Chromatin structure of integrated T-DNA in crown gall tumors

Coates, David; Taliercio, Earl; Gelvin, Stanton B.

doi:10.1007/bf00025327

Cited by 21 publications

(15 citation statements)

References 32 publications

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“…It is becoming increasingly apparent that high levels of heritability and gene expression may be dependent on the genomic environment and local topology of chromosome structure (Bennett, 1982;Chyi et aL, 1986;Coates, Taliercio & Gelvin, 1987). Thus, in addition to detailed information at the coding level, a knowledge of the relevant higher-order characteristics of compatible genomes will be of assistance.…”

Section: Discussionmentioning

confidence: 99%

Genome Heterogeneity and Classification of the Poaceae

King

Ingrouille

1987

New Phytologist

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SUMMARYIntragenomic base composition heterogeneity was investigated in 35 species of the grass family Poaceae, using high-resolution thermal denaturation of DNA to produce base composition distributions. These show a pattern of peaks and shoulders which represent overlapping components of discrete base composition and provide a 'fingerprint' of the genome of a species. Quantitative comparison of distribution by distance matrix and cluster analysis supported traditional groupings within the Poaceae and allowed clarification of previous artificial relationships between taxa. The technique was most successful in distinguishing between taxa within subfamily, from tribal to generic level. Use of an absolute measure of all sequences present in a genome avoids problems inherent in commonly used DNA/DNA hybridization methods for determining homology. The non-random distribution of DNA base composition components conserved among related genomes is discussed in relation to chromosome architecture and to exploitation of the gene pool of the Poaceae.

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Section: Discussionmentioning

confidence: 99%

Genome Heterogeneity and Classification of the Poaceae

King

Ingrouille

1987

New Phytologist

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“…DNAs (10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20) ,ug) were suspended in 400 ,uL 88% of formic acid, then hydrolyzed to individual bases by incubation at 120°C for 90 min. The bases were separated on a BeckmanUltrasphere IP C18 column (4.6 x 150 mm) in 10 mm potassium phosphate (pH 5.6), 5 mM hexanesulfonic acid, 0.7% methanol at a flow rate of 1 mL/min.…”

Section: Determination Of the M5c Levels By Hplc Analysismentioning

confidence: 99%

“…A similar correlation was found for pea rRNA genes (29). However, it has not always been possible to correlate patterns of DNA methylation with expression of specific genes or with nuclease accessibility of chromatin in plants (10,22,28).In this study, we examined the relationship between chromatin structure and DNA methylation on a genome-wide level. We found that a DNaseI-sensitive chromatin configuration is associated with a reduced level of DNA methylation.…”

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DNA Methylation is Reduced in DNasel-Sensitive Regions of Plant Chromatin

Klaas¹,

Amasino²

1989

Plant Physiol.

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Pea, barley, and com chromatin was isolated and subjected to limited digestion with DNasel. The preferentially degraded, small molecular weight fraction, presumably consisting of sequences in an active state of expression, was isolated and its 5-methylcytosine content determined. The DNasel-sensitive chromatin fraction from all three plant species investigated contained a markedly reduced level of DNA methylation compared to total DNA.The DNA of higher animals and plants contains the modified base m5C4 in the sequence CG and, in plants, CNG (N = any base). Only a fraction of the cytosines occurring in these sequences are methylated (13), and the distribution of cytosine methylation is not random. High levels of m5C are found in unexpressed regions ofgenomes, such as centromeric and heterochromatic areas of animal chromosomes (20), several types of satellite DNA (6), and inactive mammalian Xchromosomes (14). A number of studies have demonstrated that certain genes are undermethylated in tissues where they are actively expressed, but highly methylated in tissues (or different developmental stages of the same tissue) where the genes are silent (8). Thus, DNA methylation is postulated to be a determinant of gene expression.Chromatin containing actively expressed genes (or genes that are poised for expression) is maintained in a structure that renders it more susceptible to nuclease attack, and presumably more accessible to transcription factors, than chromatin containing inactive genes (30). This nuclease-sensitive fraction of animal chromatin has been shown to have a reduced level of methylation (I1, 21). In addition, the nuclease-sensitive fraction of animal chromatin is enriched in HMG-proteins and depleted in histone HI (4,31 'Abbreviation: m5C, 5-methylcytosine. 451Plant genomes are methylated to a far greater extent than animal genomes. Up to 40% of the cytosine residues are modified in certain plant species, compared to 4 to 6% in mammals (1). The role, however, of DNA methylation in the plant genome is not well understood. The relationship between plant DNA methylation and gene expression has been primarily examined for specific T-DNA (2, 12, 15, 23) and transposon insertions (9,25). In all of these cases, expression has been found to correlate with reduced methylation. In addition, the methylation state ofa maize seed storage protein gene was recently found to correlate with its expression at different developmental stages (7). Although a relationship between chromatin structure and gene activity has been found for a number of plant genes (17 and references therein), and HMG-like proteins have been implicated in the determination of plant chromatin structure (26), little is known about the relationship between DNA methylation and plant chromatin structure. In a study of T-DNA expression in tobacco cells, Reid et al. (24) found a correlation between nuclease-sensitive chromatin, gene expression, and reduced methylation of the T-DNA insertion. A similar correlation was found for pea rRNA genes (29). H...

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“…A high frequency of reporter gene activity is observed after integration of promoterless reporter genes which is obviously due to gene fusions to endogenous promoters (16)(17)(18). Moreover, it has been shown for crown gall tumor lines (19) as well as for transgenic tobacco plants (20) that genes which are transferred by the Agrobacterium Ti plasmid are integrated in DNase I-sensitive domains and hence are associated with an 'open' chromatin conformation.…”

Section: Introductionmentioning

confidence: 99%

A plant scaffold attached region detected close to a T-DNA integration site is active in mammalian cells

et al. 1994

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Integration of foreign genes into plant genomes by the Agrobacterlum T-DNA transfer system has been considered to occur at random. It has been speculated that the chromosomal structure of the integration site might affect the expression pattern of the introduced genes. To gain insight into the molecular structure of T-DNA integration sites and its possible impact on gene expression, we have examined plant DNA sequences In the vicinity of T-DNA borders. Analysis of a transgenic petunia plant containing a chloramphenicol acetyltransferase (CAT) gene regulated by the hemoglobin promoter (PAR) from Parasponia andersonii revealed a scaffold attachment region (SAR) close to one T-DNA end. In addition to having strong binding affinities for both animal and plant nuclear scaffolds this petunia SAR element is as active in mammalian cells as the authentic elements from mammalian sources.

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Chromatin structure of integrated T-DNA in crown gall tumors

Cited by 21 publications

References 32 publications

Genome Heterogeneity and Classification of the Poaceae

Genome Heterogeneity and Classification of the Poaceae

DNA Methylation is Reduced in DNasel-Sensitive Regions of Plant Chromatin

A plant scaffold attached region detected close to a T-DNA integration site is active in mammalian cells

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