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A molecular-cytogenetic method for locating genes to pericentromeric regions facilitates a genomewide comparison of synteny between the centromeric regions of wheat and rice.

ABSTRACT: 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 + 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.

SUBMITTER: Qi L

PROVIDER: S-EPMC2787417 | biostudies-literature | 2009 Dec

REPOSITORIES: biostudies-literature

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A molecular-cytogenetic method for locating genes to pericentromeric regions facilitates a genomewide comparison of synteny between the centromeric regions of wheat and rice.

Qi Lili L Friebe Bernd B Zhang Peng P Gill Bikram S BS

Genetics 20090921 4

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 Ce ...[more]

PMID: 19797045

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Project description:BACKGROUND:The centromeric and pericentromeric regions of plant chromosomes are colonized by Ty3/gypsy retrotransposons, which, on the basis of their reverse transcriptase sequences, form the chromovirus CRM clade. Despite their potential importance for centromere evolution and function, they have remained poorly characterized. In this work, we aimed to carry out a comprehensive survey of CRM clade elements with an emphasis on their diversity, structure, chromosomal distribution and transcriptional activity. RESULTS:We have surveyed a set of 190 CRM elements belonging to 81 different retrotransposon families, derived from 33 host species and falling into 12 plant families. The sequences at the C-terminus of their integrases were unexpectedly heterogeneous, despite the understanding that they are responsible for targeting to the centromere. This variation allowed the division of the CRM clade into the three groups A, B and C, and the members of each differed considerably with respect to their chromosomal distribution. The differences in chromosomal distribution coincided with variation in the integrase C-terminus sequences possessing a putative targeting domain (PTD). A majority of the group A elements possess the CR motif and are concentrated in the centromeric region, while members of group C have the type II chromodomain and are dispersed throughout the genome. Although representatives of the group B lack a PTD of any type, they appeared to be localized preferentially in the centromeres of tested species. All tested elements were found to be transcriptionally active. CONCLUSIONS:Comprehensive analysis of the CRM clade elements showed that genuinely centromeric retrotransposons represent only a fraction of the CRM clade (group A). These centromeric retrotransposons represent an active component of centromeres of a wide range of angiosperm species, implying that they play an important role in plant centromere evolution. In addition, their transcriptional activity is consistent with the notion that the transcription of centromeric retrotransposons has a role in normal centromere function.

Project description:Nuclear structures ND10/PML NBs are linked to multiple processes, including the maintenance of intranuclear homeostasis by sequestering proteins into "nuclear depot." This function presumes release of proteins from PML NBs and their redistribution to the alternative, supposedly "active" locations, in response to the external stress application. To further investigate this nuclear depot function, we focused on the intranuclear distribution of protein Daxx that in normal conditions is mainly accumulated at PML NBs, and has a minor association with centromeres and pericentromeres (CEN/periCEN). Here we report that application of physiological Heat Shock (HS) changes this balance forcing very robust and reversible accumulation of Daxx on CEN/periCEN heterochromatin. Heterochromatin architecture is essential for the proper orchestration of nuclear processes, while transcription from this part of genome is required for its maintenance. To understand functional consequences of Daxx deposition at CEN/periCEN, we tested for Daxx-dependency of heterochromatin transcription. Depletion of Daxx reduces accumulation of CEN RNA in normal conditions and periCEN RNA after HS application. Searching for the mechanism of Daxx-dependent regulation of heterochromatin transcription, we found that depletion of Daxx decreases incorporation of transcription-associated histone H3 variant, H3.3, into both CEN and periCEN. Surprisingly, HS-induced deposition of Daxx does not further elevate incorporation of H3.3 into CEN/periCEN that remained steady during stress and recovery. Instead, depletion of Daxx leads to HS-induced changes in the balance of epigenetic modifications at heterochromatin, most dramatically elevating levels of active H3K4Me2 modification at periCEN. We propose dualistic function of Daxx-containing complexes at CEN/periCEN: (1) regulation of H3.3 loading in normal conditions and (2) protection of epigenetic status upon stress-induced accumulation, thus collectively guarding epigenetic identity of CEN/periCEN heterochromatin.

Dataset Information

A molecular-cytogenetic method for locating genes to pericentromeric regions facilitates a genomewide comparison of synteny between the centromeric regions of wheat and rice.

Publications

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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