Unique Features of Plant Cleavage and Polyadenylation Specificity Factor Revealed by Proteomic Studies

Zhao, Hongwei; Xing, Denghui; Li, Qingshun Quinn

doi:10.1104/pp.109.142729

Cited by 31 publications

(28 citation statements)

References 50 publications

(91 reference statements)

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“…In plants, a similar set of poly(A) factors were identified, albeit with some differences in the number of encoding genes and domain structures (Hunt et al 2008. Genetic and biochemical analysis of these factors also revealed similar, but distinct, and sometimes unique, functions to their animal counterparts (Zhao et al 2009(Zhao et al , 2011Thomas et al 2012;Xing et al 2013;Liu et al 2014).…”

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confidence: 96%

Genome-wide dynamics of alternative polyadenylation in rice

Yang

et al. 2016

Genome Res.

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Alternative polyadenylation (APA), in which a transcript uses one of the poly(A) sites to define its 3′-end, is a common regulatory mechanism in eukaryotic gene expression. However, the potential of APA in determining crop agronomic traits remains elusive. This study systematically tallied poly(A) sites of 14 different rice tissues and developmental stages using the poly(A) tag sequencing (PAT-seq) approach. The results indicate significant involvement of APA in developmental and quantitative trait loci (QTL) gene expression. About 48% of all expressed genes use APA to generate transcriptomic and proteomic diversity. Some genes switch APA sites, allowing differentially expressed genes to use alternate 3′ UTRs. Interestingly, APA in mature pollen is distinct where differential expression levels of a set of poly(A) factors and different distributions of APA sites are found, indicating a unique mRNA 3′-end formation regulation during gametophyte development. Equally interesting, statistical analyses showed that QTL tends to use APA for regulation of gene expression of many agronomic traits, suggesting a potential important role of APA in rice production. These results provide thus far the most comprehensive and high-resolution resource for advanced analysis of APA in crops and shed light on how APA is associated with trait formation in eukaryotes.

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confidence: 96%

Genome-wide dynamics of alternative polyadenylation in rice

Yang

et al. 2016

Genome Res.

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“…The endonuclease activity is attributable to the C-terminal zinc finger motif. Beyond these biochemical activities, the Arabidopsis CPSF30 sits at the center of a hub of protein-protein interactions involving other CPSF subunits as well as other components of the polyadenylation complex Zhao et al, 2009).…”

Section: Introductionmentioning

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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“…Future directions should include the identification of the plant cleavage/ polyadenylation factors that are responsible for the activities, and the roles of those potential factors revealed through bioinformatic and genetic studies, as confirmed by protein-protein interactions (Xu et al, 2006;Hunt et al, 2008;Xing et al, 2008aXing et al, , 2008bZhao et al, 2009). Several approaches can be employed to identify the plant polyadenylation factors through this type of biochemical assay.…”

Section: Discussionmentioning

confidence: 99%

“…While studying the proteomics of plant polyadenylation factors, we overexpressed Arabidopsis CPSF73-I (for CPSF 73-kD subunit-I; At1g61010) using a tandem affinity purification tagging approach and isolated the protein complexes formed with it (Zhao et al, 2009). Arabidopsis CPSF73-I is a homolog of mammalian CPSF73 that was shown to be the endonuclease that plays a direct role in the cleavage step of pre-mRNA 3#-end formation (Dominski et al, 2005;Mandel et al, 2006).…”

Section: Establishment Of a Plant In Vitro Pre-mrna Cleavage System Umentioning

confidence: 99%

“…To address this, numerous efforts were made in establishing a plant cleavage and polyadenylation in vitro assay system by using the nuclear extracts of different plants, such as peas (Pisum sativum), cauliflower (Brassica oleracea), and Arabidopsis (Arabidopsis thaliana), but without success. Over the past few years, through bioinformatics, phylogenetics, protein interactions, and proteomic analysis, we and others have identified the conserved polyadenylation factors (Simpson et al, 2003;Herr et al, 2006;Hunt et al, 2008;Zhao et al, 2009). However, the biochemical efficacy of these proteins remains largely elusive.…”

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A Novel Plant in Vitro Assay System for Pre-mRNA Cleavage during 3′-End Formation

Zhao

Zheng

2011

Plant Physiol.

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Messenger RNA (mRNA) maturation in eukaryotic cells requires the formation of the 3# end, which includes two tightly coupled steps: the committing cleavage reaction that requires both correct cis-element signals and cleavage complex formation, and the polyadenylation step that adds a polyadenosine [poly(A)] tract to the newly generated 3# end. An in vitro biochemical assay plays a critical role in studying this process. The lack of such an assay system in plants hampered the study of plant mRNA 3#-end formation for the last two decades. To address this, we have now established and characterized a plant in vitro cleavage assay system, in which nuclear protein extracts from Arabidopsis (Arabidopsis thaliana) suspension cell cultures can accurately cleave different pre-mRNAs at expected in vivo authenticated poly(A) sites. The specific activity is dependent on appropriate cis-elements on the substrate RNA. When complemented by yeast (Saccharomyces cerevisiae) poly(A) polymerase, about 150-nucleotide poly(A) tracts were added specifically to the newly cleaved 3# ends in a cooperative manner. The reconstituted polyadenylation reaction is indicative that authentic cleavage products were generated. Our results not only provide a novel plant pre-mRNA cleavage assay system, but also suggest a cross-kingdom functional complementation of yeast poly(A) polymerase in a plant system.Gene expression in eukaryotes requires the transcription of DNA into mRNA in the nucleus. The newly transcribed pre-mRNAs undergo extensive processing, such as 5#-end capping and removal of introns and 3#-end polyadenylation before they are ready to be transported to the cytoplasm for translation. Among pre-mRNA processing events, 3#-end formation and polyadenylation are known to regulate transcription termination, affect intron splicing, promote mRNA transportation and translation initiation, and protect mature mRNAs from unregulated degradation (Buratowski, 2005;Moore and Proudfoot, 2009). In addition, studies on alternative polyadenylation show that more than half of plant and mammal genes can be alternatively processed at different locations, resulting in distinct mature mRNAs from the same pre-mRNA transcripts (Tian et al., 2005;Xing and Li, 2010;Wu et al., 2011). More recently, the choice of alternative polyadenylation sites at 3#-untranslated region (UTR) of many genes has been linked to gene expression level control and cancer development (Mayr and Bartel, 2009). Thus, a theme of gene expression regulation through pre-mRNA polyadenylation is emerging. Due to its tight connections to transcription, translation, and RNA decay, mRNA 3#-end polyadenylation appears to act as a hub for fine tuning gene expression and forming a regulation network (Danckwardt et al., 2008).The 3#-end processing of mRNA includes two coupled steps: cleavage at a specific site at the 3#-UTR and an addition of a polyadenosine [poly(A)] tract to the newly formed 3# end. The biochemical process of polyadenylation is relatively well studied in mammals and yeast (Saccharo...

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Unique Features of Plant Cleavage and Polyadenylation Specificity Factor Revealed by Proteomic Studies

Cited by 31 publications

References 50 publications

Genome-wide dynamics of alternative polyadenylation in rice

Genome-wide dynamics of alternative polyadenylation in rice

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

A Novel Plant in Vitro Assay System for Pre-mRNA Cleavage during 3′-End Formation

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