Bartel, D. P. Metazoan microRNAs. Cell 173, 20–51 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wang, X., Ramat, A., Simonelig, M. & Liu, M. F. Emerging roles and functional mechanisms of PIWI-interacting RNAs. Nat. Rev. Mol. Cell Biol. 24, 123–141 (2023).

Article  CAS  PubMed  Google Scholar 

Shi, J., Zhou, T. & Chen, Q. Exploring the expanding universe of small RNAs. Nat. Cell Biol. 24, 415–423 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen, Q., Zhang, X., Shi, J., Yan, M. & Zhou, T. Origins and evolving functionalities of tRNA-derived small RNAs. Trends Biochem. Sci. 46, 790–804 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Costa, B. et al. Nicked tRNAs are stable reservoirs of tRNA halves in cells and biofluids. Proc. Natl Acad. Sci. USA 120, e2216330120 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen, X. & Wolin, S. L. Transfer RNA halves are found as nicked tRNAs in cells: evidence that nicked tRNAs regulate expression of an RNA repair operon. RNA https://doi.org/10.1261/rna.079575.122 (2023).

Article  PubMed  PubMed Central  Google Scholar 

Drino, A. et al. Identification of RNA helicases with unwinding activity on angiogenin-processed tRNAs. Nucleic Acids Res. 51, 1326–1352 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Akiyama, Y. et al. RTCB complex regulates stress-induced tRNA cleavage. Int. J. Mol. Sci. 23, 13100 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Spitale, R. C. & Incarnato, D. Probing the dynamic RNA structurome and its functions. Nat. Rev. Genet. 24, 178–196 (2023).

Article  CAS  PubMed  Google Scholar 

Giraldez, M. D. et al. Comprehensive multi-center assessment of small RNA-seq methods for quantitative miRNA profiling. Nat. Biotechnol. 36, 746–757 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hafner, M. et al. RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries. RNA 17, 1697–1712 (2011).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hu, J. F. et al. Quantitative mapping of the cellular small RNA landscape with AQRNA-seq. Nat. Biotechnol. 39, 978–988 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Song, Y., Liu, K. J. & Wang, T. H. Elimination of ligation dependent artifacts in T4 RNA ligase to achieve high efficiency and low bias microRNA capture. PLoS ONE 9, e94619 (2014).

Article  PubMed  PubMed Central  Google Scholar 

Zhang, Z., Lee, J. E., Riemondy, K., Anderson, E. M. & Yi, R. High-efficiency RNA cloning enables accurate quantification of miRNA expression by deep sequencing. Genome Biol. 14, R109 (2013).

Article  PubMed  PubMed Central  Google Scholar 

Turchinovich, A. et al. Capture and amplification by tailing and switching (CATS): an ultrasensitive ligation-independent method for generation of DNA libraries for deep sequencing from picogram amounts of DNA and RNA. RNA Biol. 11, 817–828 (2014).

Article  PubMed  PubMed Central  Google Scholar 

Zhu, Y. Y., Machleder, E. M., Chenchik, A., Li, R. & Siebert, P. D. Reverse transcriptase template switching: a SMART approach for full-length cDNA library construction. Biotechniques 30, 892–897 (2001).

Article  CAS  PubMed  Google Scholar 

Upton, H. E. et al. Low-bias ncRNA libraries using ordered two-template relay: serial template jumping by a modified retroelement reverse transcriptase. Proc. Natl Acad. Sci. USA 118, e2107900118 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wulf, M. G. et al. Non-templated addition and template switching by Moloney murine leukemia virus (MMLV)-based reverse transcriptases co-occur and compete with each other. J. Biol. Chem. 294, 18220–18231 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dard-Dascot, C. et al. Systematic comparison of small RNA library preparation protocols for next-generation sequencing. BMC Genomics 19, 118 (2018).

Article  PubMed  PubMed Central  Google Scholar 

Mohr, S. et al. Thermostable group II intron reverse transcriptase fusion proteins and their use in cDNA synthesis and next-generation RNA sequencing. RNA 19, 958–970 (2013).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zheng, G. et al. Efficient and quantitative high-throughput tRNA sequencing. Nat. Methods 12, 835–837 (2015).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Nottingham, R. M. et al. RNA-seq of human reference RNA samples using a thermostable group II intron reverse transcriptase. RNA 22, 597–613 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Xu, H., Yao, J., Wu, D. C. & Lambowitz, A. M. Improved TGIRT-seq methods for comprehensive transcriptome profiling with decreased adapter dimer formation and bias correction. Sci. Rep. 9, 7953 (2019).

Article  PubMed  PubMed Central  Google Scholar 

Behrens, A., Rodschinka, G. & Nedialkova, D. D. High-resolution quantitative profiling of tRNA abundance and modification status in eukaryotes by mim-tRNAseq. Mol. Cell 81, 1802–1815.e7 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Heyer, E. E., Ozadam, H., Ricci, E. P., Cenik, C. & Moore, M. J. An optimized kit-free method for making strand-specific deep sequencing libraries from RNA fragments. Nucleic Acids Res. 43, (2015).

Cozen, A. E. et al. ARM-seq: AlkB-facilitated RNA methylation sequencing reveals a complex landscape of modified tRNA fragments. Nat. Methods 12, 879–884 (2015).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wang, H. et al. CPA-seq reveals small ncRNAs with methylated nucleosides and diverse termini. Cell Discov. 7, 25 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Shi, J. et al. PANDORA-seq expands the repertoire of regulatory small RNAs by overcoming RNA modifications. Nat. Cell Biol. 23, 424–436 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Pinkard, O., McFarland, S., Sweet, T. & Coller, J. Quantitative tRNA-sequencing uncovers metazoan tissue-specific tRNA regulation. Nat. Commun. 11, 4104 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Shigematsu, M. et al. YAMAT-seq: an efficient method for high-throughput sequencing of mature transfer RNAs. Nucleic Acids Res. 45, e70 (2017).

CAS  PubMed  PubMed Central  Google Scholar 

Nolte’T Hoen, E. N. M. et al. Deep sequencing of RNA from immune cell-derived vesicles uncovers the selective incorporation of small non-coding RNA biotypes with potential regulatory functions. Nucleic Acids Res. 40, 9272–9285 (2012).

Article  PubMed  Google Scholar 

Tosar, J. P. et al. Assessment of small RNA sorting into different extracellular fractions revealed by high-throughput sequencing of breast cell lines. Nucleic Acids Res. 43, 5601–5616 (2015).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sharma, U. et al. Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals. Science 351, 391–396 (2016).

Article  CAS  PubMed  Google Scholar 

Shurtleff, M. J. et al. Broad role for YBX1 in defining the small noncoding RNA composition of exosomes. Proc. Natl Acad. Sci. USA 114, E8987–E8995 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Tosar, J. P. et al. Fragmentation of extracellular ribosomes and tRNAs shapes the extracellular RNAome. Nucleic Acids Res. 48, 12874–12888 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gogakos, T. et al. Characterizing expression and processing of precursor and mature human tRNAs by hydro-tRNAseq and PAR-CLIP. Cell Rep. 20, 1463–1475 (2017).

Article