James Birchler

..The probes were demonstrated to produce signals in several wild relatives of maize, including Zea luxurians, Z. diploperennis, and Tripsacum dactyloides...

..These results demonstrate that telomere-mediated chromosomal truncation operates in plant species. This technology will be useful for chromosomal engineering in maize as well as other plant species...

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..Gene balance effects are hypothesized to result from stoichiometric differences among members of macromolecular complexes, the interactome, and signaling pathways. The implications of gene balance are discussed...

..These and other studies described suggest there are negative fitness consequences when an imbalance occurs for members of macromolecular complexes including regulatory functions...

..In a recent report in Nature, de Vanssay and colleagues (2012) describe in Drosophila an operationally analogous phenomenon to paramutation that is mediated by piwi-interacting RNAs...

..In two different Arabidopsis species, a related element was recognized in which the specificity for such targeting was altered. These observations provide a partial explanation for how homogenization of centromere DNA sequences occurs...

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..Several groups have recently succeeded in analyzing centromeric sequences in human, Drosophila and Arabidopsis, providing new insights into the importance of DNA sequence for centromere function...

..In this article we will summarize the evidence for this potential synthesis...

..1,2) The results suggest that a common mechanism might operate in these different cases...

..The uses of engineered minichromosomes are discussed...

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..Under some circumstances, inactive centromeres can exhibit reactivation at their formerly inactive sites. This observation suggests that a DNA-based topological component also operates for centromere identity...

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..The discovery of a novel RNA-dependent RNA polymerase activity with a eukaryote-wide distribution raises new questions about the roles and mechanisms of gene silencing by small RNAs...

..A careful documentation of the modulations of gene expression in aneuploids should provide insight into the nature of cancerous cells and the basis of aneuploid syndromes...

..While we do not provide a comprehensive model to explain the phenomenology of heterosis, we provide the details of what needs to be explained and a direction of pursuit that we feel should be fruitful...

..Here we present evidence for epigenetic and structural aspects involved with centromere activity in plants...

..These observations are not consistent with the hypothesis that the MSL complex conditions dosage compensation. A synthesis is described that can account for these observations...

..In this article, we discuss the potential contribution of regulatory balance to the control of quantitative traits, hybrid vigor, genome evolution and post-zygotic speciation mechanisms...

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..The silencing mechanisms potentially act as a protection against high expression of transposons and viruses...

..Moreover, because the majority of dosage-dependent regulators act negatively, this property can account for the up-regulation of genes in monosomics and hemizygous sex chromosomes to achieve dosage compensation...

..RNA silencing processes in Drosophila are described...

..These mutations result in reduction of H3 Lys9 methylation and delocalization of HP1 and HP2, most dramatically in spindle-E mutants...

..Mutations in piwi, which belongs to a gene family with members required for RNAi, block PTGS and one aspect of TGS, indicating a connection between the two types of silencing...

..These analyses suggest that meiotic centromeric cohesion is compromised in minichromosomes depending on their size and cannot be maintained by the mechanisms used by normal-sized chromosomes...

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..Later the active component was found to be a dsRNA (Fire et al. 1998). In subsequent years, it has been found to occur in diverse eukaryotes..

..Finally, we detected small interfering RNAs (siRNAs) in plants carrying C2-Idf, but not in plants homozygous for the wild-type C2 allele. Together, our results indicate that the inhibitory effect of C2-Idf occurs through RNA silencing...

..These Pc-associated sequences are involved with the control of the proper expression of developmental HOX genes...

..The results indicate the ability of the somatic karyotyping system to recognize and characterize chromosomal aberrations...

..Instead, transcript levels in the diploid hybrids correlate negatively with the levels in diploid inbreds. Although transcript levels were clearly nonadditive, transcript levels in triploid hybrids were affected by genomic dosage...

..Also, intergenic regions are implicated as targets in Arabidopsis...

..The other source is genotype specific and results in a response to ploidy change that varies among inbred lines. This finding demonstrates the existence of genetic variation for the morphological response to ploidy change in Zea mays...

..Lethal hybrid rescue (Lhr), which allows hybrid males from this cross to survive, corrects the SXL and MSL defects. The reciprocal cross of D. simulans mothers by D. melanogaster males exhibits underexpression of Sxl in embryos...

..Using the LTR divergence of retroelements interrupting the B-specific sequences, the minimum age of the StarkB repeat array and, by inference, of the B chromosome, was estimated to be 2 million years...

..The placement of the cre/lox site-specific recombination system in many locations in the maize genome will be valuable materials for gene targeting and chromosome engineering...

..Overall, the results indicate that the heterotic response of tetraploid maize lines differs significantly from that of the diploid...

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..Interploidy crosses between diploid and tetraploid derivatives of the same inbred exhibit changes in the chromatin organization of centromeres and heterochromatic knobs...

..These findings also indicate a structural aspect to centromere specification revealed by the gain of activity at the site of the previously inactive sequences...

..Overall, we find that gene expression trends mirror observations from the phenotypic studies; however, obvious mechanistic connections remain unknown...

..Therefore, the B's non-disjunctive capacity, previously thought to be primarily restricted to the gametophyte, is present in sporophytic cells...

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..We conclude that healing of broken maize centromeres can be achieved through the mechanisms of addition or fusion of telomeric repeat sequences to the broken centromere...

..This work demonstrates the utility of FISH and karyotyping in the study of transposon activity and its consequences...

..Although the homologous centromeres were not paired, they were always correctly oriented at anaphase and migrated to opposite poles. Additionally, recombination on 8L was severely repressed in the hybrid...

..Recently, it was demonstrated that the introduction of telomere sequences into plants cells causes truncation of the chromosomes, and that this technique can be used to produce artificial chromosome platforms...

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..The inactivation of the centromeres was stable for at least four generations. By using dicentrics from dispensable chromosomes, centromere inactivation was found to be quite common under these circumstances...

..These platforms will provide avenues for studies on plant chromosome structure and function and for future developments in biotechnology and agriculture...

..The successful tetraploid inbred lines were from the A188, B73, H99, Oh43, Stock 6, and W22 genetic backgrounds. Aneuploids, plants with broken chromosomes and chimeras, were also found among the treated materials...

..Root-tip chromosome karyotype analysis was also performed on material with and without Cre expression. Chromosomal aberrations in Cre+ material were not observed above the background level...

..Such karyotype analysis opens new avenues for the study of chromosomal variation and behavior, as well as for the localization of individual genes and transgenes to genomic position...

..The probe collection can be used as chromosomal landmarks or as a "banding paint" for the physical mapping of sequences including transgenes and BAC clones and for studying chromosomal rearrangements...

..The data confirm that this translocation is widespread in G. soja accessions and likely accounts for the semi-sterility found in some G. soja by G. max crosses...

..Differences were detectable, suggesting either that mtDNA is being incorporated or lost from the maize nuclear genome continuously. The results indicate that mtDNA insertions represent a major source of nuclear chromosomal variation...

..With long exposures, smaller sites of hybridization are detected at the ends of chromosomes, adjacent to the telomere tract. This distal position for knob satellites is conserved among Zea and Tripsacum species...

..The same probe mixture identifies meiotic pachytene, late prophase I, and metaphase I chromosomes. The procedure could facilitate the study of chromosomal structure and behavior and be adapted for other plant species...

..Thus, this technique can be easily extended to all plant species. The engineered minichromosome technology can also be used in combination with site-specific recombination systems to facilitate the stacking of multiple transgenes...

..Our results demonstrate that the amount of CENH3 at the B centromere can be varied, but with decreasing amounts, the function of the centromere becomes impaired...

..Furthermore, in some organisms RNAi silences unpaired DNA regions during meiosis. These mechanisms facilitate the directed silencing of specific genomic regions...

..CR elements as well as their flanking centromeric satellite DNA are actively transcribed in maize. These data suggest that the deposition of centromeric histones might be a transcription-coupled event...

..New research approaches are being used to study these mechanisms and the results should provide a more complete understanding of polyploidy...

..Approximately 38 and 33% of CentC and CRM are precipitated in the chromatin immunoprecipitation assay, consistent with data showing that much, but not all, of CENH3 colocalizes with CentC...

..The proposed project will contribute to an understanding of how chromatin modifications become established along the length of the chromosome and how they affect gene expression. ..

..The single active X chromosome in humans of both males and females must be up-regulated for viability. The proposed project will examine the type of mechanism responsible for this up-regulation. ..