Sequence specificity of methylation in higher plant DNA

Gruenbaum, Yosef; Naveh-Many, Tally; Cedar, Howard; Razin, Aharon

doi:10.1038/292860a0

Cited by 694 publications

(362 citation statements)

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“…2A, right panel). These results therefore imply that A. carterae DNA is hypermethylated at CpG motifs, as has been reported for a few higher plants (Gruenbaum et al, 1981) and algae (Jarvis et al 1992).…”

Section: Pcp and Lhc Loci Are Normally Hypermethylated At Cpg Motifs supporting

confidence: 54%

Light-Regulated Transcription of Genes Encoding Peridinin Chlorophyll a Proteins and the Major Intrinsic Light-Harvesting Complex Proteins in the DinoflagellateAmphidinium carterae Hulburt (Dinophycae)1

Lohuis

Miller

1998

Plant Physiology

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In the dinoflagellate Amphidinium carterae, photoadaptation involves changes in the transcription of genes encoding both of the major classes of light-harvesting proteins, the peridinin chlorophyll a proteins (PCPs) and the major a/c-containing intrinsic lightharvesting proteins (LHCs). PCP and LHC transcript levels were increased up to 86-and 6-fold higher, respectively, under low-light conditions relative to cells grown at high illumination. These increases in transcript abundance were accompanied by decreases in the extent of methylation of CpG and CpNpG motifs within or near PCP-and LHC-coding regions. Cytosine methylation levels in A. carterae are therefore nonstatic and may vary with environmental conditions in a manner suggestive of involvement in the regulation of gene expression. However, chemically induced undermethylation was insufficient in activating transcription, because treatment with two methylation inhibitors had no effect on PCP mRNA or protein levels. Regulation of gene activity through changes in DNA methylation has traditionally been assumed to be restricted to higher eukaryotes (deuterostomes and green plants); however, the atypically large genomes of dinoflagellates may have generated the requirement for systems of this type in a relatively "primitive" organism. Dinoflagellates may therefore provide a unique perspective on the evolution of eukaryotic DNA-methylation systems.In many respects dinoflagellates are an unusual group of chromophytic algae, their closest relatives being the apicomplexans (van der Peer et al., 1993). For example, uniquely among eukaryotes, their chromatin appears to be entirely devoid of histones (Rizzo, 1981(Rizzo, , 1991 and is not organized in the normal nucleosomal structure (Herzog and Soyer, 1981). Light harvesting is mediated in dinoflagellates by two classes of proteins, the PCPs and the LHCs. PCP, a water-soluble protein containing the carotenoid peridinin, is unique to dinoflagellates and appears to be unrelated to any other light-harvesting protein (Norris and Miller, 1994), whereas the LHCs are related to the cab proteins of higher plants (Hiller et al., 1993) and their algal homologs (for review, see Grossman et al., 1990). Both PCPs and LHCs are present in multiple forms in dinoflagellates. The functional significance of this and the nature of the interaction between these two classes of lightharvesting proteins are completely unknown. Chromophyte chloroplasts appear to lack many of the mechanisms known to be central to photoadaptation in chlorophytes, such as lateral mobility of photosynthetic complexes and stacking/unstacking of thylakoids. One hypothesis is that the multiple forms of light-harvesting proteins fulfill related roles in dinoflagellates, i.e. that the synthesis of different PCP and LHC complements facilitates photoadaptation.In Amphibinium carterae, both PCPs and LHCs are encoded by nuclear genes (Hiller et al., 1995;Sharples et al., 1996) and synthesized with N-terminal transit peptides directing chloroplast translocation (Norris and...

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Section: Pcp and Lhc Loci Are Normally Hypermethylated At Cpg Motifs supporting

confidence: 54%

Light-Regulated Transcription of Genes Encoding Peridinin Chlorophyll a Proteins and the Major Intrinsic Light-Harvesting Complex Proteins in the DinoflagellateAmphidinium carterae Hulburt (Dinophycae)1

Lohuis

Miller

1998

Plant Physiology

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“…If the enzyme used has cleavage sites within the element, but at a distance of more than 1 kb from the end containing its transcription initiation site, the observed fragments are those expected if all of the sites are methylated and therefore resistant to digestion. This is true both for enzymes inhibited by the methylation of the C residue in the dinucleotide CG and for those inhibited by methylation of the C residue in the trinucleotide CNG, which is c o m m o n l y methylated in plant DNA (Gruenbaum et al 1981). Representative blots illustrating the outcome of such experiments with the restriction endonucleases PstI and PvuII are shown in Figure 3B.…”

Section: The Spm Element Is Methylated Extensively But the A Gene Ismentioning

confidence: 99%

Molecular mechanisms in the developmental regulation of the maize Suppressor-mutator transposable element.

Banks¹,

Masson²,

Fedoroff³

1988

Genes Dev.

199

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The maize Suppressor-mutator (Spm) element can exist in one of three heritable forms: (1) a stably active form, (2) a stably inactive form, termed cryptic, and (3) a labile form, here termed programmable, in which the element exhibits one of a variety of heritable developmental programs of expression. Active elements are transcribed and are hypomethylated at sites upstream of the transcription start site, whereas inactive elements are transcriptionally silent and largely methylated at the upstream sites. Active (both stable and programmable), inactive programmable, and cryptic elements are unmethylated, partially methylated, and fully methylated, respectively, at sites within an 0.35-kb 80% G + C region just downstream from the transcription start site. An active Spin element in a genome with a cryptic element promotes its partial demethylation but not its transcriptional activation. In contrast, a trans-acting Spin promotes extensive demethylation and transcriptional activation of an inactive programmable element, as well as its heritable reactivation. These observations define the molecular components of the Spin element's developmental regulatory mechanism. We discuss their general relevance to the developmental regulation of gene expression.[ 1957, 1958, 1959, 1965aPeterson 1966;Fowler and Peterson 1978). These include the cryptic form, in which the element is genetically silent. Both McClintock and Peterson also identified elements that were capable of undergoing reversible transitions between the active and inactive phases in a characteristic and heritable pattern during development (McClintock 1957(McClintock , 1958(McClintock , 1962(McClintock , 1965a(McClintock , b, 1971Peterson 1966;Fowler and Peterson 1978). We showed recently that the genetic mechanism responsible for the developmental control of Spin expression has two components, which we designated the phase setting and the phase program (Fedoroff and Banks 1988). The phase setting determines whether the element is genetically active or inactive. The phase program determines the heritability of the phase setting, as well as when, where, and how frequently it will be reversed during plant development. The underlying genetic mechanism is heritable, reversible, and capable of promoting the incremental transition of the element from a stably active to a stably inactive (cryptic) form, implying the involvement of multiple epigenetic events (Fedoroff and Banks 1988). In view of the accumulating evidence that the inactivation of gene expression, in general (for reviews, see Razin et al. 1984;Adams and Burdon 1985;Holliday 1987;Cedar 1988), and maize transposable elements, in particular Bennetzen 1985;Chandler and Walbot 1986;Schwartz and Dennis 1986;Chomet et al. 1987; Fedoroff et al. 1988a, b)

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“…In plants, 5-methyl cytosine is the most common methylated base occurring in up to 30 per cent of all C (Gruenbaum et al, 1981) in plants and an estimated 25.7 per cent in barley (Amasino et a!., 1990b). Changes in methylation status have been reported previously in barley when HpaII-and MspIdigested DNA from anther-culture derived doubled haploids of cv.…”

Section: Location Of Quantitative Traitsmentioning

confidence: 99%

Analysis of quantitative traits in barley by the use of Amplified Fragment Length Polymorphisms

Powell¹,

Thomas²,

Baird³

et al. 1997

Heredity

120

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Amplified fragment length polymorphisms (AFLPs) produced with EcoRI and PstI both in combination with MseI restriction enzymes have been studied in the parents of four barley mapping populations. Averages of 15.9 and 18.7 polymorphic products per assay were produced for the EcoRI/MseI and PstI/MseI combinations, respectively. There was some evidence of interaction between cross combinations and restriction enzyme combinations, with PstI/MseI generating relatively more polymorphic products than EcoRI/MseI in the Blenheim x E224/3 cross combination, the least polymorphic of the four. Three hundred and ninety-eight AFLP products, using both restriction enzyme combinations, were generated in a doubled haploid population of 68 lines produced from the Blenheim x E224/3 cross. These were added to existing marker data for the cross to study the effects of incorporation of AFLPs produced by different restriction enzyme combinations upon genetic maps. Addition of the AFLP data resulted in greater genome coverage, both through linking previously separate groups and extensions to other groups. This increase in coverage appeared to result from AFLPs sampling some different regions of the genome compared to RAPDs and RFLPs, as the map distances spanned by the RAPD and RFLP linkage groups were similar with and without incorporation of AFLPs. There was also evidence that the EcoRI and PstI restriction enzymes sampled different regions of the genome. The revised maps were used in scanning for QTLs controlling a subset of 12 economically important traits measured in the cross. Overall, the QTLs accounted for an average of 53 per cent of the phenotypic variation for the characters. Positive and negative alleles were present in each parent for each character, apart from hot water extract corrected to 1.5 per cent nitrogen (HWEc). Several regions of the genome appeared to be involved in the control of several characters, notably chromosome 2, the denso locus on chromosome 3, the short arm of chromosome 5 and chromosome 7.Although there was considerable similarity to previous results of QTL mapping for the subset of characters, the greater genome coverage afforded by the inclusion of the AFLPs revealed some new QTL locations.Keywords: AFLPs, barley, genes, mapping, markers, QTL.Introduction this technology has been widely deployed in plants (Helentjaris & Burr, 1989). However, the RFLP AFLPS AND QUANTITATIVE TRAITS IN BARLEY 49& Vos, 1993). Two important aspects of a marker system's utility are: information content and multiplex ratio . Standard measures of diversity may be used to evaluate information content and the multiplex ratio is the number of loci simultaneously analysed per experiment. These two metrics have been used to compare RFLPs, AFLPs, SSRPs and RAPDs in common soybean and barley genotypes (Powell et a!., , 1995. Multiplex ratio and the diversity index were combined to provide an overall measure of marker utility defined as the Marker Index. To date, all comparative studies concur in identifying AFLP as an unique tec...

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Sequence specificity of methylation in higher plant DNA

Cited by 694 publications

References 17 publications

Light-Regulated Transcription of Genes Encoding Peridinin Chlorophyll a Proteins and the Major Intrinsic Light-Harvesting Complex Proteins in the DinoflagellateAmphidinium carterae Hulburt (Dinophycae)1

Light-Regulated Transcription of Genes Encoding Peridinin Chlorophyll a Proteins and the Major Intrinsic Light-Harvesting Complex Proteins in the DinoflagellateAmphidinium carterae Hulburt (Dinophycae)1

Molecular mechanisms in the developmental regulation of the maize Suppressor-mutator transposable element.

Analysis of quantitative traits in barley by the use of Amplified Fragment Length Polymorphisms

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