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Krishna S, Raghavan S, DasGupta R, Palakodeti D. tRNA-derived fragments (tRFs): establishing their turf in post-transcriptional gene regulation. Cell Mol Life Sci 2021; 78:2607-2619. [PMID: 33388834 PMCID: PMC11073306 DOI: 10.1007/s00018-020-03720-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/02/2020] [Accepted: 11/24/2020] [Indexed: 02/06/2023]
Abstract
Transfer RNA (tRNA)-derived fragments (tRFs) are an emerging class of conserved small non-coding RNAs that play important roles in post-transcriptional gene regulation. High-throughput sequencing of multiple biological samples have identified heterogeneous species of tRFs with distinct functionalities. These small RNAs have garnered a lot of scientific attention due to their ubiquitous expression and versatility in regulating various biological processes. In this review, we highlight our current understanding of tRF biogenesis and their regulatory functions. We summarize the diverse modes of biogenesis through which tRFs are generated and discuss the mechanism through which different tRF species regulate gene expression and the biological implications. Finally, we conceptualize research areas that require focus to strengthen our understanding of the biogenesis and function of tRFs.
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Affiliation(s)
- Srikar Krishna
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
- SASTRA University, Thirumalaisamudram, Thanjavur, India
| | - Srikala Raghavan
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India.
| | - Ramanuj DasGupta
- Precision Oncology, Genome Institute of Singapore, Singapore City, Singapore.
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Tosar JP, Gámbaro F, Castellano M, Cayota A. RI-SEC-seq: Comprehensive Profiling of Nonvesicular Extracellular RNAs with Different Stabilities. Bio Protoc 2021; 11:e3918. [PMID: 33732805 DOI: 10.21769/bioprotoc.3918] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/24/2020] [Accepted: 12/26/2020] [Indexed: 12/13/2022] Open
Abstract
Exosomes and other extracellular vesicles (EVs) are considered the main vehicles transporting RNAs in extracellular samples, including human bodily fluids. However, a major proportion of extracellular RNAs (exRNAs) do not copurify with EVs and remain in ultracentrifugation supernatants of cell-conditioned medium or blood serum. We have observed that nonvesicular exRNA profiles are highly biased toward those RNAs with intrinsic resistance to extracellular ribonucleases. These highly resistant exRNAs are interesting from a biomarker point of view, but are not representative of the actual bulk of RNAs released to the extracellular space. In order to understand exRNA dynamics and capture both stable and unstable RNAs, we developed a method based on size-exclusion chromatography (SEC) fractionation of RNase inhibitor (RI)-treated cell-conditioned medium (RI-SEC-seq). This method has allowed us to identify and study extracellular ribosomes and tRNAs, and offers a dynamical view of the extracellular RNAome which can impact biomarker discovery in the near future. Graphical abstract: Overview of the RI-SEC-seq protocol: sequencing of size-exclusion chromatography fractions from nonvesicular extracellular samples treated or not with RNase inhibitors (+/- RI).
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Affiliation(s)
- Juan Pablo Tosar
- Analytical Bichemistry Unit, Nuclear Research Center, School of Science, Universidad de la República, Uruguay.,Functional Genomics Unit, Institut Pasteur de Montevideo, Uruguay
| | - Fabiana Gámbaro
- Functional Genomics Unit, Institut Pasteur de Montevideo, Uruguay
| | - Mauricio Castellano
- Functional Genomics Unit, Institut Pasteur de Montevideo, Uruguay.,Biochemistry Department, School of Science, Universidad de la República, Uruguay
| | - Alfonso Cayota
- Functional Genomics Unit, Institut Pasteur de Montevideo, Uruguay.,University Hospital, Universidad de la República, Uruguay
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Tosar JP, Witwer K, Cayota A. Revisiting Extracellular RNA Release, Processing, and Function. Trends Biochem Sci 2021; 46:438-445. [PMID: 33413996 DOI: 10.1016/j.tibs.2020.12.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/26/2020] [Accepted: 12/09/2020] [Indexed: 02/06/2023]
Abstract
It is assumed that RNAs enriched in extracellular samples were selected for release by their parental cells. However, recent descriptions of extracellular RNA (exRNA) biogenesis and their differential stabilities question this assumption, as they could produce identical outcomes. Here, we share our opinion about the importance of considering both selective and nonselective mechanisms for RNA release into the extracellular environment. In doing so, we provide new perspectives on RNA-mediated intercellular communication, including an analogy to communication through social media. We also argue that technical limitations have restricted the study of some of the most abundant exRNAs, both inside and outside extracellular vesicles (EVs). These RNAs may be better positioned to induce a response in recipient cells compared with low abundance miRNAs.
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Affiliation(s)
- Juan Pablo Tosar
- Analytical Biochemistry Unit, Nuclear Research Center, School of Science, Universidad de la República, Montevideo, Uruguay; Functional Genomics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay.
| | - Kenneth Witwer
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alfonso Cayota
- Functional Genomics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay; Department of Medicine, University Hospital, Universidad de la República, Montevideo, Uruguay
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Tosar JP, Cayota A. Extracellular tRNAs and tRNA-derived fragments. RNA Biol 2020; 17:1149-1167. [PMID: 32070197 PMCID: PMC7549618 DOI: 10.1080/15476286.2020.1729584] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/05/2020] [Accepted: 02/10/2020] [Indexed: 01/08/2023] Open
Abstract
Fragmentation of tRNAs generates a family of small RNAs collectively known as tRNA-derived fragments. These fragments vary in sequence and size but have been shown to regulate many processes involved in cell homoeostasis and adaptations to stress. Additionally, the field of extracellular RNAs (exRNAs) is rapidly growing because exRNAs are a promising source of biomarkers in liquid biopsies, and because exRNAs seem to play key roles in intercellular and interspecies communication. Herein, we review recent descriptions of tRNA-derived fragments in the extracellular space in all domains of life, both in biofluids and in cell culture. The purpose of this review is to find consensus on which tRNA-derived fragments are more prominent in each extracellular fraction (including extracellular vesicles, lipoproteins and ribonucleoprotein complexes). We highlight what is becoming clear and what is still controversial in this field, in order to stimulate future hypothesis-driven studies which could clarify the role of full-length tRNAs and tRNA-derived fragments in the extracellular space.
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Affiliation(s)
- Juan Pablo Tosar
- Analytical Biochemistry Unit, Nuclear Research Center, Faculty of Science, Universidad de la República, Montevideo, Uruguay
- Functional Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Alfonso Cayota
- Functional Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Department of Medicine, University Hospital, Universidad de la República, Montevideo, Uruguay
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Xiao Y, Driedonks T, Witwer KW, Wang Q, Yin H. How does an RNA selfie work? EV-associated RNA in innate immunity as self or danger. J Extracell Vesicles 2020; 9:1793515. [PMID: 32944182 PMCID: PMC7480420 DOI: 10.1080/20013078.2020.1793515] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Innate immunity is a first line of defence against danger. Exogenous pathogen- or microbe-associated molecular patterns (PAMPs or MAMPs) trigger innate immune responses through well-understood cellular pathways. In contrast, endogenous damage-associated molecular patterns (DAMPs) convey “danger signals” via their (mis)localization or modification. Both MAMPs and DAMPs are often communicated on or within extracellular vesicles (EVs). Despite growing evidence for the importance of EVs and their cargo in modulating innate immune responses, in some cases, it is unclear how EV-transported molecules are sensed as abnormal. In particular, EVs constitutively carry RNA, which is also abundant in the cytoplasm. How, then, would RNA convey a danger signal as a cargo of EVs? In this Perspective, we offer some thoughts on how EV-associated RNAs might raise the alarm for innate immune responses – or silence them.
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Affiliation(s)
- Yu Xiao
- Zhujiang Hospital, Laboratory of Medicine Center, Southern Medical University, Guangzhou, Guangdong, China
| | - Tom Driedonks
- Department of Molecular and Comparative Pathobiology, Baltimore, USA
| | - Kenneth W Witwer
- Department of Molecular and Comparative Pathobiology, Baltimore, USA.,Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, USA
| | - Qian Wang
- Zhujiang Hospital, Laboratory of Medicine Center, Southern Medical University, Guangzhou, Guangdong, China
| | - Hang Yin
- Tsinghua University-Peking University Joint Center for Life Sciences, Tsinghua University, Beijing, China.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China.,School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
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