Alternative polyadenylation and gene expression regulation in plants

Xing, Denghui; Li, Qingshun Quinn

doi:10.1002/wrna.59

Cited by 91 publications

(88 citation statements)

References 88 publications

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“…Beyond the links with mRNA synthesis, transport, and function, polyadenylation also affects gene expression by determining the coding and regulatory potential of an mRNA. Especially with genes whose mRNAs may be polyadenylated at more than one position within the primary transcript, poly(A) site choice has the potential to contribute to regulation and ultimately to gene function (Lutz and Moreira, 2011;Xing and Li, 2011).…”

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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Section: Introductionmentioning

confidence: 99%

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

et al. 2012

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“…In plants, there are many documented cases of APA (11)(12)(13). Perhaps the best-studied example of APA in plants involves the network of genes that control flowering time in Arabidopsis.…”

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confidence: 99%

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.

273

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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“…In human, alternative polyadenylation is very widespread, and the broad modulation of alternative polyadenylation has been associated with processes as diverse as cell proliferation and differentiation, neural function, and cancer (Elkon et al, 2013). Likewise in Arabidopsis, alternative polyadenylation may affect 60% to 70% of all genes (Shen et al, 2011;Xing and Li, 2011;Sherstnev et al, 2012). Using a genome-wide approach to assess the role of CPSF30 in alternative polyadenylation in Arabidopsis, poly(A) site choice in the oxt6 mutant was surveyed (Thomas et al, 2012).…”

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confidence: 99%

The Polyadenylation Factor Subunit CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR30: A Key Factor of Programmed Cell Death and a Regulator of Immunity in Arabidopsis

et al. 2014

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Programmed cell death (PCD) is essential for several aspects of plant life, including development and stress responses. Indeed, incompatible plant-pathogen interactions are well known to induce the hypersensitive response, a localized cell death. Mutational analyses have identified several key PCD components, and we recently identified the mips1 mutant of Arabidopsis (Arabidopsis thaliana), which is deficient for the key enzyme catalyzing the limiting step of myoinositol synthesis. One of the most striking features of mips1 is the light-dependent formation of lesions on leaves due to salicylic acid (SA)-dependent PCD, revealing roles for myoinositol or inositol derivatives in the regulation of PCD. Here, we identified a regulator of plant PCD by screening for mutants that display transcriptomic profiles opposing that of the mips1 mutant. Our screen identified the oxt6 mutant, which has been described previously as being tolerant to oxidative stress. In the oxt6 mutant, a transfer DNA is inserted in the CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR30 (CPSF30) gene, which encodes a polyadenylation factor subunit homolog. We show that CPSF30 is required for lesion formation in mips1 via SA-dependent signaling, that the prodeath function of CPSF30 is not mediated by changes in the glutathione status, and that CPSF30 activity is required for Pseudomonas syringae resistance. We also show that the oxt6 mutation suppresses cell death in other lesion-mimic mutants, including lesion-simulating disease1, mitogen-activated protein kinase4, constitutive expressor of pathogenesis-related genes5, and catalase2, suggesting that CPSF30 and, thus, the control of messenger RNA 39 end processing, through the regulation of SA production, is a key component of plant immune responses.

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Alternative polyadenylation and gene expression regulation in plants

Cited by 91 publications

References 88 publications

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

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

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

The Polyadenylation Factor Subunit CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR30: A Key Factor of Programmed Cell Death and a Regulator of Immunity in Arabidopsis

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