loci. For example, when chromosome 1U of Aegilops umbellulata is introduced into the hexaploid wheat cultivar "Chinese Spring" the A. umbellulata NOR accounts for most of the nucleolar activity and seems to suppress the activity of the wheat NOR loci. Even in wild-type "Chinese Spring", the NOR on chromosome 1B is partially dominant to that on chromosome 6B, since the 1B locus is more active in spite of having fewer genes. We have previously shown that these and other examples of nucleolar dominance in wheat are associated with undermethylation of cytosine residues in certain regions of the dominant rDNA. Here, we show that rRNA genes at dominant loci are organized in a chromatin conformation that renders them more sensitive to DNase I digestion than other rRNA genes. In addition, we have mapped several DNase I-hypersensitive sites in the intergenic spacer region of the rDNA repeating unit. Some of these sites are located near the initiation region for the 45 S rRNA precursor, while others are associated with a series of short direct repeats 5' to the 45 S rRNA initiation site. The results are discussed in terms of a model in which repeated sequences in the wheat intergenic DNA are presumed to function as upstream promoters and transcriptional enhancers similar to those in Xenopus.