Abstract
Alternative polyadenylation (APA) is an important layer of gene regulation that produces mRNAs that have different 3′ ends and/or encode diverse protein isoforms. Up to 70% of annotated genes in plants undergo APA. Increasing numbers of poly(A) sites collected in various plant species demand new methods and tools to access and mine these data. We have created an open-access web service called PlantAPA (http://bmi.xmu.edu.cn/plantapa) to visualize and analyze genome-wide poly(A) sites in plants. PlantAPA provides various interactive and dynamic graphics and seamlessly integrates a genome browser that can profile heterogeneous cleavage sites and quantify expression patterns of poly(A) sites across different conditions. Particularly, through PlantAPA, users can analyze poly(A) sites in extended 3′ UTR regions, intergenic regions, and ambiguous regions owing to alternative transcription or RNA processing. In addition, it also provides tools for analyzing poly(A) site selections, 3′ UTR lengthening or shortening, non-canonical APA site switching, and differential gene expression between conditions, making it more powerful for the study of APA-mediated gene expression regulation. More importantly, PlantAPA offers a bioinformatics pipeline that allows users to upload their own short reads or ESTs for poly(A) site extraction, enabling users to further explore poly(A) site selection using stored PlantAPA poly(A) sites together with their own poly(A) site datasets. To date, PlantAPA hosts the largest database of APA sites in plants, including Oryza sativa, Arabidopsis thaliana, Medicago truncatula, and Chlamydomonas reinhardtii. As a user-friendly web service, PlantAPA will be a valuable addition to the community of biologists studying APA mechanisms and gene expression regulation in plants.
Highlights
Messenger RNA 3′ end formation, including cleavage and polyadenylation, is a vital step in post-transcriptional processing in eukaryotic cells
PlantAPA details poly(A) sites in different genic regions, extended 3′ UTRs, intergenic regions, and ambiguous regions owing to alternative transcription or RNA processing
PlantAPA is intended to leverage our enormous wealth of existing poly(A) site data and genome annotations in plants by providing users with easy-to-use web services for the study of alternative polyadenylation (APA)-related mechanisms and functions in plants
Summary
Messenger RNA (mRNA) 3′ end formation, including cleavage and polyadenylation, is a vital step in post-transcriptional processing in eukaryotic cells. 64% of Medicago truncatula (referred as Medicago ) genes possess more than one poly(A) site (Wu et al, 2014), and ∼70% of annotated genes undergo APA in Arabidopsis and rice (Shen et al, 2008a, 2011; Wu et al, 2011; Sherstnev et al, 2012). As data accumulate, such increasingly high numbers of APA sites should be made accessible in a user-friendly manner to facilitate investigation of important biological questions
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