The Polyadenylation of RNA in Plants

Li, Qingshun Quinn; Hunt, Arthur G.

doi:10.1104/pp.115.2.321

Cited by 72 publications

(74 citation statements)

References 33 publications

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“…To this end, we constructed a working model based on the characterized plant poly(A) signals by conventional genetic or biochemical approaches on a few genes, including the cauliflower mosaic virus (CaMV) 35S transcript, the pea (Pisum sativum) small subunit of Rubisco (rbcS), the Agrobacterium T-DNA ocs gene, and the maize (Zea mays) 27-kD protein gene (Rothnie, 1996;Li and Hunt, 1997). There are only a few genes from which poly(A) signals were analyzed in detail through mutagenesis.…”

Section: The Nuementioning

confidence: 99%

“…The NUE is defined as a signal element located between 213 nt to 230 nt upstream of the CS (position 21 anchored at the last nucleotide of the 3#-end of each cDNA sequence; thus the upstream sequence and the downstream sequence will have a ''2'' or ''1'' designation, respectively; Rothnie, 1996;Li and Hunt, 1997). The first approach was to expand the NUE region and to search for all possible patterns and signals in the subregion from 21 to 250 nt for all the sequences.…”

Section: The Nuementioning

confidence: 99%

“…Conventional genetic mutagenesis studies revealed that plant poly(A) signals are composed of three major groups: far upstream elements (FUE), near upstream elements (NUE; an AAUAAA-like element), and cleavage sites (CSs; Rothnie, 1996;Li and Hunt, 1997;Rothnie et al, 2001). The composition of plant consensus signals, such as CSs, is a YA (CA or UA) dinucleotide situated within a U-rich region.…”

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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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Section: The Nuementioning

confidence: 99%

Section: The Nuementioning

confidence: 99%

mentioning

confidence: 99%

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

et al. 2005

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“…8 It remains a formal possibility that 3'-end processing in plants is fundamentally different from same process in yeast and mammals. 9 To our knowledge, this is the first time to systematically analyze the pre-mRNA cleavage sites in plant. This bioinformatic analysis, in contrast to exclusively experimental mutagenesis approaches, allows a much broader sampling of genes for cleavage assays, thereby providing statistical data beyond the range of feasible experiments and important information for a mechanistic understanding of 3'-end processing in plant.…”

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confidence: 99%

“…In addition, progress in understanding plant 3' RNA processing mechanism has lagged behind that in mammalian and yeast, mainly due to the lack of in vitro assays, for 3'-end processing. 8,9 The availability of complete genome sequences has made possible large-scale sequence analysis to identify and model the cleavage sites. [6][7][8][10][11][12] Several tools have been designed to locate unknown cleavage sites in a genomic sequence of the Saccharomyces cerevisiae and Caenorhabditis elegans.…”

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Determination and Analysis of the Pre-mRNA Cleavage sites inArabidopsis

Jin

Chen²,

Gong³

2005

RNA Biology

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Alternative polyadenylation and gene expression regulation in plants

Xing

2010

WIREs RNA

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Functioning as an essential step of pre-mRNA processing, polyadenylation has been realized in recent years to play an important regulatory role during eukaryotic gene expression. Such regulation occurs mostly through the use of alternative polyadenylation (APA) sites and generates different transcripts with altered coding capacity for proteins and/or RNA. However, the molecular mechanisms that underlie APAs are poorly understood. Besides APA cases demonstrated in animal embryo development, cancers, and other diseases, there are a number of APA examples reported in plants. The best-known ones are related to flowering time control pathways and stress responses. Genome-wide studies have revealed that plants use APA extensively to generate diversity in their transcriptomes. Although each transcript produced by RNA polymerase II has a poly(A) tail, over 50% of plant genes studied possess multiple APA sites in their transcripts. The signals defining poly(A) sites in plants were mostly studied through classical genetic means. Our understanding of these poly(A) signals is enhanced by the tallies of whole plant transcriptomes. The profiles of these signals have been used to build computer models that can predict poly(A) sites in newly sequenced genomes, potential APA sites in genes of interest, and/or to identify, and then mutate, unwanted poly(A) sites in target transgenes to facilitate crop improvements. In this review, we provide readers an update on recent research advances that shed light on the understanding of polyadenylation, APA, and its role in gene expression regulation in plants.

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The Polyadenylation of RNA in Plants

Cited by 72 publications

References 33 publications

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

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

Determination and Analysis of the Pre-mRNA Cleavage sites inArabidopsis

Alternative polyadenylation and gene expression regulation in plants

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