Organization of retro-element and stem-loop repeat families in the genomes and nuclei of cereals

Abbo, Shahal; Dunford, Roy P.; Foote, Tracie; Reader, S. M.; Flavell, R. B.; Moore, Graham

doi:10.1007/bf00711156

Cited by 31 publications

(27 citation statements)

References 26 publications

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“…Recently, these repeats have been found to be nested retrotransposons that comprise a small number of families of highly re-iterated transposons of conserved structure and therefore relatively recent origin (19)(20)(21). Similar observations have been made in other cereals including wheat (22)(23)(24). These transposons are heavily methylated, when compared with genes (25).…”

mentioning

confidence: 54%

Functional genomics: Probing plant gene function and expression with transposons

Martienssen

1998

Proc. Natl. Acad. Sci. U.S.A.

206

128

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Transposable elements provide a convenient and f lexible means to disrupt plant genes, so allowing their function to be assessed. By engineering transposons to carry reporter genes and regulatory signals, the expression of target genes can be monitored and to some extent manipulated. Two strategies for using transposons to assess gene function are outlined here: First, the PCR can be used to identify plants that carry insertions into specific genes from among pools of heavily mutagenized individuals (site-selected transposon mutagenesis). This method requires that high copy transposons be used and that a relatively large number of reactions be performed to identify insertions into genes of interest. Second, a large library of plants, each carrying a unique insertion, can be generated. Each insertion site then can be amplified and sequenced systematically. These two methods have been demonstrated in maize, Arabidopsis, and other plant species, and the relative merits of each are discussed in the context of plant genome research.

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mentioning

confidence: 54%

Functional genomics: Probing plant gene function and expression with transposons

Martienssen

1998

Proc. Natl. Acad. Sci. U.S.A.

206

128

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“…Searching in the GenBank database did not find any significant matches to these sequences except for pRCH2. Bases 39-102 and 204-232 in pRCH2 had sequence identities to the centromeric CCS1 sequence isolated from B. sylvaticum (16,25). Interestingly, about 120 bp (bases 8-130) of this element had 80% sequence identity to the spacer sequence that separates the rice 5S rRNA genes.…”

Section: Isolation Of Bac Clones Derived From Rice Centromericmentioning

confidence: 94%

Rice ( Oryza sativa ) centromeric regions consist of complex DNA

Dong

Miller

Jackson

et al. 1998

Proc. Natl. Acad. Sci. U.S.A.

202

158

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Rice bacterial artificial chromosome clones containing centromeric DNA were isolated by using a DNA sequence (pSau3A9) that is present in the centromeres of Gramineae species. Seven distinct repetitive DNA elements were isolated from a 75-kilobase rice bacterial artificial chromosome clone. All seven DNA elements are present in every rice centromere as demonstrated by f luorescence in situ hybridization. Six of the elements are middle repetitive, and their copy numbers range from Ϸ50 to Ϸ300 in the rice genome. Five of these six middle repetitive DNA elements are present in all of the Gramineae species, and the other element is detected only in species within the Bambusoideae subfamily of Gramineae. All six middle repetitive DNA elements are dispersed in the centromeric regions. The seventh element, the RCS2 family, is a tandem repeat of a 168-bp sequence that is represented Ϸ6,000 times in the rice genome and is detected only in Oryza species. Fiber-f luorescence in situ hybridization analysis revealed that the RCS2 family is organized into long uninterrupted arrays and resembles previously reported tandem repeats located in the centromeres of human and Arabidopsis thaliana chromosomes. We characterized a large DNA fragment derived from a plant centromere and demonstrated that rice centromeres consist of complex DNA, including both highly and middle repetitive DNA sequences.Centromeres are one of the most characteristic landmarks of eukaryotic chromosomes. The centromeric region is the site for mitotic and meiotic spindle fiber attachment and is responsible for sister chromatid association. Thus centromeres play a central role in the process of chromosomal segregation and transmission in cell divisions. The molecular organization of centromeres has been studied extensively in yeast, Drosophila melanogaster, and humans. Whereas the centromeres of budding yeast (Saccharomyces cerevisiae) chromosomes are structurally simple, specified by only a 125-bp, single-copy DNA sequence (1-2), the centromeres from higher eukaryotic species, such as D. melanogaster and humans, encompass several hundred kilobases (kb) or even megabases of DNA and contain repetitive DNA sequences (3-7).Thus far, only limited information is available for the organization of plant centromeres. Peacock et al. (8) first isolated a repetitive DNA element from the maize knobs that can act as neocentromeres in certain genetic backgrounds. A repetitive DNA element also was cloned from the centromeres of the supernumerary B chromosomes of maize (9-10). Part of this B-specific DNA element shows strong homology to the maize knob sequences. A 180-bp tandem repeat (pAL1 family) is the major component of the centromeric regions of Arabidopsis thaliana chromosomes. The genomic organization of this repeat family shares similarities to the alpha satellite DNA at the human centromeres (11)(12)(13)(14). Recently, two repetitive DNA elements, pSau3A9 and CCS1, were isolated from sorghum (Sorghum bicolor) (15) and Brachypodium sylvaticum (16), respectivel...

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“…Positive BAC clones for specific genes digested with HindIII were first screened with three centromere-specific clones pAet6-09, Hi10, and pRCS1 to reveal their potential centromeric locations (Abbo et al 1995;Dong et al 1998;P. Zhang et al 2004).…”

Section: Methodsmentioning

confidence: 99%

A Molecular-Cytogenetic Method for Locating Genes to Pericentromeric Regions Facilitates a Genomewide Comparison of Synteny Between the Centromeric Regions of Wheat and Rice

Friebe

Zhang³

et al. 2009

Genetics

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Centromeres, because of their repeat structure and lack of sequence conservation, are difficult to assemble and compare across organisms. It was recently discovered that rice centromeres often contain genes. This suggested a method for studying centromere homologies between wheat and rice chromosomes by mapping rice centromeric genes onto wheat aneuploid stocks. Three of the seven cDNA clones of centromeric genes from rice centromere 8 (Cen8), 6729.t09, 6729.t10, and 6730.t11 which lie in the Cen8 kinetochore region, and three wheat ESTs, BJ301191, BJ305475, and BJ280500, with similarity to sequences of rice centromeric genes, were mapped to the centromeric regions of the wheat group-7 (W7) chromosomes. A possible pericentric inversion in chromosome 7D was detected. Genomewide comparison of wheat ESTs that mapped to centromeric regions against rice genome sequences revealed high conservation and a one-to-one correspondence of centromeric regions between wheat and rice chromosome pairs W1-R5, W2-R7, W3-R1, W5-R12, W6-R2, and W7-R8. The W4 centromere may share homology with R3 only or with R3 1 R11. Wheat ESTs that mapped to the pericentromeric region of the group-5 long arm anchored to the rice BACs located in the recently duplicated region at the distal ends of the short arms of rice chromosomes 11 and 12. A pericentric inversion specific to the rice lineage was detected. The depicted framework provides a working model for further studies on the structure and evolution of cereal chromosome centromeres.

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Organization of retro-element and stem-loop repeat families in the genomes and nuclei of cereals

Cited by 31 publications

References 26 publications

Functional genomics: Probing plant gene function and expression with transposons

Functional genomics: Probing plant gene function and expression with transposons

Rice ( Oryza sativa ) centromeric regions consist of complex DNA

A Molecular-Cytogenetic Method for Locating Genes to Pericentromeric Regions Facilitates a Genomewide Comparison of Synteny Between the Centromeric Regions of Wheat and Rice

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