Genome-wide dynamics of alternative polyadenylation in rice

Abstract

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.

Noncanonical Alternative Polyadenylation Contributes to Gene Regulation in Response to Hypoxia

“…In plants, a majority of genes that possess multiple poly(A) sites have at least one site situated upstream of the 39-UTR, proximal to the associated promoter (Shen et al, 2011;Wu et al, 2011Wu et al, , 2014Fu et al, 2016). The results presented in this study indicate that the products of proximal poly(A) site choice (collectively, noncanonical mRNA isoforms) may be differentiated according to the location of the poly(A) site within the transcriptional unit.…”

Tissue‐specific mechanisms of alternative polyadenylation: Testis, brain, and beyond (2018 update)

“…Similarly, FPA (an RNA‐binding protein of the spen gene family) controls APA of antisense FCA transcripts (Hornyik, Terzi, & Simpson, ); CstF‐64 and CstF‐77 are probably also involved in this mechanism (F. Liu, Marquardt, Lister, Swiezewski, & Dean, ). Recent high‐throughput studies in Arabidopsis, red clover ( Trifolium pratense L.), and rice have uncovered suggestive patterns in tissue‐specific APA in those species (Chakrabarti, Dinkins, & Hunt, ; de Lorenzo, Sorenson, Bailey‐Serres, & Hunt, ; Fu et al, ). Finally, we would remiss if not to mention the considerable research into polyadenylation mechanisms in Arabidopsis and other plants, which affect gene expression in embryo and gametophyte development, flowers, leaves, and other plant tissues (Hunt et al, ; Lorkovic, ; Xing, Zhao, & Li, ).…”

3′ UTR lengthening as a novel mechanism in regulating cellular senescence

“…Importantly, both microRNAs (miRNAs) and RNA binding proteins (RBPs) targeting 3 ′ UTRs are able to regulate translational efficiency, degradation, and subcellular localization of mRNA or protein (Di Giammartino et al 2011;Berkovits and Mayr 2015;Tian and Manley 2017). It is well known that APA plays important roles in a wide range of biological processes such as cell differentiation (Ji et al 2009;Mangone et al 2010;Hilgers et al 2011;Ulitsky et al 2012;Fu et al 2016;Hu et al 2017), cell proliferation Elkon et al 2012;Hoffman et al 2016), cell/tissue identity Derti et al 2012;Smibert et al 2012;Ni et al 2013), and carcinogenesis (Mayr and Bartel 2009;Fu et al 2011;Lin et al 2012;Xia et al 2014). However, whether APA is involved in senescenceassociated gene expression and contributes to cellular senescence remains to be answered.…”