title: Experimental Genome-Wide Determination of RNA Polyadenylation in Chlamydomonas reinhardtii.
abstract: The polyadenylation of RNA is a near-universal feature of RNA metabolism in eukaryotes. This process has been studied in the model alga Chlamydomonas reinhardtii using low-throughput (gene-by-gene) and high-throughput (transcriptome sequencing) approaches that recovered poly(A)-containing sequence tags which revealed interesting features of this critical process in Chlamydomonas. In this study, RNA polyadenylation has been studied using the so-called Poly(A) Tag Sequencing (PAT-Seq) approach. Specifically, PAT-Seq was used to study poly(A) site choice in cultures grown in four different media types-Tris-Phosphate (TP), Tris-Phosphate-Acetate (TAP), High-Salt (HS), and High-Salt-Acetate (HAS). The results indicate that: 1. As reported before, the motif UGUAA is the primary, and perhaps sole, cis-element that guides mRNA polyadenylation in the nucleus; 2. The scope of alternative polyadenylation events with the potential to change the coding sequences of mRNAs is limited; 3. Changes in poly(A) site choice in cultures grown in the different media types are very few in number and do not affect protein-coding potential; 4. Organellar polyadenylation is considerable and affects primarily ribosomal RNAs in the chloroplast and mitochondria; and 5. Organellar RNA polyadenylation is a dynamic process that is affected by the different media types used for cell growth.
authors.affiliation: Department of Plant and Soil Sciences, University of Kentucky, Lexington, Kentucky, United States of America.
authors.forename: Stephen A
authors.initials: SA
authors.lastname: Bell
authors.affiliation: Division of Computer Science, Kentucky State University, Frankfort, Kentucky, United States of America.
authors.forename: Chi
authors.initials: C
authors.lastname: Shen
authors.affiliation: Division of Computer Science, Kentucky State University, Frankfort, Kentucky, United States of America.
authors.forename: Alishea
authors.initials: A
authors.lastname: Brown
authors.affiliation: Department of Plant and Soil Sciences, University of Kentucky, Lexington, Kentucky, United States of America.
authors.forename: Arthur G
authors.initials: AG
authors.lastname: Hunt
mesh_terms: D020121:5' Untranslated Regions / Q000235:genetics; D017398:Alternative Splicing; D001483:Base Sequence; D002467:Cell Nucleus / Q000235:genetics / Q000378:metabolism; D016825:Chlamydomonas reinhardtii / Q000235:genetics* / Q000378:metabolism; D019295:Computational Biology / Q000379:methods; D018506:Gene Expression Regulation, Plant; D054628:Genome, Chloroplast / Q000235:genetics; D054629:Genome, Mitochondrial / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D008957:Models, Genetic; D008969:Molecular Sequence Data; D059372:Nucleotide Motifs / Q000235:genetics; D016366:Open Reading Frames / Q000235:genetics; D011061:Poly A / Q000235:genetics* / Q000378:metabolism; D026723:Polyadenylation; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics* / Q000378:metabolism
chemical_list: D020121:5' Untranslated Regions; D012333:RNA, Messenger; D018749:RNA, Plant; D011061:Poly A