Tags

Type your tag names separated by a space and hit enter

Genome-wide identification and characterization of tRNA-derived RNA fragments in land plants.
Plant Mol Biol 2017; 93(1-2):35-48PM

Abstract

KEY MESSAGE

The manuscript by Alves et al. entitled "Genome-wide identification and characterization of tRNA-derived RNA fragments in land plants" describes the identification and characterization of tRNAderived sRNA fragments in plants. By combining bioinformatic analysis and genetic and molecular approaches, we show that tRF biogenesis does not rely on canonical microRNA/siRNA processing machinery (i.e., independent of DICER-LIKE proteins). Moreover, we provide evidences that the Arabidopsis S-like Ribonuclease 1 (RNS1) might be involved in the biogenesis of tRFs. Detailed analyses showed that plant tRFs are sorted into different types of ARGONAUTE proteins and that they have potential target candidate genes. Our work advances the understanding of the tRF biology in plants by providing evidences that plant and animal tRFs shared common features and raising the hypothesis that an interplay between tRFs and other sRNAs might be important to fine-tune gene expression and protein biosynthesis in plant cells. Small RNA (sRNA) fragments derived from tRNAs (3'-loop, 5'-loop, anti-codon loop), named tRFs, have been reported in several organisms, including humans and plants. Although they may interfere with gene expression, their biogenesis and biological functions in plants remain poorly understood. Here, we capitalized on small RNA sequencing data from distinct species such as Arabidopsis thaliana, Oryza sativa, and Physcomitrella patens to examine the diversity of plant tRFs and provide insight into their properties. In silico analyzes of 19 to 25-nt tRFs derived from 5' (tRF-5s) and 3'CCA (tRF-3s) tRNA loops in these three evolutionary distant species showed that they are conserved and their abundance did not correlate with the number of genomic copies of the parental tRNAs. Moreover, tRF-5 is the most abundant variant in all three species. In silico and in vivo expression analyses unraveled differential accumulation of tRFs in Arabidopsis tissues/organs, suggesting that they are not byproducts of tRNA degradation. We also verified that the biogenesis of most Arabidopsis 19-25 nt tRF-5s and tRF-3s is not primarily dependent on DICER-LIKE proteins, though they seem to be associated with ARGONAUTE proteins and have few potential targets. Finally, we provide evidence that Arabidopsis ribonuclease RNS1 might be involved in the processing and/or degradation of tRFs. Our data support the notion that an interplay between tRFs and other sRNAs might be important to fine tune gene expression and protein biosynthesis in plant cells.

Authors+Show Affiliations

Departamento de Genetica, Instituto de Biociencias, Universidade Estadual Paulista (UNESP), Distrito de Rubião Jr., s/n, Botucatu, SP, 18618-970, Brazil. Laboratorio de Genetica Molecular do Desenvolvimento Vegetal, Departamento de Ciencias Biologicas, ESALQ/USP, Avenida Pádua Dias s/n, 11, Piracicaba, SP, 13418-900, Brazil.Laboratorio de Bioinformatica e Biologia de Sistemas, Departamento de Genetica, Evoluçao e Bioagentes, Universidade Estadual de Campinas (Unicamp), Campinas, SP, Brazil.Centro de Biologia Molecular e Engenharia Genetica (CBMEG), Universidade Estadual de Campinas (Unicamp), Campinas, SP, Brazil.Departamento de Genetica, Instituto de Biociencias, Universidade Estadual Paulista (UNESP), Distrito de Rubião Jr., s/n, Botucatu, SP, 18618-970, Brazil.Centro de Biologia Molecular e Engenharia Genetica (CBMEG), Universidade Estadual de Campinas (Unicamp), Campinas, SP, Brazil.Laboratorio de Genetica Molecular do Desenvolvimento Vegetal, Departamento de Ciencias Biologicas, ESALQ/USP, Avenida Pádua Dias s/n, 11, Piracicaba, SP, 13418-900, Brazil. ftsnogue@usp.br.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

27681945

Citation

Alves, Cristiane S., et al. "Genome-wide Identification and Characterization of tRNA-derived RNA Fragments in Land Plants." Plant Molecular Biology, vol. 93, no. 1-2, 2017, pp. 35-48.
Alves CS, Vicentini R, Duarte GT, et al. Genome-wide identification and characterization of tRNA-derived RNA fragments in land plants. Plant Mol Biol. 2017;93(1-2):35-48.
Alves, C. S., Vicentini, R., Duarte, G. T., Pinoti, V. F., Vincentz, M., & Nogueira, F. T. (2017). Genome-wide identification and characterization of tRNA-derived RNA fragments in land plants. Plant Molecular Biology, 93(1-2), pp. 35-48. doi:10.1007/s11103-016-0545-9.
Alves CS, et al. Genome-wide Identification and Characterization of tRNA-derived RNA Fragments in Land Plants. Plant Mol Biol. 2017;93(1-2):35-48. PubMed PMID: 27681945.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genome-wide identification and characterization of tRNA-derived RNA fragments in land plants. AU - Alves,Cristiane S, AU - Vicentini,Renato, AU - Duarte,Gustavo T, AU - Pinoti,Vitor F, AU - Vincentz,Michel, AU - Nogueira,Fabio T S, Y1 - 2016/09/28/ PY - 2016/05/20/received PY - 2016/09/19/accepted PY - 2016/9/30/pubmed PY - 2017/2/7/medline PY - 2016/9/30/entrez KW - Arabidopsis thaliana KW - High throughput data KW - Small RNA KW - tRF KW - tRNA-derived RNA fragment SP - 35 EP - 48 JF - Plant molecular biology JO - Plant Mol. Biol. VL - 93 IS - 1-2 N2 - KEY MESSAGE: The manuscript by Alves et al. entitled "Genome-wide identification and characterization of tRNA-derived RNA fragments in land plants" describes the identification and characterization of tRNAderived sRNA fragments in plants. By combining bioinformatic analysis and genetic and molecular approaches, we show that tRF biogenesis does not rely on canonical microRNA/siRNA processing machinery (i.e., independent of DICER-LIKE proteins). Moreover, we provide evidences that the Arabidopsis S-like Ribonuclease 1 (RNS1) might be involved in the biogenesis of tRFs. Detailed analyses showed that plant tRFs are sorted into different types of ARGONAUTE proteins and that they have potential target candidate genes. Our work advances the understanding of the tRF biology in plants by providing evidences that plant and animal tRFs shared common features and raising the hypothesis that an interplay between tRFs and other sRNAs might be important to fine-tune gene expression and protein biosynthesis in plant cells. Small RNA (sRNA) fragments derived from tRNAs (3'-loop, 5'-loop, anti-codon loop), named tRFs, have been reported in several organisms, including humans and plants. Although they may interfere with gene expression, their biogenesis and biological functions in plants remain poorly understood. Here, we capitalized on small RNA sequencing data from distinct species such as Arabidopsis thaliana, Oryza sativa, and Physcomitrella patens to examine the diversity of plant tRFs and provide insight into their properties. In silico analyzes of 19 to 25-nt tRFs derived from 5' (tRF-5s) and 3'CCA (tRF-3s) tRNA loops in these three evolutionary distant species showed that they are conserved and their abundance did not correlate with the number of genomic copies of the parental tRNAs. Moreover, tRF-5 is the most abundant variant in all three species. In silico and in vivo expression analyses unraveled differential accumulation of tRFs in Arabidopsis tissues/organs, suggesting that they are not byproducts of tRNA degradation. We also verified that the biogenesis of most Arabidopsis 19-25 nt tRF-5s and tRF-3s is not primarily dependent on DICER-LIKE proteins, though they seem to be associated with ARGONAUTE proteins and have few potential targets. Finally, we provide evidence that Arabidopsis ribonuclease RNS1 might be involved in the processing and/or degradation of tRFs. Our data support the notion that an interplay between tRFs and other sRNAs might be important to fine tune gene expression and protein biosynthesis in plant cells. SN - 1573-5028 UR - https://www.unboundmedicine.com/medline/citation/27681945/Genome_wide_identification_and_characterization_of_tRNA_derived_RNA_fragments_in_land_plants_ L2 - https://doi.org/10.1007/s11103-016-0545-9 DB - PRIME DP - Unbound Medicine ER -