Extensive profiling of the expressions of tRNAs and tRNA-derived fragments (tRFs) reveals the complexities of tRNA and tRF populations in plants. 2021

Xuan Ma, and Chunyan Liu, and Xiaocong Kong, and Jing Liu, and Siju Zhang, and Shanshan Liang, and Weijiang Luan, and Xiaofeng Cao
Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China. skyxma@tjnu.edu.cn.

Evidence is emerging that tRNA-derived fragments (tRFs) are regulatory molecules. Studies of tRFs in plants have been based on conventional small RNA sequencing, and focused on profiling of tRF-5 and tRF-3 species. A more comprehensive and quantitative analysis of the entire tRF population is highly necessary. Here, we employ tRNA-seq and YAMAT-seq, and develop a bioinformatics tool to comprehensively profile the expressions of tRNAs and tRFs in plants. We show that in Arabidopsis, approximately half of tRNA genes are extremely weakly expressed, accounting for only 1% of total tRNA abundance, while ~12% of tRNA genes contribute to ~80% of tRNA abundance. Our tRNA sequencings in various plants reveal that tRNA expression profiles exhibit a cross-species conserved pattern. By characterizing the composition of a highly heterogeneous tRF population, we show that tRNA halves and previously unnoticed 10-16-nt tiny tRFs represent substantial portions. The highly accumulated 13-nt and 16-nt tiny tRFs in Arabidopsis indicate that tiny tRFs are not random tRNA degradation products. Finally, we provide a user-friendly database for displaying the dynamic spatiotemporal expressions of tRNAs and tRFs in the model plants Arabidopsis and rice.

UI MeSH Term Description Entries
D008958 Models, Molecular Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures. Molecular Models,Model, Molecular,Molecular Model
D009154 Mutation Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations. Mutations
D009690 Nucleic Acid Conformation The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape. DNA Conformation,RNA Conformation,Conformation, DNA,Conformation, Nucleic Acid,Conformation, RNA,Conformations, DNA,Conformations, Nucleic Acid,Conformations, RNA,DNA Conformations,Nucleic Acid Conformations,RNA Conformations
D001483 Base Sequence The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence. DNA Sequence,Nucleotide Sequence,RNA Sequence,DNA Sequences,Base Sequences,Nucleotide Sequences,RNA Sequences,Sequence, Base,Sequence, DNA,Sequence, Nucleotide,Sequence, RNA,Sequences, Base,Sequences, DNA,Sequences, Nucleotide,Sequences, RNA
D012275 Oryza A genus of grass family (Poaceae) that include several rice species. Oryza sativa,Rice,Rices
D012343 RNA, Transfer The small RNA molecules, 73-80 nucleotides long, that function during translation (TRANSLATION, GENETIC) to align AMINO ACIDS at the RIBOSOMES in a sequence determined by the mRNA (RNA, MESSENGER). There are about 30 different transfer RNAs. Each recognizes a specific CODON set on the mRNA through its own ANTICODON and as aminoacyl tRNAs (RNA, TRANSFER, AMINO ACYL), each carries a specific amino acid to the ribosome to add to the elongating peptide chains. Suppressor Transfer RNA,Transfer RNA,tRNA,RNA, Transfer, Suppressor,Transfer RNA, Suppressor,RNA, Suppressor Transfer
D013045 Species Specificity The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species. Species Specificities,Specificities, Species,Specificity, Species
D017360 Arabidopsis A plant genus of the family BRASSICACEAE that contains ARABIDOPSIS PROTEINS and MADS DOMAIN PROTEINS. The species A. thaliana is used for experiments in classical plant genetics as well as molecular genetic studies in plant physiology, biochemistry, and development. Arabidopsis thaliana,Cress, Mouse-ear,A. thaliana,A. thalianas,Arabidopses,Arabidopsis thalianas,Cress, Mouse ear,Cresses, Mouse-ear,Mouse-ear Cress,Mouse-ear Cresses,thaliana, A.,thaliana, Arabidopsis,thalianas, A.
D017423 Sequence Analysis, RNA A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE. RNA Sequence Analysis,Sequence Determination, RNA,Analysis, RNA Sequence,Determination, RNA Sequence,Determinations, RNA Sequence,RNA Sequence Determination,RNA Sequence Determinations,RNA Sequencing,Sequence Determinations, RNA,Analyses, RNA Sequence,RNA Sequence Analyses,Sequence Analyses, RNA,Sequencing, RNA
D018506 Gene Expression Regulation, Plant Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants. Plant Gene Expression Regulation,Regulation of Gene Expression, Plant,Regulation, Gene Expression, Plant

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