Bioinformatics Analysis of tRNA-derived Fragments in Rice Male Gametophyte Development

doi:10.11983/CBB17169

Abstract

Abstract: tRNA derived fragments (termed tRFs) are functional RNAs produced by non-random cleavage of tRNAs. The knowledge of tRNAs’ production and function is being studied but is unknown in the rice male gametophyte. Using high-throughput sequencing with 3 stages in the rice male gametophyte development, we found tRFs with a large range of length. Next, we determined four sequence-specific and one non-sequence-specific ribonuclease cleaving sites. We also summarized the distribution profile of tRFs in the three stages. Finally, a NCBI blast search was carried out to predict the tRF target gene, revealing that the major class of targets was transposable elements. This results provid new clues for rice male gametophyte research.

Key words: rice, male gametophyte, pollen, tRFs, bioinformatics

Liu Wei, Tong Yong’ao, Bai Jie. Bioinformatics Analysis of tRNA-derived Fragments in Rice Male Gametophyte Development[J]. Chinese Bulletin of Botany, 2018, 53(5): 625-633.

Add to citation manager EndNote|Ris|BibTeX

URL: https://www.chinbullbotany.com/EN/10.11983/CBB17169

https://www.chinbullbotany.com/EN/Y2018/V53/I5/625

Figures/Tables 5

Figure 1 Length distribution of tRFs in three types of pollens in rice male gameteunm: Uni-nucleate microspore; bcp: Bi-cellular pollen; tcp : Tri-cellular pollen; RPM: Reads per million

Figure 2 tRFs’ starting and ending site distribution in tRNAs’ universal cloverleaf structure sections in three types of pollens in rice male gamete(A) Schematic view of tRNAs’ cloverleaf-like secondary structure; (B) tRFs’ starting site positions in tRNA; (C) tRFs’ ending site positions in tRNA. * indicate that the numbers before can only be regarded as a positions represented in Figure 2A instead of base ID. unm, bcp, tcp and RPM see Figure 1.

Figure 3 tRFs’ 5’ end base bias in three types of pollens in rice male gamete(A) tRF starting site’s distribution in each position of their host tRNA (The vertical axis labels’ positions were transferred according to their square root number); (B) First 8 base logo of the tRNAs that produce tRFs from the 1st base in bcp; (C) First 8 base logo of tRNAs that produce tRFs from the 2nd base in bcp; (D) First 8 base logo of the tRNAs that produce tRFs from the 1st base in tcp; (E) First 8 base logo of tRNAs that produce tRFs from the 2nd base in tcp. unm, bcp, tcp and RPM see Figure 1.

Figure 4 Sequence motif logo for tRNA 8 mer around cleavage sites in three types of pollens in rice male gamete(A), (D) Sequence logo of all tRNA’s first 7 bases of D loop and Anticodon loop; (B) For bcp tRFs ended at the 3rd base of D loop; (C) For tcp tRFs started at the 7th base of D loop; (E) For bcp tRFs ended at the 1st base of Anticodon loop; (F) For tcp tRFs started at the 6th base of Anticodon loop. The position between 4 and 5 in X axis of Figure B, C, E and F stand for cleavage site.

Table 1 tRFs targeted loci of non-TE and TE genes

Sample	No. of non-TE genes	No. of genic TEs	No. of intergenic TEs	TE Percentage (%)
unm	317	166	506	67.95
bcp	728	403	905	64.24
tcp	529	287	736	65.91

References 33

1	Abe T, Ikemura T, Ohara Y, Uehara H, Kinouchi M, Kanaya S, Yamada Y, Muto A, Inokuchi H (2009). tRNADB-CE: tRNA gene database curated manually by experts.Nucleic Acids Res 37, D163-D168.
2	Alves CS, Vicentini R, Duarte GT, Pinoti VF, Vincentz M, Nogueira FTS (2016). Genome-wide identification and characterization of tRNA-derived RNA fragments in land plants.Plant Mol Biol 93, 35-48.
3	Anderson SN, Johnson CS, Jones DS, Conrad LJ, Gou XP, Russell SD, Sundaresan V (2013). Transcriptomes of isolated Oryza sativa gametes characterized by deep sequencing: evidence for distinct sex-dependent chromatin and epigenetic states before fertilization. Plant J 76, 729-741.
4	Chen CJ, Liu Q, Zhang YC, Qu LH, Chen YQ, Gautheret D (2011). Genome-wide discovery and analysis of microRNAs and other small RNAs from rice embryogenic callus.RNA Biol 8, 538-547.
5	Cole C, Sobala A, Lu C, Thatcher SR, Bowman A, Brown JWS, Green PJ, Barton GJ, Hutvagner G (2009). Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs.RNA 15, 2147-2160.
6	Couvillion MT, Sachidanandam R, Collins K (2010). A growth-essential Tetrahymena Piwi protein carries tRNA fragment cargo. Genes Dev 24, 2742-2747.
7	Dunin-Horkawicz S, Czerwoniec A, Gajda MJ, Feder M, Grosjean H, Bujnicki JM (2006). MODOMICS: a database of RNA modification pathways.Nucleic Acids Res 34, D145-D149.
8	Emara MM, Ivanov P, Hickman T, Dawra N, Tisdale S, Kedersha N, Hu GF, Anderson P (2010). Angiogenin- induced tRNA-derived stress-induced RNAs promote stress-induced stress granule assembly.J Biol Chem 285, 10959-10968.
9	Gebetsberger J, Wyss L, Mleczko AM, Reuther J, Polacek N (2017). A tRNA-derived fragment competes with mRNA for ribosome binding and regulates translation during stress.RNA Biol 14, 1364-1373.
10	Goodarzi H, Liu XH, Nguyen HCB, Zhang S, Fish L, Tavazoie SF (2015). Endogenous tRNA-derived fragments suppress breast cancer progression via YBX1 displacement.Cell 161, 790-802.
11	Grant-Downton R, Le Trionnaire G, Schmid R, Rodriguez-Enriquez J, Hafidh S, Mehdi S, Twell D, Dickinson H (2009). MicroRNA and tasiRNA diversity in mature pollen of Arabidopsis thaliana. BMC Genomics 10, 643.
12	Hsieh LC, Lin SI, Kuo HF, Chiou TJ (2010). Abundance of tRNA-derived small RNAs in phosphate-starved Arabidopsis roots.Plant Signal Behav 5, 537-539.
13	Karaiskos S, Naqvi AS, Swanson KE, Grigoriev A (2015). Age-driven modulation of tRNA-derived fragments in Drosophila and their potential targets. Biol Direct 10, 51.
14	Keam SP, Sobala A, Ten Have S, Hutvagner G (2017). tRNA-Derived RNA fragments associate with human multisynthetase complex (MSC) and modulate ribosomal protein translation.J Proteome Res 16, 413-420.
15	Kumar P, Anaya J, Mudunuri SB, Dutta A (2014). Meta- analysis of tRNA derived RNA fragments reveals that they are evolutionarily conserved and associate with AGO proteins to recognize specific RNA targets.BMC Biol 12, 78.
16	Kumar P, Kuscu C, Dutta A (2016). Biogenesis and function of transfer RNA-related fragments (tRFs).Trends Biochem Sci 41, 679-689.
17	Loss-Morais G, Waterhouse PM, Margis R (2013). Description of plant tRNA-derived RNA fragments (tRFs) associated with argonaute and identification of their putative targets.Biol Direct 8, 6.
18	Lowe TM, Eddy SR (1997). tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.Nucleic Acids Res 25, 955-964.
19	Martinez G, Choudury SG, Slotkin RK (2017). tRNA- derived small RNAs target transposable element transcripts.Nucleic Acids Res 45, 5142-5152.
20	Nawrot B, Malkiewicz A, Smith WS, Sierzputowska-Gracz H, Agris PF (1995). RNA modified uridines VII: chemical synthesis and initial analysis of tRNA D-Loop oligomers with tandem modified uridines.Nucleos Nucleot Nud 14, 143-165.
21	Peng H, Chun J, Ai TB, Tong YA, Zhang R, Zhao MM, Chen F, Wang SH (2012). MicroRNA profiles and their control of male gametophyte development in rice.Plant Mol Biol 80, 85-102.
22	Schaefer M, Pollex T, Hanna K, Tuorto F, Meusburger M, Helm M, Lyko F (2010). RNA methylation by Dnmt2 protects transfer RNAs against stress-induced cleavage.Genes Dev 24, 1590-1595.
23	Sharma U, Conine CC, Shea JM, Boskovic A, Derr AG, Bing XY, Belleannee C, Kucukural A, Serra RW, Sun FY, Song LN, Carone BR, Ricci EP, Li XZ, Fauquier L, Moore MJ, Sullivan R, Mello CC, Garber M, Rando OJ (2016). Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals.Science 351, 391-396.
24	Slotkin RK, Vaughn M, Borges F, Tanurdžić M, Becker JD, Feijo JA, Martienssen RA (2009). Epigenetic reprogramming and small RNA silencing of transposable elements in pollen.Cell 136, 461-472.
25	Sobala A, Hutvagner G (2013). Small RNAs derived from the 5' end of tRNA can inhibit protein translation in human cells.RNA Biol 10, 553-563.
26	Stroud H, Ding B, Simon SA, Feng SH, Bellizzi M, Pellegrini M, Wang GL, Meyers BC, Jacobsen SE (2013). Plants regenerated from tissue culture contain stable epigenome changes in rice.eLife 2, e00354.
27	Thompson DM, Parker R (2009). The RNase Rny1p cleaves tRNAs and promotes cell death during oxidative stress in Saccharomyces cerevisiae. J Cell Biol 185, 43-50.
28	Tuorto F, Liebers R, Musch T, Schaefer M, Hofmann S, Kellner S, Frye M, Helm M, Stoecklin G, Lyko F (2012). RNA cytosine methylation by Dnmt2 and NSun2 promotes tRNA stability and protein synthesis.Nat Struct Mol Biol 19, 900-905.
29	Vare VYP, Eruysal ER, Narendran A, Sarachan KL, Agris PF (2017). Chemical and conformational diversity of modified nucleosides affects tRNA structure and function.Bio- molecules 7, 29.
30	Wang F, Johnson NR, Coruh C, Axtell MJ (2016a). Genome-wide analysis of single non-templated nucleotides in plant endogenous siRNAs and miRNAs.Nucleic Acids Res 44, 7395-7405.
31	Wang QH, Li TT, Xu K, Zhang W, Wang XL, Quan JL, Jin WB, Zhang MX, Fan GJ, Wang MB, Shan WX (2016b). The tRNA-derived small RNAs regulate gene expression through triggering sequence-specific degradation of target transcripts in the oomycete pathogen Phytophthora sojae. Front Plant Sci 7, 1938.
32	Wei LQ, Xu WY, Deng ZY, Su Z, Xue YB, Wang T (2010). Genome-scale analysis and comparison of gene expression profiles in developing and germinated pollen in Oryza sativa. BMC Genomics 11, 338.
33	Wei LQ, Yan LF, Wang T (2011). Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa. Genome Biol 12, R53.

[1]	Juan Cui, Xiaoyu Yu, Yuejiao Yu, Chengwei Liang, Jian Sun, Wenfu Chen. Analysis of Texture Factors and Genetic Basis Influencing the Differences in Eating Quality between Northeast China and Japanese Japonica Rice [J]. Chinese Bulletin of Botany, 2025, 60(4): 1-0.
[2]	Yang Li, Qu Xitong, Chen Zihang, Zou Tingting, Wang Quanhua, Wang Xiaoli. Identification of the Spinach AT-hook Gene Family and Analysis of Expression Profiles [J]. Chinese Bulletin of Botany, 2025, 60(3): 377-392.
[3]	Zhao Ling, Guan Ju, Liang Wenhua, Zhang Yong, Lu Kai, Zhao Chunfang, Li Yusheng, Zhang Yadong. Mapping of QTLs for Heat Tolerance at the Seedling Stage in Rice Based on a High-density Bin Map [J]. Chinese Bulletin of Botany, 2025, 60(3): 342-353.
[4]	Xinyu Li, Yue Gu, Feifei Xu, Jinsong Bao. Research Progress on Post-translational Modifications of Starch Biosynthesis-related Proteins in Rice Endosperm [J]. Chinese Bulletin of Botany, 2025, 60(2): 256-270.
[5]	Jianguo Li, Yi Zhang, Wenjun Zhang. Iron Plaque Formation and Its Effects on Phosphorus Absorption in Rice Roots [J]. Chinese Bulletin of Botany, 2025, 60(1): 132-143.
[6]	Suyan Ba, Chunyan Zhao, Yuan Liu, Qiang Fang. Constructing a pollination network by identifying pollen on insect bodies: Consistency between human recognition and an AI model [J]. Biodiv Sci, 2024, 32(6): 24088-.
[7]	Ruifeng Yao, Daoxin Xie. Activation and Termination of Strigolactone Signal Perception in Rice [J]. Chinese Bulletin of Botany, 2024, 59(6): 873-877.
[8]	Siying Qin, Yan Luo, He Zhang, Jun Hu, Jugou Liao. Optimization of Preparation and Detection Methods for Pollen Tube Cell Wall by Atomic Force Microscopy [J]. Chinese Bulletin of Botany, 2024, 59(5): 783-791.
[9]	Jinjin Lian, Luyao Tang, Yinuo Zhang, Jiaxing Zheng, Chaoyu Zhu, Yuhan Ye, Yuexing Wang, Wennan Shang, Zhenghao Fu, Xinxuan Xu, Richeng Wu, Mei Lu, Changchun Wang, Yuchun Rao. Genetic Locus Mining and Candidate Gene Analysis of Antioxidant Traits in Rice [J]. Chinese Bulletin of Botany, 2024, 59(5): 738-751.
[10]	Jiahui Huang, Huimin Yang, Xinyu Chen, Chaoyu Zhu, Yanan Jiang, Chengxiang Hu, Jinjin Lian, Tao Lu, Mei Lu, Weilin Zhang, Yuchun Rao. Response Mechanism of Rice Mutant pe-1 to Low Light Stress [J]. Chinese Bulletin of Botany, 2024, 59(4): 574-584.
[11]	Jianmin Zhou. A Combat Vehicle with a Smart Brake [J]. Chinese Bulletin of Botany, 2024, 59(3): 343-346.
[12]	Chaoyu Zhu, Chengxiang Hu, Zhenan Zhu, Zhining Zhang, Lihai Wang, Jun Chen, Sanfeng Li, Jinjin Lian, Luyao Tang, Qianqian Zhong, Wenjing Yin, Yuexing Wang, Yuchun Rao. Mapping of QTLs Associated with Rice Panicle Traits and Candidate Gene Analysis [J]. Chinese Bulletin of Botany, 2024, 59(2): 217-230.
[13]	Bao Zhu, Jiangzhe Zhao, Kewei Zhang, Peng Huang. OsCKX9 is Involved in Regulating the Rice Lamina Joint Development and Leaf Angle [J]. Chinese Bulletin of Botany, 2024, 59(1): 10-21.
[14]	Yanli Fang, Chuanyu Tian, Ruyi Su, Yapei Liu, Chunlian Wang, Xifeng Chen, Wei Guo, Zhiyuan Ji. Mining and Preliminary Mapping of Rice Resistance Genes Against Bacterial Leaf Streak [J]. Chinese Bulletin of Botany, 2024, 59(1): 1-9.
[15]	Feifei Zhang, Tianfeng Yang, Lirong Chen, Dongmei Liu, Liuyuan Yang, Duyu Yang, Peng Ju, Lu Lu. Review of pollen color diversity in Angiosperms [J]. Biodiv Sci, 2024, 32(1): 23346-.