title: Extensive translational regulation during seed germination revealed by polysomal profiling.
abstract: This work investigates the extent of translational regulation during seed germination. The polysome occupancy of each gene is determined by genome-wide profiling of total mRNA and polysome-associated mRNA. This reveals extensive translational regulation during Arabidopsis thaliana seed germination. The polysome occupancy of thousands of individual mRNAs changes to a large extent during the germination process. Intriguingly, these changes are restricted to two temporal phases (shifts) during germination, seed hydration and germination. Sequence features, such as upstream open reading frame number, transcript length, mRNA stability, secondary structures, and the presence and location of specific motifs correlated with this translational regulation. These features differed significantly between the two shifts, indicating that independent mechanisms regulate translation during seed germination. This study reveals substantial translational dynamics during seed germination and identifies development-dependent sequence features and cis elements that correlate with the translation control, uncovering a novel and important layer of gene regulation during seed germination.
authors.affiliation: Department of Molecular Plant Physiology, Utrecht University, 3584 CH, Utrecht, the Netherlands.|Wageningen Seed Laboratory, Laboratory of Plant Physiology, Wageningen University, 6708 PB, Wageningen, the Netherlands.
authors.forename: Bing
authors.initials: B
authors.lastname: Bai
authors.affiliation: Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH, Utrecht, the Netherlands.
authors.forename: Alessia
authors.initials: A
authors.lastname: Peviani
authors.affiliation: Wageningen Seed Laboratory, Laboratory of Plant Physiology, Wageningen University, 6708 PB, Wageningen, the Netherlands.|Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH, Utrecht, the Netherlands.
authors.forename: Sjors
authors.initials: S
authors.lastname: van der Horst
authors.affiliation: Department of Molecular Plant Physiology, Utrecht University, 3584 CH, Utrecht, the Netherlands.
authors.forename: Magdalena
authors.initials: M
authors.lastname: Gamm
authors.affiliation: Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH, Utrecht, the Netherlands.
authors.forename: Berend
authors.initials: B
authors.lastname: Snel
authors.affiliation: Department of Molecular Plant Physiology, Utrecht University, 3584 CH, Utrecht, the Netherlands.|Wageningen Seed Laboratory, Laboratory of Plant Physiology, Wageningen University, 6708 PB, Wageningen, the Netherlands.
authors.forename: Leónie
authors.initials: L
authors.lastname: Bentsink
authors.affiliation: Department of Molecular Plant Physiology, Utrecht University, 3584 CH, Utrecht, the Netherlands.|Umeå Plant Science Centre, Department of Plant Physiology, University of Umeå, Umeå, SE-901 87, Sweden.
authors.forename: Johannes
authors.identifier: http://orcid.org/0000-0002-5605-7984
authors.initials: J
authors.lastname: Hanson
mesh_terms: D017360:Arabidopsis / Q000196:embryology* / Q000235:genetics*; D001483:Base Sequence; D018506:Gene Expression Regulation, Plant; D018525:Germination / Q000235:genetics*; D009690:Nucleic Acid Conformation; D011132:Polyribosomes / Q000378:metabolism*; D014176:Protein Biosynthesis / Q000235:genetics*; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D018749:RNA, Plant / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012639:Seeds / Q000235:genetics*
chemical_list: D012333:RNA, Messenger; D018749:RNA, Plant
keywords: Arabidopsis; RNA structure; germination; imbibition; polysomal profiling; ribosome; seedling establishment; translatomics