Qiudeng Que - Academia.edu (original) (raw)

Papers by Qiudeng Que

Cold Spring Harbor Symposia on Quantitative Biology, 2006

We describe features of RNA silencing and associated epigenetic imprints that illustrate potentia... more We describe features of RNA silencing and associated epigenetic imprints that illustrate potential roles for RNA interference (RNAi) in maintenance and transmission of epigenetic states between cells, throughout a plant, and perhaps even across sexual generations. Three types of transgenes can trigger RNAi of homologous endogenous plant genes: (1) &amp;quot;sense&amp;quot; transgenes that overexpress translatable transcripts, (2) inverted repeat (IR) transgenes that produce double-stranded RNA (dsRNA), and (3) antisense transgenes. Each mode of RNAi produces a different characteristic developmental silencing pattern. Single-copy transgenes are sufficient for sense-RNAi and antisense-RNAi, but not inverted repeat-RNAi. A single premature termination codon dramatically attenuates sense-RNAi, but it has no effect on antisense or inverted repeat-RNAi. We report here that antisense transgenes altered by removal of nonsense codons generate silencing patterns characteristic of sense-RNAi. Duplication of a sense overexpression transgene results in two types of epigenetic events: (1) complete loss of silencing and (2) altered developmental pattern of silencing. We also report that duplicating only the transgene promoter results in complete loss of silencing, whereas duplicating only transcribed sequences produces the second class, which are vein-based patterns. We infer that the latter class is due to systemic RNA silencing signals that interact with certain epigenetic states of the transgene to imprint it with information generated at a distance elsewhere in the plant.

Frontiers in Plant Science, 2014

Maize is an important food and feed crop in many countries. It is also one of the most important ... more Maize is an important food and feed crop in many countries. It is also one of the most important target crops for the application of biotechnology. Currently, there are more biotech traits available on the market in maize than in any other crop. Generation of transgenic events is a crucial step in the development of biotech traits. For commercial applications, a high throughput transformation system producing a large number of high quality events in an elite genetic background is highly desirable. There has been tremendous progress in Agrobacterium-mediated maize transformation since the publication of the Ishida et al. (1996) paper and the technology has been widely adopted for transgenic event production by many labs around the world. We will review general efforts in establishing efficient maize transformation technologies useful for transgenic event production in trait research and development. The review will also discuss transformation systems used for generating commercial maize trait events currently on the market. As the number of traits is increasing steadily and two or more modes of action are used to control key pests, new tools are needed to efficiently transform vectors containing multiple trait genes. We will review general guidelines for assembling binary vectors for commercial transformation. Approaches to increase transformation efficiency and gene expression of large gene stack vectors will be discussed. Finally, recent studies of targeted genome modification and transgene insertion using different site-directed nuclease technologies will be reviewed.

Plant Journal, 1998

A single-copy sense Chalcone synthase (Chs) transgene driven by a strong promoter and producing a... more A single-copy sense Chalcone synthase (Chs) transgene driven by a strong promoter and producing a fully translatable transcript was converted to an allelic antisense Chs transgene by Cre-lox-mediated DNA recombination in petunia. The sense Chs allele suppressed flower pigmentation in a simple pattern determined by cells at the junctions between adjacent petals, as is typical of single-copy sense Chs transgenes of this type, whereas the antisense Chs allele produced a different pattern of Chs suppression with white petal edges and reduced pigmentation throughout the petal limbs, as is typical of antisense Chs transgenes. In plants carrying a lox-flanked Chs transgene, the presence of Cre protein can cause both sense-specific and antisense-specific patterns to be superimposed in the same flower, suggesting that sense and antisense suppression by single-copy transgenes are mediated by different mechanisms or occur in different cellular or developmental compartments. The presence of Cre also causes the production of numerous, non-clonal white spots, suggesting that the turnover state is not cell-autonomous.

Plant Physiology - PLANT PHYSIOL, 2003

Agrobacterium tumefaciens T-DNA normally integrates into random sites in the plant genome. We hav... more Agrobacterium tumefaciens T-DNA normally integrates into random sites in the plant genome. We have investigated targeting of T-DNA by nonhomologous end joining process to a specific double-stranded break created in the plant genome by I-CeuI endonuclease. Sequencing of genomic DNA/T-DNA junctions in targeted events revealed that genomic DNA at the cleavage sites was usually intact or nearly so, whereas donor T-DNA ends were often resected, sometimes extensively, as is found in random T-DNA inserts. Short filler DNAs were also present in several junctions. When an I-CeuI site was placed in the donor T-DNA, it was often cleaved by I-CeuI endonuclease, leading to precisely truncated targeted T-DNA inserts. Their structure requires that T-DNA cutting occurred before or during integration, indicating that T-DNA is at least partially double stranded before integration is complete. This method of targeting full-length T-DNA with considerable fidelity to a chosen break point in the plant ge...

Trends in Genetics, 1999

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The Plant Cell, 1997

By comparing the effects of strong and weak promoters that drive sense chalcone synthase (Chs) tr... more By comparing the effects of strong and weak promoters that drive sense chalcone synthase (Chs) transgenes in large populations of independently transformed plants, we show here that a strong transgene promoter is required for highfrequency cosuppression of Chs genes and for production of the full range of cosuppression phenotypes. In addition, sense Chs transgenes driven by a cauliflower mosaic virus 35s promoter possessing a single copy of the upstream activator region (UAR) were found to produce a significantly lower degree of cosuppression than they did when the transgene promoter possessed two or four copies of the UAR. It has been shown elsewhere that 35s promoter strength increases with increasing UAR copy number. Frameshift mutations producing early nonsense codons in the Chs transgene were found to reduce the frequency and the degree of cosuppression. These results suggest that promoter strength and transcript stability determine the degree of cosuppression, supporting the hypothesis that sense cosuppression is a response to the accumulation of transcripts at high concentrations. This conclusion was shown to apply to single-copy transgenes but not necessarily to inversely repeated transgenes. The results presented here also have significance for efficient engineering of cosuppression phenotypes for use in research and agriculture.

Plant Molecular Biology, 1996

Flower pigmentation patterns were scored in 185 sense Chalcone synthase (Chs) transgenotes and 85... more Flower pigmentation patterns were scored in 185 sense Chalcone synthase (Chs) transgenotes and 85 antisense Chs transgenotes; upon first flowering, 139 (75%) of sense transgenotes were found to be phenotypically altered, as were 70 (82%) of the antisense transgenotes. The observed patterns document the range of phenotypic variations that occur, as well as confirm and extend the finding that sense Chs constructs produce several types of morphology-based flower pigmentation patterns that antisense Chs constructs do not. Long-term monitoring for epigenetic variations in one population of 44 sense Chs transgenotes showed that 43 (98%) were capable of producing a cosuppression phenotype. The primary determinant of sense-specific patterns of cosuppression of Chs was found to be the repetitiveness and organization pattern of the transgene, not &amp;amp;amp;#39;position effects&amp;amp;amp;#39; by, or &amp;amp;amp;#39;readthrough&amp;amp;amp;#39; from, flanking plant DNA sequences. The degree of cosuppression observed in progeny of transgenotes carrying multiple, dispersed copies as compared to that observed with a single copy of the transgene suggests that sense cosuppression of Chs is subject to a transgene dosage effect.

Developmental Genetics, 1998

Plant transgenes may participate in two types of homology-based gene silencing. One requires tran... more Plant transgenes may participate in two types of homology-based gene silencing. One requires transcript homology, is post-transcriptional, and is referred to as cosuppression; the other requires promoter homology, is transcriptional, and is similar to paramutation. This paper uses flower color transgenes to address the hierarchical operation of both mechanisms in plants carrying two transgene copies. It is shown that cosuppression of homologous, endogenous flower color genes by single-copy transgenes requires that the transgene be driven by a strong promoter and that the degree of cosuppression is highly sensitive to increasing transgene dosage. Together, these observations suggest that cosuppression should be a sensitive reporter of epigenetic changes in transgene transcription, such as might be caused by paramutation-like interactions between transgene loci. Intercrosses bringing together two homologous transgene loci, one a known epimutable reporter and the other a transgene inverted repeat, result in complete loss of cosuppression in some outcross progeny and a qualitative change in morphology-based patterns of cosuppression in other outcross progeny. This paramutation-like behavior suggests that the transgenes may be altered at the transcriptional level, eliminating cosuppression altogether or changing the spatial pattern of transgene transcription to produce a new pattern of cosuppression. Dev. Genet. 22:100-109, 1998. 1998

Functional plant biology, Dec 24, 2002

Transgenes designed to overexpress anthocyanin genes An6 (encoding dihydroflavonol-4-reductase) o... more Transgenes designed to overexpress anthocyanin genes An6 (encoding dihydroflavonol-4-reductase) or Hf1 (encoding flavonoid-3′, 5′-hydroxylase) in Petunia hybrida L. produced flower colour phenotypes similar to those caused by sense ...