Splice Site Requirements and Switches in Plants

Schuler, Mary A.

doi:10.1007/978-3-540-76776-3_3

Cited by 29 publications

(30 citation statements)

References 92 publications

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“…A normal ESP transcript, and hence the 238 bp amplicon, is generated by splicing the unique ESP intron at a canonical 5 0 splice site AG-GT (exon-intron) for Mt-0 and a non-canonical AG-AT 5 0 splice site for Col-0 (Barbazuk et al 2008;Reddy 2007). Although the GT to AT mutation of the 5 0 splice site we observed for ESP in Col-0 seems to be a rather rare event, it has been reported for other plant genes leading to diverse effects including intron retention and consequently premature translation termination (Schuler 2008). The 350 bp amplicon in Col-0 is generated by the use of a distal 5 0 splice site with a CG-GT sequence and situated 110 bp downstream into the intron ( Fig.…”

Section: Characterisation Of An Alternative Splicing Event For Espmentioning

confidence: 41%

Ecotype dependent expression and alternative splicing of epithiospecifier protein (ESP) in Arabidopsis thaliana

et al. 2012

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Epithiospecifier protein (ESP) is responsible for diverting glucosinolate hydrolysis from the generation of isothiocyanates to that of epithionitriles or nitriles, and thereby negatively affects the ability of the plant to defend itself against certain insects. Despite this important role of ESP, little is known about its expression in plant tissues and the regulation thereof. We therefore investigated ESP expression by qPCR and Western blot in different organs during the growth cycle of the two Arabidopsis thaliana ecotypes Col-0 and Mt-0. Besides the fact that ESP transcript and protein levels were revealed to be much higher in Mt-0 than in Col-0 in all cases, our qPCR results also indicated that ESP expression is regulated differently in the two A. thaliana ecotypes. No ESP protein was detected by Western blot in any organ or developmental stage for Col-0. During the assays an alternative splice variant of ESP was identified in Col-0, but not Mt-0, leading to a mis-spliced transcript which could explain the low expression levels of ESP in the former ecotype. Analysis of genomic sequences containing the ESP splice sites, of ESP protein level and ESP activity from seven A. thaliana ecotypes showed a positive correlation between the presence of a non-canonical 5' splice site for ESP and the absence of detectable ESP protein levels and ESP activity. When analysing the expression of both transcript variants in Col-0 after treatment with methyl jasmonate, a condition known to "induce ESP", it was indeed the alternative splice variant that was preferentially induced.

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Section: Characterisation Of An Alternative Splicing Event For Espmentioning

confidence: 41%

Ecotype dependent expression and alternative splicing of epithiospecifier protein (ESP) in Arabidopsis thaliana

et al. 2012

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“…2A), with the only discernible difference being localized to the cleavage site. This difference probably reflects the marked tendency of plant introns to be U-rich (20,21) and thus to have a lower C content than would be seen near a "normal" poly(A) site. Other than this, the base composition profiles of 3′-UTR (as in Fig.…”

Section: Resultsmentioning

confidence: 94%

Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation

Liu

Downie³

et al. 2011

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

269

380

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Alternative polyadenylation (APA) has been shown to play an important role in gene expression regulation in animals and plants. However, the extent of sense and antisense APA at the genome level is not known. We developed a deep-sequencing protocol that queries the junctions of 3′UTR and poly(A) tails and confidently maps the poly(A) tags to the annotated genome. The results of this mapping show that 70% of Arabidopsis genes use more than one poly(A) site, excluding microheterogeneity. Analysis of the poly(A) tags reveal extensive APA in introns and coding sequences, results of which can significantly alter transcript sequences and their encoding proteins. Although the interplay of intron splicing and polyadenylation potentially defines poly(A) site uses in introns, the polyadenylation signals leading to the use of CDS protein-coding region poly(A) sites are distinct from the rest of the genome. Interestingly, a large number of poly(A) sites correspond to putative antisense transcripts that overlap with the promoter of the associated sense transcript, a mode previously demonstrated to regulate sense gene expression. Our results suggest that APA plays a far greater role in gene expression in plants than previously expected.alternative processing | antisense transcription | nonstop mRNAs

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“…Similar to other eukaryotes, plant pre-mRNA splicing is a nuclear process that involves the recognition of exon–intron junctions by the spliceosome (Brown and Simpson, 1998; Maquat, 2004; Reddy, 2007; Schuler, 2008). The spliceosome is assembled from small nuclear RNAs (snRNAs) and associated proteins that make up the small nuclear ribonucleoprotein particles (snRNPs) that recognize and splice introns.…”

Section: Resultsmentioning

confidence: 99%

Cell‐type specific analysis of translating RNAs in developing flowers reveals new levels of control

Jiao

Meyerowitz

2010

Molecular Systems Biology

164

152

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Combining translating ribosome affinity purification with RNA-seq for cell-specific profiling of translating RNAs in developing flowers.Cell type comparisons of cell type-specific hormone responses, promoter motifs, coexpressed cognate binding factor candidates, and splicing isoforms.Widespread post-transcriptional regulation at both the intron splicing and translational stages.A new class of noncoding RNAs associated with polysomes.

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Splice Site Requirements and Switches in Plants

Cited by 29 publications

References 92 publications

Ecotype dependent expression and alternative splicing of epithiospecifier protein (ESP) in Arabidopsis thaliana

Ecotype dependent expression and alternative splicing of epithiospecifier protein (ESP) in Arabidopsis thaliana

Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation

Cell‐type specific analysis of translating RNAs in developing flowers reveals new levels of control

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