title: Both endo-siRNAs and tRNA-derived small RNAs are involved in the differentiation of primitive eukaryote Giardia lamblia.
abstract: Small RNAs (sRNAs), including microRNAs and endogenous siRNAs (endo-siRNAs), regulate most important biologic processes in eukaryotes, such as cell division and differentiation. Although sRNAs have been extensively studied in various eukaryotes, the role of sRNAs in the early emergence of eukaryotes is unclear. To address these questions, we deep sequenced the sRNA transcriptome of four different stages in the differentiation of Giardia lamblia, one of the most primitive eukaryotes. We identified a large number of endo-siRNAs in this fascinating parasitic protozoan and found that they were produced from live telomeric retrotransposons and three genomic regions (i.e., endo-siRNA generating regions [eSGRs]). eSGR-derived endo-siRNAs were proven to target mRNAs in trans. Gradual up-regulation of endo-siRNAs in the differentiation of Giardia suggested that they might be involved in the regulation of this process. This hypothesis was supported by the impairment of the differentiation ability of Giardia when GLDICER, essential for the biogenesis of endo-siRNAs, was knocked down. Endo-siRNAs are not the only sRNA regulators in Giardia differentiation, because a great number of tRNAs-derived sRNAs showed more dramatic expression changes than endo-siRNAs in this process. We totally identified five novel kinds of tRNAs-derived sRNAs and found that the biogenesis in four of them might be correlated with that of stress-induced tRNA-derived RNA (sitRNA), which was discovered in our previous studies. Our studies reveal an unexpected complex panorama of sRNA in G. lamblia and shed light on the origin and functional evolution of eukaryotic sRNAs.
authors.affiliation: State Key Laboratory of Biocontrol and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, People's Republic of China;
authors.forename: Jian-You
authors.initials: JY
authors.lastname: Liao
authors.affiliation: State Key Laboratory of Biocontrol and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China;
authors.forename: Yan-Hua
authors.initials: YH
authors.lastname: Guo
authors.affiliation: State Key Laboratory of Biocontrol and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China;
authors.forename: Ling-Ling
authors.initials: LL
authors.lastname: Zheng
authors.affiliation: State Key Laboratory of Biocontrol and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China;
authors.forename: Yan
authors.initials: Y
authors.lastname: Li
authors.affiliation: State Key Laboratory of Biocontrol and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China;
authors.forename: Wen-Li
authors.initials: WL
authors.lastname: Xu
authors.affiliation: State Key Laboratory of Biocontrol and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China;
authors.forename: Yu-Chan
authors.initials: YC
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Biocontrol and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China;
authors.forename: Hui
authors.initials: H
authors.lastname: Zhou
authors.affiliation: State Key Laboratory of Biocontrol and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China; Key Laboratory of Tropical Diseases Control of the Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, People's Republic of China; and lsslzr@mail.sysu.edu.cn fjayala@uci.edu lssqlh@mail.sysu.edu.cn.
authors.forename: Zhao-Rong
authors.initials: ZR
authors.lastname: Lun
authors.affiliation: Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697 lsslzr@mail.sysu.edu.cn fjayala@uci.edu lssqlh@mail.sysu.edu.cn.
authors.forename: Francisco J
authors.initials: FJ
authors.lastname: Ayala
authors.affiliation: State Key Laboratory of Biocontrol and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China; lsslzr@mail.sysu.edu.cn fjayala@uci.edu lssqlh@mail.sysu.edu.cn.
authors.forename: Liang-Hu
authors.initials: LH
authors.lastname: Qu
mesh_terms: D001483:Base Sequence; D019143:Evolution, Molecular; D018503:Genome, Protozoan; D016829:Giardia lamblia / Q000166:cytology / Q000235:genetics* / Q000254:growth & development; D059014:High-Throughput Nucleotide Sequencing; D008957:Models, Genetic; D009690:Nucleic Acid Conformation; D016053:RNA, Protozoan / Q000737:chemistry / Q000235:genetics*; D034741:RNA, Small Interfering / Q000737:chemistry / Q000235:genetics; D012343:RNA, Transfer / Q000737:chemistry / Q000235:genetics; D018626:Retroelements / Q000235:genetics; D059467:Transcriptome
chemical_list: D016053:RNA, Protozoan; D034741:RNA, Small Interfering; D018626:Retroelements; D012343:RNA, Transfer
keywords: RNA regulation; development; ncRNA sRNA-generating region; single-cell parasite