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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

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Transcriptome Analyses of FY Mutants Reveal Its Role in mRNA Alternative Polyadenylation

Zhibo Yu1, Juncheng Lin1,2, Qingshun Quinn Li3,2

  • 1Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China 361102.

The Plant Cell
|August 21, 2019
PubMed

Insights

The flowering time regulator FY in Arabidopsis is crucial for messenger RNA (mRNA) polyadenylation, impacting alternative polyadenylation (APA) and gene expression. FY mutations disrupt poly(A) signal recognition, affecting root growth and flowering time.

Area of Science:

  • Molecular Biology
  • Plant Science
  • Genetics

Background:

  • Messenger RNA (mRNA) polyadenylation is essential for gene expression, involving the recognition of poly(A) signals by trans-acting factors.
  • In mammals, CPSF30 and WDR33 recognize the AAUAAA poly(A) signal.
  • The Arabidopsis homolog of WDR33, FY, is a flowering time regulator with a poorly understood role in mRNA polyadenylation.

Purpose of the Study:

  • To investigate the role of the Arabidopsis FY protein in mRNA polyadenylation and alternative polyadenylation (APA).
  • To determine how different domains of FY (WD40 repeat and PPLPP domain) contribute to its function in poly(A) signal recognition and APA.
  • To explore the physiological consequences of FY mutations on plant development and gene expression.

Main Methods:

  • Poly(A) tag sequencing was employed to analyze genome-wide APA events in wild-type and mutant Arabidopsis.
  • Mutations were introduced in the FY gene, including single mutants, double mutants with oxt6 (AtCPSF30), and domain-specific mutations (WD40-repeat and PPLPP domain).
  • Phenotypic analysis, including root growth and flowering time, was conducted.

Main Results:

  • Over 50% of APA events were altered in fy mutants, indicating a significant role for FY in APA.
  • Mutations in the FY WD40-repeat domain had a stronger effect on APA than mutations in the PPLPP domain.
  • FY mutations disrupted the recognition of AAUAAA and AAUAAA-like poly(A) signals, with distinct effects on A-rich signal usage and 3' untranslated region (UTR) length depending on the mutated domain.
  • FY mutations led to shortened primary roots, late flowering, and altered APA of genes involved in abiotic stress responses.

Conclusions:

  • FY plays a conserved and specific role in mRNA polyadenylation in Arabidopsis.
  • Both the WD40-repeat and PPLPP domains of FY are important for its function in poly(A) signal recognition and APA.
  • FY-mediated APA influences plant development and the response to abiotic stress.

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