Adaptive methylation pattern of ribosomal DNA in wild barley from Israel (original) (raw)
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Scientific reports, 2014
Genomic methylation is variable under biotic and abiotic stresses in plants. In particular, viral infection is thought to significantly increase genomic methylation with particularly high activity around transposable elements. Here we present the genomic methylation profiles of grains of archaeological barley (Hordeum vulgare) from several strata from a site in southern Egypt, from the Napatan to the Islamic periods (800 BCE - 1812 CE). One sample tested positive for viral infection and exhibits an unusually high degree of genomic methylation compared to the rest. A decreasing trend in global methylation levels according to deposition date shows in-situ de-methylation of 5-methylcytosine, which can be described as a diagenetic process. This is most likely a deamination mediated de-methylation process and is expected to lead to 5 mC > T base modifications in addition to the C > U modifications due to cytosine deamination, so represents a time-dependent process of DNA diagenesis...
Adaptive ribosomal DNA polymorphism in wild barley at a mosaic microsite, Newe Ya’ar in Israel
Plant Science, 2004
In eukaryotic genomes, ribosomal DNA is organized in tandem repeat units at the nucleolar organizing regions (NORs) on each satellited chromosome. Each repeat unit consists of a coding region and an intergenic spacer (IGS), the latter generally varying in length at different loci of the same genotype and also at the same locus in different genotypes. The spacer length variants (slvs) are sometimes correlated with climatic and ecological variables. In a study of 42 accessions of wild barley (Hordeum spontaneum) collected from four different microniches (sun-deep soil, sun-shallow soil, shade-deep soil and shade-shallow soil) at the Newe Ya'ar microsite (3182 m 2 ), in Israel, we observed eight slvs constituting 10 different rDNA phenotypes, correlated with edaphic conditions prevalent at the four microniches. We conclude that rDNA diversity in wild barley is distributed nonrandomly and adaptively in the four microniches of Newe Ya'ar. A novel feature in this study is also the homogenization of IGS length at the two loci located at two nonhomologous chromosomes. Fluorescence in situ hybridization (FISH), was used to rule out the possibility of loss of one of the two NOR loci.
Protoplasma, 2010
A reconstructed barley karyotype (T-35) was utilised to study the influence of chromosomal rearrangements on the DNA methylation pattern at chromosome level. Data obtained were also compared with the distribution of Giemsa N-bands and high gene density regions along the individual chromosomes that have been previously described. In comparison to the control karyotype (T-1586), the DNA methylation pattern was found to vary not only in the reconstructed chromosomes but also in the other chromosomes of the complement. Significant remodelling process of methylation pattern was found also in the residual nucleolus organiser regions (NOR) on chromosome 5H as a consequence of deletion comprising the whole NOR of chromosome 6H in T-35. Moreover, differences between corresponding segments of the homologues with respect to some other chromosome locations were also observed. Repositioning of genomic DNA methylation along the metaphase chromosomes following chromosomal reconstruction in barley seems to be essential to ensure correct chromatin organisation and function.
2012
Summary. The methylation pattern of rRNA genes in reconstructed barley karyotypes ( Hordeum vulgare L.) with altered position or structure of the two nucleolus organizers (NORs) was studied by double digestion with EcoRI and HhaI and molecular hybridization with specifi c rDNA probes. The lack of the whole rRNA gene cluster residing in chromosome 6H in the homozygous deletion line T-35 led to an increased hypomethylation of the rRNA genes in the remaining NOR5H. On the other hand, repositioning by translocation of the distant part of the split NOR6H to the short arm of the chromosome 5H in the translocation line T-21 did not correlate with any signifi cant changes in the methylation of –GCGC– sequences in rDNA units. In addition, the length of the intergenic spacer (IGS) in both reconstructed barley lines T35 and T21 was also analyzed. Our results showed the same length of IGS in the long rDNA repeat as compared with previously published rDNA clone (GenBank HQ825319). However, the s...
Plant Science, 2004
Ribosomal DNA (rDNA) repeat unit length polymorphism was examined in 285 accessions of wild barley, Hordeum spontaneum C. Koch, which were collected from 27 locations across Jordan. As many as 19 spacer length variants (slvs) or rDNA alleles were available, which formed 70 slv phenotypes. The two missing alleles (098, 099) of the series (097, 100-118) and one additional allele 119 were also discovered in the present study thus raising the number of ribosomal slvs in barley to 24. Relatively more frequent rDNA alleles were analyzed in detail, and it was shown that they occurred non-randomly at locations with different environmental factors (annual rainfall, highest and lowest temperatures, altitude, longitude, latitude) and exhibited association with specific environments. Ecogeographical factors, rather than geographical factors per se, seem to affect the distribution of rDNA alleles. The present study thus demonstrates that rDNA repeat unit length polymorphism in some cases can be adaptive in nature.
Proceedings of the National Academy of Sciences, 1990
DNA from 267 accessions of wild barley from ecologically diverse habitats in Israel and Iran and from 92 accessions of cultivated barley from throughout the world were assayed for the 20 ribosomal DNA (rDNA) spacer-length variants that have been identified in the barley species. These 20 spacer-length variants, which are detectable by Southern blot hybridization, serve as markers of rDNA alleles of two Mendelian loci, Rrnl and Rrn2. All of the populations of wild barley studied were polymorphic for both loci. In wild barley allele 112 (Rrnl) and allele 107 (Rrn2) behaved as widely adapted wild-type alleles; in our sample of cultivated barley allele 112 also behaved as a wild-type allele but allele 104 was somewhat more frequent than allele 107 in Rrn2. A few other alleles were locally frequent in wild barley. However, most of the 20 alleles were infrequent or rare and such alleles were often associated as "hitchhikers" with one of the wild-type alleles in compound two-component alleles. Allelic and genotypic frequencies differed widely in different habitats in correlation with eight of nine factors of the physical environment. Discrete log-linear multivariate analyses revealed statistically significant associations among alleles of Rrnl and Rrn2. It was concluded that natural selection acting differentially on various rDNA alleles plays a major role in the development and maintenance of observed patterns of molecular and genetic organization of rDNA variability.
Differential rRNA Genes Expression in Hexaploid Wheat Related to NOR Methylation
Plant Molecular Biology Reporter, 2010
Ribosomal RNA genes expression was analysed in 18 Portuguese bread wheat accessions (Triticum aestivum L. em Thell.), and the number of argyrophilic-nucleolar organiser regions (Ag-NORs) per cultivar was scored. Ten accessions presented six Ag-NORs per metaphase and six nucleoli per interphase, and eight accessions presented four Ag-NORs per metaphase and four nucleoli per interphase. Fluorescent in situ hybridisation with the 45S rDNA sequence pTa71 and genomic DNA from Aegilops tauschii (2n = 2x= 14, DD) confirmed the Ag-NOR location and identified the six satellited chromosomes as being the chromosome pairs 1B, 6B and 5D. The methylation pattern of the NOR region was studied by Southern blot using pTa71 as probe, which represented a complete rDNA unit of bread wheat. DNA digestions performed by MspI and HpaII resulted in different patterns revealing the high level of cytosine methylation at their recognition sequences. The total percentage values of NOR methylation indicated that wheat accessions with a maximum of four Ag-NORs were more heavily methylated at the NOR region than accessions with a maximum of six Ag-NORs.
The methylation status of DNA derived from potato plants recovered from slow growth
Plant Cell, Tissue and Organ Culture, 1994
The in vitro conservation of potato using tissue culture medium supplemented with the growth retardant mannitol causes morphological changes in the propagated material. These culture conditions seem to have an affect on the DNA extracted from the regenerated plants, when it is digested by the methylation sensitive restriction enzymes Hpa II/Msp I and Eco RII/Bst NI, compared to the control material. In most of these plants, there appears to be preferential methylation of nuclear domains that contain Eco RII/Bst NI recognition sites in contrast to those that contain Hpa II/Msp I sites. The refractory nature of the isolated DNA to these restriction enzymes was attributed to hypermethylation of genomic DNA and the ribosomal RNA genes. These findings indicate that methylation of DNA sequences may be an adaptive response to conditions of high osmotic stress. The importance of these results for the conservation of potato germplasm and international exchange is discussed.
DNA Methylation Mechanism [Working Title], 2020
The barley (Hordeum vulgare) genome comprises over 32,000 genes, with differentiated cells expressing only a subset of genes; the remainder being silent. Mechanisms by which tissue-specific genes are regulated are not entirely understood, although DNA methylation is likely to be involved. To shed light on the dynamic of DNA methylation during development and its variation between organs, methylation-sensitive genotyping by sequencing (ms-GBS) was used to generate methylation profiles for roots, leaf-blades and leaf-sheaths from five barley varieties, using seedlings at the three-leaf stage. Robust differentially methylated markers (DMMs) were characterised by pairwise comparisons of roots, leaf-blades and leaf-sheaths of three different ages. While very many DMMs were found between roots and leaf parts, only a few existed between leaf-blades and leaf-sheaths, with differences decreasing with leaf rank. Organspecific DMMs appeared to target mainly repeat regions, implying that organ differentiation partially relies on the spreading of DNA methylation from repeats to promoters of adjacent genes. Identified DMMs indicate that different organs do possess diagnostic methylation profiles and suggest that DNA methylation is important for both tissue differentiation and organ function and will provide the basis to the understanding of the role of DNA methylation in plant organ differentiation and development.