Genome-wide identification of short 2′,3′-cyclic phosphate-containing RNAs and their regulation in aging

English version

Autoři: Megumi Shigematsu ^aff001; Keisuke Morichika ^aff001; Takuya Kawamura ^aff001; Shozo Honda ^aff001; Yohei Kirino ^aff001
Působiště autorů: Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America ^aff001
Vyšlo v časopise: Genome-wide identification of short 2′,3′-cyclic phosphate-containing RNAs and their regulation in aging. PLoS Genet 15(11): e32767. doi:10.1371/journal.pgen.1008469
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pgen.1008469

Souhrn

RNA molecules generated by ribonuclease cleavage sometimes harbor a 2′,3′-cyclic phosphate (cP) at their 3′-ends. Those cP-containing RNAs (cP-RNAs) form a hidden layer of transcriptome because standard RNA-seq cannot capture them as a result of cP’s prevention of an adapter ligation reaction. Here we provide genome-wide analyses of short cP-RNA transcriptome across multiple mouse tissues. Using cP-RNA-seq that can exclusively sequence cP-RNAs, we identified numerous novel cP-RNA species which are mainly derived from cytoplasmic tRNAs, mRNAs, and rRNAs. Determination of the processing sites of substrate RNAs for cP-RNA generation revealed highly-specific RNA cleavage events between cytidine and adenosine in cP-RNA biogenesis. cP-RNAs were not evenly derived from the overall region of substrate RNAs but rather from specific sites, implying that cP-RNAs are not from random degradation but are produced through a regulated biogenesis pathway. The identified cP-RNAs were abundantly accumulated in mouse tissues, and the expression levels of cP-RNAs showed age-dependent reduction. These analyses of cP-RNA transcriptome unravel a novel, abundant class of non-coding RNAs whose expression could have physiological roles.

Klíčová slova:

Mammalian genomics – Non-coding RNA – Non-coding RNA sequences – Ribosomal RNA – RNA sequencing – Sequence assembly tools – Transfer RNA – Small nucleolar RNA

Zdroje

1. Goodwin S, McPherson JD, McCombie WR (2016) Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet 17 : 333–351. doi: 10.1038/nrg.2016.49 27184599

2. Marguerat S, Bahler J (2010) RNA-seq: from technology to biology. Cell Mol Life Sci 67 : 569–579. doi: 10.1007/s00018-009-0180-6 19859660

3. Costa V, Aprile M, Esposito R, Ciccodicola A (2013) RNA-Seq and human complex diseases: recent accomplishments and future perspectives. Eur J Hum Genet 21 : 134–142. doi: 10.1038/ejhg.2012.129 22739340

4. Shigematsu M, Kawamura T, Kirino Y (2018) Generation of 2',3'-Cyclic Phosphate-Containing RNAs as a Hidden Layer of the Transcriptome. Front Genet 9 : 562. doi: 10.3389/fgene.2018.00562 30538719

5. Yamasaki S, Ivanov P, Hu GF, Anderson P (2009) Angiogenin cleaves tRNA and promotes stress-induced translational repression. J Cell Biol 185 : 35–42. doi: 10.1083/jcb.200811106 19332886

6. Emara MM, Ivanov P, Hickman T, Dawra N, Tisdale S, et al. (2010) Angiogenin-induced tRNA-derived stress-induced RNAs promote stress-induced stress granule assembly. J Biol Chem 285 : 10959–10968. doi: 10.1074/jbc.M109.077560 20129916

7. Ivanov P, Emara MM, Villén J, Gygi SP, Anderson P (2011) Angiogenin-Induced tRNA Fragments Inhibit Translation Initiation. Molecular Cell 43 : 613–623. doi: 10.1016/j.molcel.2011.06.022 21855800

8. Ivanov P, O'Day E, Emara MM, Wagner G, Lieberman J, et al. (2014) G-quadruplex structures contribute to the neuroprotective effects of angiogenin-induced tRNA fragments. Proc Natl Acad Sci U S A 111 : 18201–18206. doi: 10.1073/pnas.1407361111 25404306

9. Blanco S, Dietmann S, Flores JV, Hussain S, Kutter C, et al. (2014) Aberrant methylation of tRNAs links cellular stress to neuro-developmental disorders. EMBO J 33 : 2020–2039. doi: 10.15252/embj.201489282 25063673

10. Honda S, Loher P, Shigematsu M, Palazzo JP, Suzuki R, et al. (2015) Sex hormone-dependent tRNA halves enhance cell proliferation in breast and prostate cancers. Proc Natl Acad Sci U S A 112: E3816–3825. doi: 10.1073/pnas.1510077112 26124144

11. Honda S, Kirino Y. (2015) SHOT-RNAs: a novel class of tRNA-derived functional RNAs expressed in hormone-dependent cancers. Mol Cell Onco 3: e1079672. doi: 10.1080/23723556.2015.1079672 27308603

12. Honda S, Morichika K, Kirino Y (2016) Selective amplification and sequencing of cyclic phosphate-containing RNAs by the cP-RNA-seq method. Nat Protoc 11 : 476–489. doi: 10.1038/nprot.2016.025 26866791

13. Dhahbi JM, Spindler SR, Atamna H, Yamakawa A, Boffelli D, et al. (2013) 5' tRNA halves are present as abundant complexes in serum, concentrated in blood cells, and modulated by aging and calorie restriction. BMC Genomics 14 : 298. doi: 10.1186/1471-2164-14-298 23638709

14. Sharma U, Conine CC, Shea JM, Boskovic A, Derr AG, et al. (2016) Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals. Science 351 : 391–396. doi: 10.1126/science.aad6780 26721685

15. Shigematsu M, Honda S, Kirino Y (2014) Transfer RNA as a source of small functional RNA. J Mol Biol Mol Imaging 1. 26389128

16. Loher P, Telonis AG, Rigoutsos I (2017) MINTmap: fast and exhaustive profiling of nuclear and mitochondrial tRNA fragments from short RNA-seq data. Sci Rep 7 : 41184. doi: 10.1038/srep41184 28220888

17. Pliatsika V, Loher P, Telonis AG, Rigoutsos I (2016) MINTbase: a framework for the interactive exploration of mitochondrial and nuclear tRNA fragments. Bioinformatics 32 : 2481–2489. doi: 10.1093/bioinformatics/btw194 27153631

18. Telonis AG, Loher P, Honda S, Jing Y, Palazzo J, et al. (2015) Dissecting tRNA-derived fragment complexities using personalized transcriptomes reveals novel fragment classes and unexpected dependencies. Oncotarget 6 : 24797–24822. doi: 10.18632/oncotarget.4695 26325506

19. Chan PP, Lowe TM (2009) GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res 37: D93–97. doi: 10.1093/nar/gkn787 18984615

20. Sprinzl M, Horn C, Brown M, Ioudovitch A, Steinberg S (1998) Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res 26 : 148–153. doi: 10.1093/nar/26.1.148 9399820

21. Shigematsu M, Kirino Y. (2017) 5'-Terminal nucleotide variations in human cytoplasmic tRNAHisGUG and its 5'-halves. RNA 23 : 161–168. doi: 10.1261/rna.058024.116 27879434

22. Czech A, Wende S, Mörl M, Pan T, Ignatova Z (2013) Reversible and rapid transfer-RNA deactivation as a mechanism of translational repression in stress. PLoS Genet 9: e1003767. doi: 10.1371/journal.pgen.1003767 24009533

23. Schutz K, Hesselberth JR, Fields S (2010) Capture and sequence analysis of RNAs with terminal 2',3'-cyclic phosphates. RNA 16 : 621–631. doi: 10.1261/rna.1934910 20075163

24. Mebius RE, Kraal G (2005) Structure and function of the spleen. Nat Rev Immunol 5 : 606–616. doi: 10.1038/nri1669 16056254

25. Wang LK, Shuman S (2002) Mutational analysis defines the 5'-kinase and 3'-phosphatase active sites of T4 polynucleotide kinase. Nucleic Acids Res 30 : 1073–1080. doi: 10.1093/nar/30.4.1073 11842120

26. Honda S, Kawamura T, Loher P, Morichika K, Rigoutsos I, et al. (2017) The biogenesis pathway of tRNA-derived piRNAs in Bombyx germ cells. Nucleic Acids Res 45 : 9108–9120. doi: 10.1093/nar/gkx537 28645172

27. Bissels U, Wild S, Tomiuk S, Holste A, Hafner M, et al. (2009) Absolute quantification of microRNAs by using a universal reference. RNA 15 : 2375–2384. doi: 10.1261/rna.1754109 19861428

28. Shapiro R, Riordan JF, Vallee BL (1986) Characteristic ribonucleolytic activity of human angiogenin. Biochemistry 25 : 3527–3532. doi: 10.1021/bi00360a008 2424496

29. Harper JW, Vallee BL (1989) A covalent angiogenin/ribonuclease hybrid with a fourth disulfide bond generated by regional mutagenesis. Biochemistry 28 : 1875–1884. doi: 10.1021/bi00430a067 2719939

30. Nikolaev Y, Deillon C, Hoffmann SR, Bigler L, Friess S, et al. (2010) The leucine zipper domains of the transcription factors GCN4 and c-Jun have ribonuclease activity. PLoS One 5: e10765. doi: 10.1371/journal.pone.0010765 20505831

31. Honda S, Kirino Y, Maragkakis M, Alexiou P, Ohtaki A, et al. (2013) Mitochondrial protein BmPAPI modulates the length of mature piRNAs. RNA 19 : 1405–1418. doi: 10.1261/rna.040428.113 23970546

32. Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25. doi: 10.1186/gb-2009-10-3-r25 19261174

33. Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, et al. (2011) Integrative genomics viewer. Nat Biotechnol 29 : 24–26. doi: 10.1038/nbt.1754 21221095

34. Lorenz R, Bernhart SH, Honer Zu Siederdissen C, Tafer H, Flamm C, et al. (2011) ViennaRNA Package 2.0. Algorithms Mol Biol 6 : 26. doi: 10.1186/1748-7188-6-26 22115189