Chromatin structure and gene regulation in higher plants

Transgene expression variability (position effect) of CAT and GUS reporter genes driven by linked divergent T-DNA promoters

Forty-five individually transformed clonal tobacco callus lines were simultaneously assayed for both chloramphenicol acetyltransferase (CAT) and beta-glucuronidase (GUS) activity resulting from expression of introduced reporter genes driven by the adjacent and divergent mannopine (mas) promoters. Excluding lines in which one or both of the enzyme activities was essentially zero, the activities of the reporter genes varied by as much as a factor of 136 (CAT) and 175 (GUS) between individual transformants. Superimposed upon the high degree of inter-clonal expression variability was an intra-clonal variability of 3-4-fold. The observed degree of intra-clonal reporter gene activity may be more extreme because of the regulatory characteristics of the mannopine promoters, but must still be addressed when considering the limitations of reporter gene-based analysis of transgene function and structure. There was no consistent correlation between the expression levels of the introduced CAT and GUS genes since the ratio of GUS to CAT activities (nmol min-1 mg-1) within individual lines varied from 0.05 to 49. Even divergent transcription from two directly adjacent promoter regions (both contained within a 479 bp TR-DNA fragment) is insufficient to guarantee concurrent expression of two linked transgenes. Our quantitative data were compared to published data of transgene expression variability to examine the overall distribution of expression levels in individual transformants. The resulting frequency distribution indicates that most transformants express introduced transgenes at relatively low levels, suggesting that a potentially large number of Agrobacterium-mediated transformation events may result in silent transgenes.

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.

Electrophoretic heterogeneity of maize histones

Histones from maize embryos and seedlings have been isolated using a fast extraction procedure. Three different electrophoretic systems have been applied for the study of the heterogeneity of maize core histones. Electrophoresis in acetic acid/urea polyacrylamide gels, containing high concentrations of urea, resulted in optimum fractionation of the core histones and especially of histone H4. Sodium dodecyl sulfate-containing polyacrylamide gels were not useful for the fractionation of maize histone classes H2a and H2b, nor for the various subfractions of H3 and H4. Gels containing Triton X-100, used for the dimension in two-dimensional electrophoresis proved to be efficient for the separation of all histone classes, as well as their structural variants and chemical modifications. Maize core histones have been oxidized in an attempt to define which of the Triton X-100 resolved subfractions represent oxidation forms.

The primary structure of the histone H2A(2) type from wheat germ. A core histone type with both, N-terminal and C-terminal extensions

The histone H2A(2) type from wheat germ comprises at least two highly homologous isohistones with 151 amino acid residues. Microheterogeneity occurs mainly at the N-terminal and C-terminal regions. These isohistones have both N-terminal (7 amino acid residues) and C-terminal (15 amino acid residues) extensions relative to calf thymus histone H2A.

The amino acid sequence of wheat histone H2B(2). A core histone with a novel repetitive N-terminal extension

Two of the four electrophoretic histone H2B variants present in wheat embryos have been isolated. The complete primary structure of the H2B(2) variant has been deduced from sets of overlapping peptides generated by CNBr cleavage, Staphylococcus aureus V8 protease, endoproteinase Arg-C, the post-proline cleaving enzyme, chymotrypsin and cleavage in dilute acid. A minimum of 17 peptides were required to establish the sequence. This variant has a blocked N terminus and comprises a total of 149 amino acids. The C-terminal two-thirds of the protein are highly homologous to vertebrate H2B. In contrast, the N-terminal third is entirely different and contains an N-terminal extension of 23 residues in which the sequence Ala-Glu-Lys or variants are repeated several times. This region is also highly homologous to the H2B from Tetrahymena pyriformis. It shows in addition similarities to wheat H2A(1) and bovine H1.

DNase I hypersensitive sites in the 5'-region of the maize Shrunken gene in nuclei from different organs

The chromatin structure of the 5'-upstream region of the Shrunken (Sh) gene in Zea mays has been examined. We have identified a region of DNase I hypersensitivity extending at least from the 3'-end of exon 1 for 2 kb into the 5'-flanking region. This region is composed of a set of closely spaced hypersensitive sites separated by small regions that are less accessible to DNase I. The most sensitive sites are located within 300 bp upstream of the transcription start site. Hypersensitive sites are found essentially at the same positions in kernels, roots and leaves, although the latter display different relative intensities. No changes are found in roots within the tested region upon anaerobic induction. Testing protein-free plasmid DNA containing the 5' upstream region of the Sh gene, we found a site sensitive to the single strand specific nuclease S1 located very close to a DNase I hypersensitive site identified in chromatin. Several hypersensitive sites are flanking in vitro binding sites of nuclear proteins as determined by Werr et al. (1988; accompanying paper).

DNase I hypersensitivity and expression of the Shrunken-1 gene of maize

The local chromatin structure of the Shrunken-1 (Sh) gene of maize was probed by analyzing DNase I hypersensitivity. Sh encodes the gene for sucrose synthetase, a major starch biosynthetic enzyme, which is maximally expressed in the endosperm during seed maturation. In addition to general DNase I sensitivity, specific DNase I hypersensitive sites were identified in endosperm chromatin that mapped near the 5' end of the Sh gene. The pattern of hypersensitive sites and their relative sensitivity were altered in other non-dormant tissues that produce little or no enzyme. However, some changes in chromatin structure appear to be independent of Sh gene expression and may reflect general alterations associated with plant development. The chromatin structure of several sh mutations, induced by Ds controlling element insertions, was also analyzed. Although the insertions perturbed expression of the gene, there were no notable effects on local chromatin structure.

Chromatin structure of integrated T-DNA in crown gall tumors

We have investigated the chromatin structure of the integrated T-DNA in two N. tabacum crown gall tumor lines, and compared the results to those obtained in a previous study of the methylation patterns of these same integrated DNA sequences (Gelvin et al., Nucleic Acids Res. 11:159-174, 1983). The E9 octopine-type tumor contains a single copy of TL, whose transcription is essential for tumor maintenance, and 15-30 copies of TR, a non-essential region. The HT37#15 nopaline type teratoma contains a single copy of the nopaline T-DNA. All these integrated sequences can be found associated with nucleosomes, although the diffuse nature of the nucleosome bands on Southern transfers implies an 'open' chromatin conformation. In addition, all the sequences are more sensitive to digestion with deoxyribonuclease I than the bulk of the chromatin. We present evidence suggesting that, despite the previously published data that the majority of copies of the TR-DNA are highly methylated at the sequence CCGG whereas the TL-DNA is not, the majority of copies of the TR-DNA in the E9 tumor line are in the same chromatin conformation as TL. These data therefore suggest that most of the copies of TR-DNA are likely to be transcriptionally competent.

A study on the heterogeneity of histone H1 from dry maize embryos

Maize dry embryo cells have been chosen as model for the study of H1 histone complement of metabolically inactive plant chromatin. H1 has been fractionated into two distinct bands in acetic acid/urea gels. Analysis of each of these bands in SDS-containing gels has shown that maize embryo H1 is heterogeneous, consisting of at least six proteins. Cross-reactivity of maize H1 species with antibodies against mouse liver total H1 and against its individual variants indicates that they share common immunological determinants but differ substantially from each other when compared by peptide mapping. It is concluded that a couple of the plant H1 subfractions are related to animal H1A histone and that another one is related to H1B histone. The other three maize H1 variants are closely related to each other and they also share common immunological determinants with mouse H1A, and possibly with H1B. All maize H1 species slightly cross-react with antibodies against H1 degree, suggesting that no one of the plant subfractions could be characterized as H1 degree in particular. One of the proteins co-extracted and comigrating with H1 is most probably an embryo storage protein.

Insertion of the Mu1 transposable element into the first intron of maize Adh1 interferes with transcript elongation but does not disrupt chromatin structure

The presence of the Mu1 transposable element within the first intervening sequence of the maize Adh1 gene interfered with transcription through that gene. Insertion of the element did not have an apparent effect on transcription initiation or chromatin structure. In nuclei isolated from anaerobically induced roots, in which Adh1 is transcriptionally active, a subset of the Adh1 chromatin is arranged in a unique conformation characterized by a generalized sensitivity to nucleases, specific DNAase I sensitive sites and a nucleosome array distinct from the inactive configuration present in leaf nuclei. The chromatin organization of the Mu1-induced mutant alleles is indistinguishable from that of the progenitor Adh1-S allele and a point mutant allele that is null for ADH1 activity. The initiation of transcription also proved to be unaffected in these mutants. Nuclear runoff experiments indicated that Adh1 sequences upstream from the point of Mu1 insertion were transcribed normally, but sequences downstream to the insertion were drastically reduced relative to a reference gene expressed in anaerobic root nuclei. Thus, it was concluded that the defect in these Mu1-induced mutants does not reside at the level of gene accessibility or transcript initiation. Rather, Mu1 presents an impediment to the progress of the polymerase II complex during transcript elongation.

Tissue-specific and light-dependent changes of chromatin organization in barley (Hordeum vulgare)

The DNase I sensitivity of the nuclear genes encoding the NADPH-protochlorophyllide oxidoreductase, the light-harvesting chlorophyll a/b protein (LHCP), the hordeins and a 15-kDa protein of unknown function was assayed in chromatin of etiolated and green leaves and endosperm tissue of barley (Hordeum vulgare L.). A tissue-specific differentiation of chromatin structure was found for the LHCP, hordein and 15-kDa protein genes. The genes for the LHCP and the 15-kDa protein, which are expressed in leaf tissue, display DNase I sensitivity in leaves but not in endosperm. Hordein genes which are expressed solely in endosperm, were insensitive to low levels of digestion with DNase I in leaves but sensitive in endosperm. The effect of light on chromatin structure was determined by comparing leaves of etiolated plants and plants which had been grown under a day/night cycle. Only in the case of the 15-kDa protein is there a remarkable change from a DNAse-I-sensitive configuration in etiolated leaves to a more resistant one in leaves from illuminated plants. The gene for the NADPH-protochlorophyllide oxidoreductase was found to be equally sensitive to DNase I in leaves and endosperm.

A simple and efficient procedure for isolating plant chromatin which is suitable for studies of DNase I-sensitive domains and hypersensitive sites

A simple and rapid procedure has been developed for the isolation of chromatin from plant leaves. The molecular weight of the DNA extracted from these chromatin preparations is comparable to that of DNA isolated by a conventional purification procedure (CTAB-CsCl-method). These results suggest that almost no degradation occurs during the isolation procedure. The effect of DNase I on three different groups of genes was studied; one of them, encoding the NADPH-protochlorophyllide oxidoreductase (PCR), represents a gene which is actively transcribed in etiolated leaf tissue. The other genes examined encode the hordein seed storage protein and 26S ribosomal RNA. The hordein genes are known to be inactive in leaves.The hordein and rDNA genes were found to be resistant to low levels of DNase I, while the gene for the PCR was highly sensitive to DNase I. During the course of digestion of the PCR gene, discrete cleavage products are generated. These indicate the presence of DNase I hypersensitive sites in the vicinity of the PCR gene in etiolated leaves. As a control 'naked' DNA has been digested with DNase I. No differences in sensitivity between the PCR gene and the hordein genes can be detected.