Revisiting CPSF30-mediated alternative polyadenylation in Arabidopsis thaliana

Guijie Hao; Lichun Zhou; Huazhen Liu; Pradeep Kachroo; Arthur G. Hunt

doi:10.1371/journal.pone.0319180

Revisiting CPSF30-mediated alternative polyadenylation in Arabidopsis thaliana

Guijie Hao
, Lichun Zhou
, Huazhen Liu
, Pradeep Kachroo
, Arthur G. Hunt

Research output: Contribution to journal › Article › peer-review

Abstract

Alternative polyadenylation (APA) is an important contributor to the regulation of gene expression in plants. One subunit of the complex that cleaves and polyadenylates mRNAs in the nucleus, CPSF30 (for the 30 kD subunit of the mammalian Cleavage and Polyadenylation Specificity Factor), has been implicated in a wide-ranging network of regulatory events. CPSF30 plays roles in root development, flowering time, and response to biotic and abiotic stresses. CPSF30 also is a conduit that links cellular signaling and RNA modification with alternative RNA processing events and transcriptional dynamics. While much is known about CPSF30 and its roles in plants, questions remain regarding the connections between CPSF30-mediated APA and the downstream events that lead to specific phenotypic outcomes. To address these, we conducted a detailed analysis of poly(A) site usage in the CPSF30 mutant. Our results corroborate earlier reports that link CPSF30 with a distinctive cis element (AAUAAA) that is present 10-30 nts upstream of some, but not all, plant pre-mRNAs. Interestingly, our results reveal a distinctive shift in poly(A) site in mutants deficient in CPSF30, resulting in cleavage and polyadenylation at the location of motifs similar to AAUAAA. Importantly, CPSF30-associated APA had at best a small impact on mRNA functionality. These results necessitate the formulation of new hypotheses for mechanisms by which CPSF30-mediated APA influences physiological processes.

Original language	English
Article number	e0319180
Journal	PLoS ONE
Volume	20
Issue number	2 February
DOIs	https://doi.org/10.1371/journal.pone.0319180
State	Published - Feb 2025

Bibliographical note

Publisher Copyright:
© 2025 Hao et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Funding

This research was supported by the National Science Foundation (www.nsf. gov; Awards MCB-1243849 (AGH), 2347539 (AGH), 0421914 (PK) and IOS-1353354 (AGH), 051909 (PK), and 0817818 (AGH)), by the USDA National Institute of Food and Agriculture (www.nifa.usda.gov; GRANT13323564 (PK) and Hatch projects 1014539 (PK) and KY006150 (AGH)). The sponsors played no role in study design, data collection and analysis, decision to publish, and preparation of the manuscript. The authors gratefully acknowledge the technical and administrative support provided by Carol Von Lanken.

Funders	Funder number
Carol Von Lanken
AGH	2347539, IOS-1353354, 0421914, 0817818, 051909
US Department of Agriculture National Institute of Food and Agriculture, Agriculture and Food Research Initiative	GRANT13323564, KY006150, 1014539
National Science Foundation Arctic Social Science Program	MCB-1243849

ASJC Scopus subject areas

General

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abstract = "Alternative polyadenylation (APA) is an important contributor to the regulation of gene expression in plants. One subunit of the complex that cleaves and polyadenylates mRNAs in the nucleus, CPSF30 (for the 30 kD subunit of the mammalian Cleavage and Polyadenylation Specificity Factor), has been implicated in a wide-ranging network of regulatory events. CPSF30 plays roles in root development, flowering time, and response to biotic and abiotic stresses. CPSF30 also is a conduit that links cellular signaling and RNA modification with alternative RNA processing events and transcriptional dynamics. While much is known about CPSF30 and its roles in plants, questions remain regarding the connections between CPSF30-mediated APA and the downstream events that lead to specific phenotypic outcomes. To address these, we conducted a detailed analysis of poly(A) site usage in the CPSF30 mutant. Our results corroborate earlier reports that link CPSF30 with a distinctive cis element (AAUAAA) that is present 10-30 nts upstream of some, but not all, plant pre-mRNAs. Interestingly, our results reveal a distinctive shift in poly(A) site in mutants deficient in CPSF30, resulting in cleavage and polyadenylation at the location of motifs similar to AAUAAA. Importantly, CPSF30-associated APA had at best a small impact on mRNA functionality. These results necessitate the formulation of new hypotheses for mechanisms by which CPSF30-mediated APA influences physiological processes.",

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Revisiting CPSF30-mediated alternative polyadenylation in Arabidopsis thaliana

Abstract

Bibliographical note

Funding

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