Generation of enhancer trap lines in <i>Arabidopsis</i> and characterization of expression patterns in the inflorescence

Campisi, Lauren; Yang, Yingzhen; Yi, Young-Byung; Heilig, Elizabeth; Herman, Bram; Cassista, A J; Allen, David W.; Xiang, Hongjun; Jack, Thomas

doi:10.1046/j.1365-313x.1999.00409.x

Cited by 161 publications

(125 citation statements)

References 44 publications

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“…The reporter gene will be activated if the construct is integrated into a position adjacent to an enhancer (or a promoter). A large number of enhancer/ promoter trapping lines were developed in several plant species, including Arabidopsis (Sundaresan et al, 1995;Campisi et al, 1999), rice (Oryza sativa) (Wu et al, 2003;Yang et al, 2004;Johnson et al, 2005), and poplar (Populus trichocarpa) (Groover et al, 2004). Unfortunately, the enhancer trapping approach has a major drawback.…”

Section: Efficiency Of Dhs-based Enhancer Prediction In Arabidopsismentioning

confidence: 99%

Genome-Wide Prediction and Validation of Intergenic Enhancers in Arabidopsis Using Open Chromatin Signatures

et al. 2015

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Enhancers are important regulators of gene expression in eukaryotes. Enhancers function independently of their distance and orientation to the promoters of target genes. Thus, enhancers have been difficult to identify. Only a few enhancers, especially distant intergenic enhancers, have been identified in plants. We developed an enhancer prediction system based exclusively on the DNase I hypersensitive sites (DHSs) in the Arabidopsis thaliana genome. A set of 10,044 DHSs located in intergenic regions, which are away from any gene promoters, were predicted to be putative enhancers. We examined the functions of 14 predicted enhancers using the b-glucuronidase gene reporter. Ten of the 14 (71%) candidates were validated by the reporter assay. We also designed 10 constructs using intergenic sequences that are not associated with DHSs, and none of these constructs showed enhancer activities in reporter assays. In addition, the tissue specificity of the putative enhancers can be precisely predicted based on DNase I hypersensitivity data sets developed from different plant tissues. These results suggest that the open chromatin signature-based enhancer prediction system developed in Arabidopsis may serve as a universal system for enhancer identification in plants.

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Section: Efficiency Of Dhs-based Enhancer Prediction In Arabidopsismentioning

confidence: 99%

Genome-Wide Prediction and Validation of Intergenic Enhancers in Arabidopsis Using Open Chromatin Signatures

et al. 2015

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“…1G). As abscission zones are thought to be specified in the proximal regions of the floral organs as they differentiate, enhancer trap lines with early expression profiles at the bases of wild-type floral organs (Campisi et al, 1999) were examined in nev flowers (see Fig. S1 in the supplementary material).…”

Section: Mutations In Nev Prevent Floral Organ Sheddingmentioning

confidence: 99%

Regulation of membrane trafficking and organ separation by the NEVERSHED ARF-GAP protein

et al. 2009

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Cell separation, or abscission, is a highly specialized process in plants that facilitates remodeling of their architecture and reproductive success. Because few genes are known to be essential for organ abscission, we conducted a screen for mutations that alter floral organ shedding in Arabidopsis. Nine recessive mutations that block shedding were found to disrupt the function of an ADP-ribosylation factor-GTPase-activating protein (ARF-GAP) we have named NEVERSHED (NEV). As predicted by its homology to the yeast Age2 ARF-GAP and transcriptional profile, NEV influences other aspects of plant development, including fruit growth. Colocalization experiments carried out with NEV-specific antiserum and a set of plant endomembrane markers revealed that NEV localizes to the trans-Golgi network and endosomes in Arabidopsis root epidermal cells. Interestingly, transmission electron micrographs of abscission zone regions from wild-type and nev flowers reveal defects in the structure of the Golgi apparatus and extensive accumulation of vesicles adjacent to the cell walls. Our results suggest that NEV ARF-GAP activity at the trans-Golgi network and distinct endosomal compartments is required for the proper trafficking of cargo molecules required for cell separation.

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“…The remaining reporter gene constructs were generated by placing AG DNA fragments upstream of a deletion derivative ( Ϫ 60) of the cauliflower mosaic virus (CaMV) 35S promoter (Benfey and Chua, 1990). This minimal promoter does not itself confer a GUS staining pattern and thus has been a useful tool in enhancer-trap experiments (Campisi et al, 1999).We transformed each of these constructs into Arabidopsis (ecotype Landsberg erecta ) and characterized the GUS staining pattern of the transgenic plants (Figure 1). We observed some variability in stain intensity between independently transformed plants.…”

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confidence: 99%

Separable Whorl-Specific Expression and Negative Regulation by Enhancer Elements within the AGAMOUS Second Intron

2000

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We analyzed the 4-kb intragenic control region of the AGAMOUS ( AG ) gene to gain insight into the mechanisms controlling its expression during early flower development. We identified three major expression patterns conferred by 19 AG ::reporter gene constructs: the normal AG pattern, a stamen-specific pattern, and a predominantly carpel pattern. To determine whether these three expression patterns were under negative control by APETALA2 ( AP2 ) or LEUNIG ( LUG ), we analyzed ␤ -glucuronidase staining patterns in Arabidopsis plants homozygous for strong ap2 and lug mutations. Our results indicated that the stamen-specific pattern was independent of AP2 but dependent on LUG; conversely, the carpel-specific pattern was independent of LUG but dependent on AP2. These results lead to a model of control of AG expression such that expression in each of the two inner whorls is under independent positive and negative control. INTRODUCTIONSpatial and temporal control of expression of genes responsible for floral organ identity is critical for normal flower development. Three classes of organ identity genes (classes A, B, and C) have been characterized both genetically and molecularly (reviewed in Irish, 1999;Ng and Yanofsky, 2000). Phenotypic analyses of plants that are mutant for an organ identity gene have shown that genes from each of these classes contribute to the specification of organ identity in two adjacent whorls. Furthermore, except for APETALA2 ( AP2 ), RNA coding for the organ identity genes also is predominantly expressed in a two-whorl domain. The importance of restricting expression to the normal domains is illustrated by the altered identities of organs observed in flowers of transgenic plants engineered to misexpress organ identity genes (Mandel et al., 1992;Mizukami and Ma, 1992;Krizek and Meyerowitz, 1996;Jack et al., 1997).Expression patterns of the class C organ identity gene AGAMOUS ( AG ) have been carefully documented (Bowman et al., 1991b;Drews et al., 1991). Early in flower development, AG RNA is first detected in the central apical region of late stage 3 floral meristems. As the organs emerge, AG RNA is found throughout the third-and fourth-whorl organ primordia (which give rise to stamens and carpels, respectively) but not in the two outer whorls (the sources of sepals and petals). As the floral organs are maturing, AG continues to be expressed in the third-and fourth-whorl organs. However, rather than the uniform pattern observed during early stages, by the time the flower opens, AG RNA is found only in specific types of stamen and carpel cells.How is the early flower expression pattern of AG RNA achieved? Genes that control AG expression were first identified on the basis of mutant phenotypes that suggested AG misexpression (Bowman et al., 1991a; Weigel et al., 1992;Weigel and Meyerowitz, 1993;Liu and Meyerowitz, 1995;Goodrich et al., 1997). Subsequent in situ hybridization analyses confirmed altered expression of AG and led investigators to distinguish between genes that function as either ...

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Generation of enhancer trap lines in Arabidopsis and characterization of expression patterns in the inflorescence

Cited by 161 publications

References 44 publications

Genome-Wide Prediction and Validation of Intergenic Enhancers in Arabidopsis Using Open Chromatin Signatures

Genome-Wide Prediction and Validation of Intergenic Enhancers in Arabidopsis Using Open Chromatin Signatures

Regulation of membrane trafficking and organ separation by the NEVERSHED ARF-GAP protein

Separable Whorl-Specific Expression and Negative Regulation by Enhancer Elements within the AGAMOUS Second Intron

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