title: Transcriptome-Wide Identification of RNA Targets of Arabidopsis SERINE/ARGININE-RICH45 Uncovers the Unexpected Roles of This RNA Binding Protein in RNA Processing.
abstract: Plant SR45 and its metazoan ortholog RNPS1 are serine/arginine-rich (SR)-like RNA binding proteins that function in splicing/postsplicing events and regulate diverse processes in eukaryotes. Interactions of SR45 with both RNAs and proteins are crucial for regulating RNA processing. However, in vivo RNA targets of SR45 are currently unclear. Using RNA immunoprecipitation followed by high-throughput sequencing, we identified over 4000 Arabidopsis thaliana RNAs that directly or indirectly associate with SR45, designated as SR45-associated RNAs (SARs). Comprehensive analyses of these SARs revealed several roles for SR45. First, SR45 associates with and regulates the expression of 30% of abscisic acid (ABA) signaling genes at the postsplicing level. Second, although most SARs are derived from intron-containing genes, surprisingly, 340 SARs are derived from intronless genes. Expression analysis of the SARs suggests that SR45 differentially regulates intronless and intron-containing SARs. Finally, we identified four overrepresented RNA motifs in SARs that likely mediate SR45's recognition of its targets. Therefore, SR45 plays an unexpected role in mRNA processing of intronless genes, and numerous ABA signaling genes are targeted for regulation at the posttranscriptional level. The diverse molecular functions of SR45 uncovered in this study are likely applicable to other species in view of its conservation across eukaryotes.
authors.affiliation: Department of Biology and Program in Molecular Plant Biology, Colorado State University, Fort Collins, Colorado 80523.
authors.forename: Denghui
authors.identifier: http://orcid.org/0000-0003-0283-4247
authors.initials: D
authors.lastname: Xing
authors.affiliation: Department of Biology and Program in Molecular Plant Biology, Colorado State University, Fort Collins, Colorado 80523.
authors.forename: Yajun
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Computer Science Department, Colorado State University, Fort Collins, Colorado 80523.
authors.forename: Michael
authors.initials: M
authors.lastname: Hamilton
authors.affiliation: Computer Science Department, Colorado State University, Fort Collins, Colorado 80523.
authors.forename: Asa
authors.initials: A
authors.lastname: Ben-Hur
authors.affiliation: Department of Biology and Program in Molecular Plant Biology, Colorado State University, Fort Collins, Colorado 80523 reddy@colostate.edu.
authors.forename: Anireddy S N
authors.initials: AS
authors.lastname: Reddy
mesh_terms: D000040:Abscisic Acid / Q000378:metabolism*; D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism*; D001120:Arginine / Q000378:metabolism; D007438:Introns / Q000235:genetics; D059372:Nucleotide Motifs; D010937:Plant Growth Regulators / Q000378:metabolism*; D012326:RNA Splicing; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D012694:Serine / Q000378:metabolism; D015398:Signal Transduction; D059467:Transcriptome
chemical_list: D029681:Arabidopsis Proteins; D010937:Plant Growth Regulators; D012333:RNA, Messenger; D018749:RNA, Plant; D016601:RNA-Binding Proteins; C483303:SR45 protein, Arabidopsis; D012694:Serine; D000040:Abscisic Acid; D001120:Arginine