Experimental genome-wide determination of RNA Polyadenylation in Chlamydomonas reinhardtii

Stephen A. Bell, Chi Shen, Alishea Brown, Arthur G. Hunt

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16 Scopus citations

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 lowthroughput (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.

Original languageEnglish
Article numbere0146107
JournalPLoS ONE
Volume11
Issue number1
DOIs
StatePublished - Jan 5 2016

Bibliographical note

Funding Information:
The authors thank Patrick Thomas for helpful guidance in preparing the PAT-Seq libraries, and in subsequent computational analysis. They also thank Carol Von Lanken for superior technical and logistical support for this project. This research was supported by NSF Award MCB-1243849 and an REU Supplement to NSF Award IOS-0817818.

Publisher Copyright:
© 2016 Bell et al.This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

ASJC Scopus subject areas

  • General

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