Characterization of the polyadenyllationm signal from the T-DNA-encoded octopine sysnthase gene

MacDonald, Margaret H.; Mogen, Bradley D.; Hunt, Arthur G.

doi:10.1093/nar/19.20.5575

Cited by 45 publications

(58 citation statements)

References 18 publications

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“…has been documented with at least one other plant poly(A) signal (MacDonald et al, 1991), suggesting that the situation depicted in Figure 2 is a general one for plant genes.…”

Section: Polyadenylation Sicnals In Plant Nuclear Mrna Precursorsmentioning

confidence: 64%

The Polyadenylation of RNA in Plants

Li¹,

Hunt²

1997

Plant Physiology

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“…has been documented with at least one other plant poly(A) signal (MacDonald et al, 1991), suggesting that the situation depicted in Figure 2 is a general one for plant genes.…”

Section: Polyadenylation Sicnals In Plant Nuclear Mrna Precursorsmentioning

confidence: 64%

The Polyadenylation of RNA in Plants

Li¹,

Hunt²

1997

Plant Physiology

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“…For example, a downstream element was found to affect the precision of cleavage, but did not influence the processing efficiency (Sanfacon et al, 1991). More dramatic effect was noted in the analysis of ocs and rbcS 3#-UTR, in which the deletion of the downstream element alters or eliminates the use of the poly(A) site (Hunt and MacDonald, 1989;MacDonald et al, 1991). These notions were not pursued further, and hence remained unresolved, but are revisited in this article.…”

Section: Discussionmentioning

confidence: 95%

Compilation of mRNA Polyadenylation Signals in Arabidopsis Revealed a New Signal Element and Potential Secondary Structures

et al. 2005

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Using a novel program, SignalSleuth, and a database containing authenticated polyadenylation [poly(A)] sites, we analyzed the composition of mRNA poly(A) signals in Arabidopsis (Arabidopsis thaliana), and reevaluated previously described cis-elements within the 3#-untranslated (UTR) regions, including near upstream elements and far upstream elements. As predicted, there are absences of high-consensus signal patterns. The AAUAAA signal topped the near upstream elements patterns and was found within the predicted location to only approximately 10% of 3#-UTRs. More importantly, we identified a new set, named cleavage elements, of poly(A) signals flanking both sides of the cleavage site. These cis-elements were not previously revealed by conventional mutagenesis and are contemplated as a cluster of signals for cleavage site recognition. Moreover, a singlenucleotide profile scan on the 3#-UTR regions unveiled a distinct arrangement of alternate stretches of U and A nucleotides, which led to a prediction of the formation of secondary structures. Using an RNA secondary structure prediction program, mFold, we identified three main types of secondary structures on the sequences analyzed. Surprisingly, these observed secondary structures were all interrupted in previously constructed mutations in these regions. These results will enable us to revise the current model of plant poly(A) signals and to develop tools to predict 3#-ends for gene annotation.Messenger RNA polyadenylation is a crucial step during the maturation of most eukaryotic mRNA, in which a polyadenine [poly(A)] tract is added to the cleaved 3#-end of a precursor mRNA (pre-mRNA) posttranscriptionally. Such a modification of mRNA has been shown to affect its stability, translatability, and nuclear-to-cytoplasmic export (Zhao et al., 1999). The posttranscriptional processing of mRNA is an event that has also been found tightly coupled with splicing and transcription termination (Proudfoot et al., 2002;Proudfoot, 2004). Thus, it is an essential processing event and the integral part of gene expression.The polyadenylation process requires two major components: the cis-elements or poly(A) signals of the pre-mRNA, and the trans-acting factors that carry out the cleavage and addition of the poly(A) tail at the 3#-end. These trans-acting factors are a complex of about 25 to 30 proteins involved in signal recognition, cleavage, and polyadenylation (Proudfoot, 2004). These proteins seem to be conserved among eukaryotic organisms. However, the poly(A) signals have been found to differ widely among yeast (Saccharomyces cerevisiae), animals, and plants in terms of signal locations and sequence content. The highly conserved AAUAAA element in mammals becomes a minor signal in plant and yeast genes, and the ubiquitous downstream elements of mammalian pre-mRNAs are nowhere to be found in yeast and plants. The latter two possess an enhancing element located far upstream of the cleavage site (Zhao et al., 1999).Previous understanding of these signal elements was derived mostly...

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“…All of these elements are somewhat degenerate in terms of sequence composition; thus, the FUE consists of an extended U+G-rich region situated more than 50 nucleotides upstream from the poly(A) site, the near-upstream element (NUE) is an A-rich region of 6 to 10 nucleotides situated 10 to 30 nucleotides upstream from the poly(A) site, and the CE is a U-rich region centered around the poly(A) site that itself is typically a YA dinucleotide. While mutational analysis has shown that each element contributes to a high-efficiency signal (Mogen et al, 1990(Mogen et al, , 1992MacDonald et al, 1991;Sanfacon et al, 1991;Rothnie et al, 1994;Li and Hunt, 1995), most aspects of the functioning of these elements have not been defined. The results presented in this article indicate that one polyadenylation factor subunit, CPSF30, plays a role of the functioning of the NUE; this is based on the observations that poly(A) sites that are used only in the wild type, and not the oxt6 mutant, possess the characteristic A-rich NUE signature, while sites used only in the oxt6 mutant lack (C) PACs that fall in intergenic regions.…”

Section: Insight Into the Nature Of Plant Polyadenylation Signalsmentioning

confidence: 99%

Genome-Wide Control of Polyadenylation Site Choice by CPSF30 in Arabidopsis

et al. 2012

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The Arabidopsis thaliana ortholog of the 30-kD subunit of the mammalian Cleavage and Polyadenylation Specificity Factor (CPSF30) has been implicated in the responses of plants to oxidative stress, suggesting a role for alternative polyadenylation. To better understand this, poly(A) site choice was studied in a mutant (oxt6) deficient in CPSF30 expression using a genomescale approach. The results indicate that poly(A) site choice in a large majority of Arabidopsis genes is altered in the oxt6 mutant. A number of poly(A) sites were identified that are seen only in the wild type or oxt6 mutant. Interestingly, putative polyadenylation signals associated with sites that are seen only in the oxt6 mutant are decidedly different from the canonical plant polyadenylation signal, lacking the characteristic A-rich near-upstream element (where AAUAAA can be found); this suggests that CPSF30 functions in the handling of the near-upstream element. The sets of genes that possess sites seen only in the wild type or mutant were enriched for those involved in stress and defense responses, a result consistent with the properties of the oxt6 mutant. Taken together, these studies provide new insights into the mechanisms and consequences of CPSF30-mediated alternative polyadenylation.

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Characterization of the polyadenyllationm signal from the T-DNA-encoded octopine sysnthase gene

Cited by 45 publications

References 18 publications

The Polyadenylation of RNA in Plants

The Polyadenylation of RNA in Plants

Compilation of mRNA Polyadenylation Signals in Arabidopsis Revealed a New Signal Element and Potential Secondary Structures

Genome-Wide Control of Polyadenylation Site Choice by CPSF30 in Arabidopsis

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