title: Analysis of Ribosome-Associated mRNAs in Rice Reveals the Importance of Transcript Size and GC Content in Translation.
abstract: Gene expression is controlled at transcriptional and post-transcriptional levels including decoding of messenger RNA (mRNA) into polypeptides via ribosome-mediated translation. Translational regulation has been intensively studied in the model dicot plant Arabidopsis thaliana, and in this study, we assessed the translational status [proportion of steady-state mRNA associated with ribosomes] of mRNAs by Translating Ribosome Affinity Purification followed by mRNA-sequencing (TRAP-seq) in rice (Oryza sativa), a model monocot plant and the most important food crop. A survey of three tissues found that most transcribed rice genes are translated whereas few transposable elements are associated with ribosomes. Genes with short and GC-rich coding regions are overrepresented in ribosome-associated mRNAs, suggesting that the GC-richness characteristic of coding sequences in grasses may be an adaptation that favors efficient translation. Transcripts with retained introns and extended 5' untranslated regions are underrepresented on ribosomes, and rice genes belonging to different evolutionary lineages exhibited differential enrichment on the ribosomes that was associated with GC content. Genes involved in photosynthesis and stress responses are preferentially associated with ribosomes, whereas genes in epigenetic regulation pathways are the least enriched on ribosomes. Such variation is more dramatic in rice than that in Arabidopsis and is correlated with the wide variation of GC content of transcripts in rice. Taken together, variation in the translation status of individual transcripts reflects important mechanisms of gene regulation, which may have a role in evolution and diversification.
authors.affiliation: Department of Horticulture, Michigan State University, East Lansing, Michigan 48824.|Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824.
authors.forename: Dongyan
authors.identifier: 0000-0002-2080-8416
authors.initials: D
authors.lastname: Zhao
authors.affiliation: Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824.
authors.forename: John P
authors.identifier: 0000-0002-8682-5526
authors.initials: JP
authors.lastname: Hamilton
authors.affiliation: Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824.
authors.forename: Michael
authors.initials: M
authors.lastname: Hardigan
authors.affiliation: Department of Horticulture, Michigan State University, East Lansing, Michigan 48824.
authors.forename: Dongmei
authors.initials: D
authors.lastname: Yin
authors.affiliation: Department of Statistics and Probability, Michigan State University, East Lansing, Michigan 48824.|Department of Mathematics, San Francisco State University, California 94132.
authors.forename: Tao
authors.initials: T
authors.lastname: He
authors.affiliation: Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824.
authors.forename: Brieanne
authors.initials: B
authors.lastname: Vaillancourt
authors.affiliation: Center for Plant Cell Biology, University of California, Riverside, California 92521.|Department of Botany and Plant Sciences, University of California, Riverside, California 92521.
authors.forename: Mauricio
authors.identifier: 0000-0002-9990-5808
authors.initials: M
authors.lastname: Reynoso
authors.affiliation: Center for Plant Cell Biology, University of California, Riverside, California 92521.|Department of Botany and Plant Sciences, University of California, Riverside, California 92521.
authors.forename: Germain
authors.initials: G
authors.lastname: Pauluzzi
authors.affiliation: Genetics Program, Michigan State University, East Lansing, Michigan 48824.
authors.forename: Scott
authors.identifier: 0000-0001-7798-6830
authors.initials: S
authors.lastname: Funkhouser
authors.affiliation: Department of Statistics and Probability, Michigan State University, East Lansing, Michigan 48824.
authors.forename: Yuehua
authors.initials: Y
authors.lastname: Cui
authors.affiliation: Center for Plant Cell Biology, University of California, Riverside, California 92521.|Department of Botany and Plant Sciences, University of California, Riverside, California 92521.
authors.forename: Julia
authors.identifier: 0000-0002-8568-7125
authors.initials: J
authors.lastname: Bailey-Serres
authors.affiliation: Department of Horticulture, University of Wisconsin-Madison, Wisconsin 53705.
authors.forename: Jiming
authors.initials: J
authors.lastname: Jiang
authors.affiliation: Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 buell@msu.edu jiangn@msu.edu.
authors.forename: C Robin
authors.identifier: 0000-0002-6727-4677
authors.initials: CR
authors.lastname: Buell
authors.affiliation: Department of Horticulture, Michigan State University, East Lansing, Michigan 48824 buell@msu.edu jiangn@msu.edu.|Genetics Program, Michigan State University, East Lansing, Michigan 48824.|Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, Michigan 48824.
authors.forename: Ning
authors.identifier: 0000-0002-2776-6669
authors.initials: N
authors.lastname: Jiang
mesh_terms: D020121:5' Untranslated Regions / Q000235:genetics; D017360:Arabidopsis / Q000235:genetics; D001482:Base Composition / Q000235:genetics; D044127:Epigenesis, Genetic; D018506:Gene Expression Regulation, Plant; D012275:Oryza / Q000235:genetics*; D014176:Protein Biosynthesis; D012333:RNA, Messenger / Q000235:genetics*; D012270:Ribosomes / Q000235:genetics*; D017423:Sequence Analysis, RNA
chemical_list: D020121:5' Untranslated Regions; D012333:RNA, Messenger
keywords: GC content; Oryza sativa; mRNA length; translating ribosome affinity purification sequencing