1
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Guo LT, Grinko A, Olson S, Leipold AM, Graveley B, Saliba AE, Pyle AM. Characterization and implementation of the MarathonRT template-switching reaction to expand the capabilities of RNA-seq. RNA (NEW YORK, N.Y.) 2024; 30:1495-1512. [PMID: 39174298 PMCID: PMC11482623 DOI: 10.1261/rna.080032.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 08/08/2024] [Indexed: 08/24/2024]
Abstract
End-to-end RNA-sequencing methods that capture 5'-sequence content without cumbersome library manipulations are of great interest, particularly for analysis of long RNAs. While template-switching methods have been developed for RNA sequencing by distributive short-read RTs, such as the MMLV RTs used in SMART-Seq methods, they have not been adapted to leverage the power of ultraprocessive RTs, such as those derived from group II introns. To facilitate this transition, we dissected the individual processes that guide the enzymatic specificity and efficiency of the multistep template-switching reaction carried out by RTs, in this case, by MarathonRT. Remarkably, this is the first study of its kind, for any RT. First, we characterized the nucleotide specificity of nontemplated addition (NTA) reaction that occurs when the RT extends past the RNA 5'-terminus. We then evaluated the binding specificity of specialized template-switching oligonucleotides, optimizing their sequences and chemical properties to guide efficient template-switching reaction. Having dissected and optimized these individual steps, we then unified them into a procedure for performing RNA sequencing with MarathonRT enzymes, using a well-characterized RNA reference set. The resulting reads span a six-log range in transcript concentration and accurately represent the input RNA identities in both length and composition. We also performed RNA-seq from total human RNA and poly(A)-enriched RNA, with short- and long-read sequencing demonstrating that MarathonRT enhances the discovery of unseen RNA molecules by conventional RT. Altogether, we have generated a new pipeline for rapid, accurate sequencing of complex RNA libraries containing mixtures of long RNA transcripts.
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Affiliation(s)
- Li-Tao Guo
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
| | - Anastasiya Grinko
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Sara Olson
- Genetics and Genome Sciences, University of Connecticut Health, Farmington, Connecticut 06030, USA
| | - Alexander M Leipold
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), 97080 Würzburg, Germany
- University of Würzburg, Faculty of Medicine, Institute of Molecular Infection Biology (IMIB), 97070 Würzburg, Germany
| | - Brenton Graveley
- Genetics and Genome Sciences, University of Connecticut Health, Farmington, Connecticut 06030, USA
| | - Antoine-Emmanuel Saliba
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), 97080 Würzburg, Germany
- University of Würzburg, Faculty of Medicine, Institute of Molecular Infection Biology (IMIB), 97070 Würzburg, Germany
| | - Anna Marie Pyle
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
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2
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Wilkinson ME, Li D, Gao A, Macrae RK, Zhang F. Phage-triggered reverse transcription assembles a toxic repetitive gene from a noncoding RNA. Science 2024; 386:eadq3977. [PMID: 39208082 DOI: 10.1126/science.adq3977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Accepted: 08/08/2024] [Indexed: 09/04/2024]
Abstract
Reverse transcription has frequently been co-opted for cellular functions and in prokaryotes is associated with protection against viral infection, but the underlying mechanisms of defense are generally unknown. Here, we show that in the DRT2 defense system, the reverse transcriptase binds a neighboring pseudoknotted noncoding RNA. Upon bacteriophage infection, a template region of this RNA is reverse transcribed into an array of tandem repeats that reconstitute a promoter and open reading frame, allowing expression of a toxic repetitive protein and an abortive infection response. Biochemical reconstitution of this activity and cryo-electron microscopy provide a molecular basis for repeat synthesis. Gene synthesis from a noncoding RNA is a previously unknown mode of genetic regulation in prokaryotes.
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Affiliation(s)
- Max E Wilkinson
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David Li
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Alex Gao
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Rhiannon K Macrae
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Feng Zhang
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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3
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Scacchetti A, Shields EJ, Trigg NA, Lee GS, Wilusz JE, Conine CC, Bonasio R. A ligation-independent sequencing method reveals tRNA-derived RNAs with blocked 3' termini. Mol Cell 2024; 84:3843-3859.e8. [PMID: 39096899 PMCID: PMC11455606 DOI: 10.1016/j.molcel.2024.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 12/12/2023] [Accepted: 07/10/2024] [Indexed: 08/05/2024]
Abstract
Despite the numerous sequencing methods available, the diversity in RNA size and chemical modification makes it difficult to capture all RNAs in a cell. We developed a method that combines quasi-random priming with template switching to construct sequencing libraries from RNA molecules of any length and with any type of 3' modifications, allowing for the sequencing of virtually all RNA species. Our ligation-independent detection of all types of RNA (LIDAR) is a simple, effective tool to identify and quantify all classes of coding and non-coding RNAs. With LIDAR, we comprehensively characterized the transcriptomes of mouse embryonic stem cells, neural progenitor cells, mouse tissues, and sperm. LIDAR detected a much larger variety of tRNA-derived RNAs (tDRs) compared with traditional ligation-dependent sequencing methods and uncovered tDRs with blocked 3' ends that had previously escaped detection. Therefore, LIDAR can capture all RNAs in a sample and uncover RNA species with potential regulatory functions.
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Affiliation(s)
- Alessandro Scacchetti
- Epigenetics Institute and Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Emily J Shields
- Epigenetics Institute and Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Department of Urology and Institute of Neuropathology, Medical Center - University of Freiburg, 79106 Freiburg, Germany
| | - Natalie A Trigg
- Departments of Genetics and Pediatrics - Penn Epigenetics Institute, Institute of Regenerative Medicine, and Center for Research on Reproduction and Women's Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Grace S Lee
- Departments of Genetics and Pediatrics - Penn Epigenetics Institute, Institute of Regenerative Medicine, and Center for Research on Reproduction and Women's Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jeremy E Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Colin C Conine
- Departments of Genetics and Pediatrics - Penn Epigenetics Institute, Institute of Regenerative Medicine, and Center for Research on Reproduction and Women's Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Roberto Bonasio
- Epigenetics Institute and Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
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4
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Wylie D, Wang X, Yao J, Xu H, Ferrick-Kiddie EA, Iwase T, Krishnamurthy S, Ueno NT, Lambowitz AM. TGIRT-seq of Inflammatory Breast Cancer Tumor and Blood Samples Reveals Widespread Enhanced Transcription Impacting RNA splicing and Intronic RNAs in Plasma. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.05.26.23290469. [PMID: 37398275 PMCID: PMC10312853 DOI: 10.1101/2023.05.26.23290469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Inflammatory breast cancer (IBC) is the most aggressive and lethal breast cancer subtype but lacks unequivocal genomic differences or robust biomarkers that differentiate it from non-IBC. Here, Thermostable Group II intron Reverse Transcriptase RNA-sequencing (TGIRT-seq) revealed myriad differences in tumor samples, Peripheral Blood Mononuclear Cells (PBMCs), and plasma that distinguished IBC from non-IBC patients and healthy donors across all tested receptor-based subtypes. These included numerous differentially expressed protein-coding gene and non-coding RNAs in all three sample types, a granulocytic immune response in IBC PBMCs, and over-expression of repeat element and antisense RNAs, suggesting wide-spread enhanced transcription in both IBC tumors and PBMCs. By using TGIRT-seq to quantitate Intron-exon Depth Ratios (IDRs) and mapping reads to both genome and transcriptome reference sequences, we developed methods for parallel analysis of transcriptional and post-transcriptional gene regulation. This analysis identified numerous differentially and non-differentially expressed protein-coding genes in IBC tumors and PBMCs with high IDRs, reflecting rate-limiting RNA splicing that negatively impacts mRNA production. Mirroring gene expression differences in tumors and PBMCs, over-represented protein-coding gene RNAs in IBC patient plasma were largely intronic RNAs, while those in non-IBC patients and healthy donor plasma were largely mRNA fragments. Potential IBC biomarkers in plasma included T-cell receptor pre-mRNAs and intronic, LINE-1, and antisense RNAs. Our findings provide new insights into IBC and set the stage for monitoring disease progression and response to treatment by liquid biopsy. The methods developed for parallel transcriptional and post-transcriptional gene regulation analysis have potentially broad RNA-seq and clinical applications.
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Affiliation(s)
- Dennis Wylie
- Departments of Molecular Biosciences and Oncology, University of Texas at Austin, Austin, TX 78712
| | - Xiaoping Wang
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
- Inflammatory Breast Cancer Research Program and Clinic, University of Hawai i Cancer Center, Honolulu, HI 96813
- Cancer Biology Research Program, University of Hawai i Cancer Center, Honolulu, HI 96813
| | - Jun Yao
- Departments of Molecular Biosciences and Oncology, University of Texas at Austin, Austin, TX 78712
| | - Hengyi Xu
- Departments of Molecular Biosciences and Oncology, University of Texas at Austin, Austin, TX 78712
| | | | - Toshiaki Iwase
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
- Inflammatory Breast Cancer Research Program and Clinic, University of Hawai i Cancer Center, Honolulu, HI 96813
- Translational Clinical Research Program, University of Hawai i Cancer Center, Honolulu, HI 96813
| | - Savitri Krishnamurthy
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Naoto T Ueno
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
- Inflammatory Breast Cancer Research Program and Clinic, University of Hawai i Cancer Center, Honolulu, HI 96813
- Cancer Biology Research Program, University of Hawai i Cancer Center, Honolulu, HI 96813
- Translational Clinical Research Program, University of Hawai i Cancer Center, Honolulu, HI 96813
| | - Alan M Lambowitz
- Departments of Molecular Biosciences and Oncology, University of Texas at Austin, Austin, TX 78712
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5
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Mestre-Fos S, Ferguson L, Trinidad M, Ingolia NT, Cate JHD. eIF3 engages with 3'-UTR termini of highly translated mRNAs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.11.566681. [PMID: 37986910 PMCID: PMC10659435 DOI: 10.1101/2023.11.11.566681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Stem cell differentiation involves a global increase in protein synthesis to meet the demands of specialized cell types. However, the molecular mechanisms underlying this translational burst and the involvement of initiation factors remains largely unknown. Here, we investigate the role of eukaryotic initiation factor 3 (eIF3) in early differentiation of human pluripotent stem cell (hPSC)-derived neural progenitor cells (NPCs). Using Quick-irCLIP and alternative polyadenylation (APA) Seq, we show eIF3 crosslinks predominantly with 3' untranslated region (3'-UTR) termini of multiple mRNA isoforms, adjacent to the poly(A) tail. Furthermore, we find that eIF3 engagement at 3'-UTR ends is dependent on polyadenylation. High eIF3 crosslinking at 3'-UTR termini of mRNAs correlates with high translational activity, as determined by ribosome profiling. The results presented here show that eIF3 engages with 3'-UTR termini of highly translated mRNAs, likely reflecting a general rather than specific regulatory function of eIF3, and supporting a role of mRNA circularization in the mechanisms governing mRNA translation.
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Affiliation(s)
- Santi Mestre-Fos
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Lucas Ferguson
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Marena Trinidad
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Nicholas T Ingolia
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
| | - Jamie H D Cate
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
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6
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Shaffer JF, Gupta A, Kharkwal G, Linares EE, Holmes AD, Katzman S, Sharma U. Epididymis-specific RNase A family genes regulate fertility and small RNA processing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.26.608813. [PMID: 39253511 PMCID: PMC11383283 DOI: 10.1101/2024.08.26.608813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Sperm small RNAs are implicated in intergenerational transmission of paternal environmental effects. Small RNAs generated by cleavage of tRNAs, known as tRNA fragments (tRFs), are an abundant class of RNAs in mature sperm, and can be modulated by environmental conditions. The ribonuclease(s) responsible for the biogenesis of tRFs in the male reproductive tract remains unknown. Angiogenin, a member of the Ribonuclease A superfamily (RNase A), cleaves tRNAs to generate tRFs in response to cellular stress. Four paralogs of Angiogenin, namely Rnase9, Rnase10, Rnase11, and Rnase12, are specifically expressed in the epididymis-a long, convoluted tubule where sperm mature and acquire fertility and motility. The biological functions of these genes remain largely unknown. Here, by generating mice deleted for all four genes (Rnase9-12-/-, termed "KO" for Knock Out), we report that these genes regulate fertility and RNA processing. KO mice showed complete male sterility. KO sperm fertilized oocytes in vitro but failed to efficiently fertilize oocytes in vivo, likely due to an inability of sperm to pass through the utero-tubular junction. Intriguingly, there were decreased levels of fragments of tRNAs (tRFs) and rRNAs (rRNA-derived small RNAs or rsRNAs) in the KO epididymis and epididymal luminal fluid, implying that Rnase9-12 regulate the biogenesis and/or stability of tRFs and rsRNAs. Importantly, KO sperm showed a dramatic decrease in the levels of tRFs, demonstrating a role of Rnase9-12 in regulating sperm RNA composition. Together, our results reveal an unexpected role of four epididymis-specific non-canonical RNase A family genes in fertility and RNA processing.
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Affiliation(s)
- Joshua F Shaffer
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California, 95064
| | - Alka Gupta
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California, 95064
| | - Geetika Kharkwal
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California, 95064
| | - Edgardo E Linares
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California, 95064
| | - Andrew D Holmes
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California, 95064
| | - Sol Katzman
- Genomics Institute, University of California, Santa Cruz, California, 95064
| | - Upasna Sharma
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California, 95064
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7
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Liu S, Holmes AD, Katzman S, Sharma U. A sperm-enriched 5'fragment of tRNA-Valine regulates preimplantation embryonic transcriptome and development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.08.607197. [PMID: 39211093 PMCID: PMC11361008 DOI: 10.1101/2024.08.08.607197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Sperm small RNAs have been implicated in intergenerational epigenetic inheritance of paternal environmental effects; however, their biogenesis and functions remain poorly understood. We previously identified a 5' fragment of tRNA-Valine-CAC-2 (tRFValCAC) as one of the most abundant small RNA in mature sperm. tRFValCAC is specifically enriched in sperm during post-testicular maturation in the epididymis, and we found that it is delivered to sperm from epididymis epithelial cells via extracellular vesicles. Here, we investigated the mechanistic basis of tRFValCAC delivery to sperm and its functions in the early embryo. We show that tRFValCAC interacts with an RNA binding protein, heterogeneous nuclear ribonucleoprotein A/B (hnRNPAB), in the epididymis, and this interaction regulates the sorting and packing of tRFValCAC into extracellular vesicles. In the embryo, we found that tRFValCAC regulates early embryonic mRNA processing and splicing. Inhibition of tRFValCAC in preimplantation embryos altered the transcript abundance of genes involved in RNA splicing and mRNA processing. Importantly, tRFValCAC-inhibited embryos showed altered mRNA splicing, including alternative splicing of various splicing factors and genes important for proper preimplantation embryonic development. Finally, we find that inhibition of tRFValCAC in zygotes delayed preimplantation embryonic development. Together, our results reveal a novel function of a sperm-enriched tRF in regulating alternating splicing and preimplantation embryonic development and shed light on the mechanism of sperm small RNA-mediated epigenetic inheritance.
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Affiliation(s)
- Simeiyun Liu
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California, 95064
| | - Andrew D. Holmes
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California, 95064
| | - Sol Katzman
- Genomics Institute, University of California, Santa Cruz, California, 95064
| | - Upasna Sharma
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California, 95064
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Rodríguez-Vargas A, Collins K. Distinct and overlapping RNA determinants for binding and target-primed reverse transcription by Bombyx mori R2 retrotransposon protein. Nucleic Acids Res 2024; 52:6571-6585. [PMID: 38499488 PMCID: PMC11194090 DOI: 10.1093/nar/gkae194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/08/2024] [Accepted: 03/09/2024] [Indexed: 03/20/2024] Open
Abstract
Eukaryotic retrotransposons encode a reverse transcriptase that binds RNA to template DNA synthesis. The ancestral non-long terminal repeat (non-LTR) retrotransposons encode a protein that performs target-primed reverse transcription (TPRT), in which the nicked genomic target site initiates complementary DNA (cDNA) synthesis directly into the genome. The best understood model system for biochemical studies of TPRT is the R2 protein from the silk moth Bombyx mori. The R2 protein selectively binds the 3' untranslated region of its encoding RNA as template for DNA insertion to its target site in 28S ribosomal DNA. Here, binding and TPRT assays define RNA contributions to RNA-protein interaction, template use for TPRT and the fidelity of template positioning for TPRT cDNA synthesis. We quantify both sequence and structure contributions to protein-RNA interaction. RNA determinants of binding affinity overlap but are not equivalent to RNA features required for TPRT and its fidelity of template positioning for full-length TPRT cDNA synthesis. Additionally, we show that a previously implicated RNA-binding protein surface of R2 protein makes RNA binding affinity dependent on the presence of two stem-loops. Our findings inform evolutionary relationships across R2 retrotransposon RNAs and are a step toward understanding the mechanism and template specificity of non-LTR retrotransposon mobility.
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Affiliation(s)
- Anthony Rodríguez-Vargas
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kathleen Collins
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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9
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Scheepbouwer C, Aparicio-Puerta E, Gómez-Martin C, van Eijndhoven MA, Drees EE, Bosch L, de Jong D, Wurdinger T, Zijlstra JM, Hackenberg M, Gerber A, Pegtel DM. Full-length tRNAs lacking a functional CCA tail are selectively sorted into the lumen of extracellular vesicles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.12.593148. [PMID: 38765958 PMCID: PMC11100784 DOI: 10.1101/2024.05.12.593148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Small extracellular vesicles (sEVs) are heterogenous lipid membrane particles typically less than 200 nm in size and secreted by most cell types either constitutively or upon activation signals. sEVs isolated from biofluids contain RNAs, including small non-coding RNAs (ncRNAs), that can be either encapsulated within the EV lumen or bound to the EV surface. EV-associated microRNAs (miRNAs) are, despite a relatively low abundance, extensively investigated for their selective incorporation and their role in cell-cell communication. In contrast, the sorting of highly-structured ncRNA species is understudied, mainly due to technical limitations of traditional small RNA sequencing protocols. Here, we adapted ALL-tRNAseq to profile the relative abundance of highly structured and potentially methylated small ncRNA species, including transfer RNAs (tRNAs), small nucleolar RNAs (snoRNAs), and Y RNAs in bulk EV preparations. We determined that full-length tRNAs, typically 75 to 90 nucleotides in length, were the dominant small ncRNA species (>60% of all reads in the 18-120 nucleotides size-range) in all cell culture-derived EVs, as well as in human plasma-derived EV samples, vastly outnumbering 21 nucleotides-long miRNAs. Nearly all EV-associated tRNAs were protected from external RNAse treatment, indicating a location within the EV lumen. Strikingly, the vast majority of luminal-sorted, full-length, nucleobase modification-containing EV-tRNA sequences, harbored a dysfunctional 3' CCA tail, 1 to 3 nucleotides truncated, rendering them incompetent for amino acid loading. In contrast, in non-EV associated extracellular particle fractions (NVEPs), tRNAs appeared almost exclusively fragmented or 'nicked' into tRNA-derived small RNAs (tsRNAs) with lengths between 18 to 35 nucleotides. We propose that in mammalian cells, tRNAs that lack a functional 3' CCA tail are selectively sorted into EVs and shuttled out of the producing cell, offering a new perspective into the physiological role of secreted EVs and luminal cargo-selection.
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Affiliation(s)
- Chantal Scheepbouwer
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Center, VU University, Amsterdam, Netherlands
- Cancer Center Amsterdam, Cancer Biology, Amsterdam, Netherlands
- Department of Pathology, Cancer Center Amsterdam, Amsterdam University Medical Center, VU University, Amsterdam, Netherlands
| | - Ernesto Aparicio-Puerta
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY, USA
| | - Cristina Gómez-Martin
- Department of Pathology, Cancer Center Amsterdam, Amsterdam University Medical Center, VU University, Amsterdam, Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, Netherlands
| | - Monique A.J. van Eijndhoven
- Department of Pathology, Cancer Center Amsterdam, Amsterdam University Medical Center, VU University, Amsterdam, Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, Netherlands
| | - Esther E.E. Drees
- Department of Pathology, Cancer Center Amsterdam, Amsterdam University Medical Center, VU University, Amsterdam, Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, Netherlands
- Department of Hematology, Cancer Center Amsterdam, Amsterdam University Medical Center, VU University, Amsterdam, Netherlands
| | - Leontien Bosch
- Department of Pathology, Cancer Center Amsterdam, Amsterdam University Medical Center, VU University, Amsterdam, Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, Netherlands
| | - Daphne de Jong
- Department of Pathology, Cancer Center Amsterdam, Amsterdam University Medical Center, VU University, Amsterdam, Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, Netherlands
| | - Thomas Wurdinger
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Center, VU University, Amsterdam, Netherlands
- Cancer Center Amsterdam, Cancer Biology, Amsterdam, Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, Netherlands
| | - Josée M. Zijlstra
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, Netherlands
- Department of Hematology, Cancer Center Amsterdam, Amsterdam University Medical Center, VU University, Amsterdam, Netherlands
| | - Michael Hackenberg
- Bioinformatics Laboratory, Biomedical Research Centre (CIBM), Biotechnology Institute, PTS, Avda. del Conocimiento s/n, 18100 Granada, Spain
- Genetics Department, Faculty of Science, Universidad de Granada, Campus de Fuentenueva s/n, 18071 Granada, Spain
- Excellence Research Unit “Modeling Nature” (MNat), University of Granada, Spain
- Instituto de Investigación Biosanitaria ibs. Granada, University Hospitals of Granada-University of Granada, Spain; Conocimiento s/n 18100, Granada. Spain
| | - Alan Gerber
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Center, VU University, Amsterdam, Netherlands
- Cancer Center Amsterdam, Cancer Biology, Amsterdam, Netherlands
| | - D. Michiel Pegtel
- Department of Pathology, Cancer Center Amsterdam, Amsterdam University Medical Center, VU University, Amsterdam, Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, Netherlands
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10
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Manning AC, Bashir MM, Jimenez AR, Upton HE, Collins K, Lowe TM, Tucker JM. Gammaherpesvirus infection triggers the formation of tRNA fragments from premature tRNAs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.592122. [PMID: 38746336 PMCID: PMC11092647 DOI: 10.1101/2024.05.01.592122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Transfer RNAs (tRNAs) are fundamental for both cellular and viral gene expression during viral infection. In addition, mounting evidence supports biological function for tRNA cleavage products, including in the control of gene expression during conditions of stress and infection. We previously reported that infection with the model murine gammaherpesvirus, MHV68, leads to enhanced tRNA transcription. However, whether this has any influence on tRNA transcript processing, viral replication, or the host response is not known. Here, we combined two new approaches, sequencing library preparation by Ordered Two Template Relay (OTTR) and tRNA bioinformatic analysis by tRAX, to quantitatively profile full-length tRNAs and tRNA fragment (tRF) identities during MHV68 infection. We find that MHV68 infection triggers both pre-tRNA and mature tRNA cleavage, resulting in the accumulation of specific tRFs. OTTR-tRAX revealed not only host tRNAome changes, but also the expression patterns of virally-encoded tRNAs (virtRNAs) and virtRFs made from the MHV68 genome, including their base modification signatures. Because the transcript ends of several host tRFs matched tRNA splice junctions, we tested and confirmed the role of tRNA splicing factors TSEN2 and CLP1 in MHV68-induced tRF biogenesis. Further, we show that CLP1 kinase, and by extension tRNA splicing, is required for productive MHV68 infection. Our findings provide new insight into how gammaherpesvirus infection both impacts and relies on tRNA transcription and processing.
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Affiliation(s)
- Aidan C. Manning
- Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Mahmoud M. Bashir
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Ariana R. Jimenez
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
- Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA, 52242, USA
| | - Heather E. Upton
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Kathleen Collins
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Todd M. Lowe
- Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Jessica M. Tucker
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
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11
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Shen Z, Naveed M, Bao J. Untacking small RNA profiling and RNA fragment footprinting: Approaches and challenges in library construction. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1852. [PMID: 38715192 DOI: 10.1002/wrna.1852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 06/06/2024]
Abstract
Small RNAs (sRNAs) with sizes ranging from 15 to 50 nucleotides (nt) are critical regulators of gene expression control. Prior studies have shown that sRNAs are involved in a broad range of biological processes, such as organ development, tumorigenesis, and epigenomic regulation; however, emerging evidence unveils a hidden layer of diversity and complexity of endogenously encoded sRNAs profile in eukaryotic organisms, including novel types of sRNAs and the previously unknown post-transcriptional RNA modifications. This underscores the importance for accurate, unbiased detection of sRNAs in various cellular contexts. A multitude of high-throughput methods based on next-generation sequencing (NGS) are developed to decipher the sRNA expression and their modifications. Nonetheless, distinct from mRNA sequencing, the data from sRNA sequencing suffer frequent inconsistencies and high variations emanating from the adapter contaminations and RNA modifications, which overall skew the sRNA libraries. Here, we summarize the sRNA-sequencing approaches, and discuss the considerations and challenges for the strategies and methods of sRNA library construction. The pros and cons of sRNA sequencing have significant implications for implementing RNA fragment footprinting approaches, including CLIP-seq and Ribo-seq. We envision that this review can inspire novel improvements in small RNA sequencing and RNA fragment footprinting in future. This article is categorized under: RNA Evolution and Genomics > Computational Analyses of RNA RNA Processing > Processing of Small RNAs Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs.
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Affiliation(s)
- Zhaokang Shen
- Department of Obstetrics and Gynecology, Center for Reproduction and Genetics, The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Hefei, Anhui, China
| | - Muhammad Naveed
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Hefei, Anhui, China
- Department of Obstetrics and Gynecology, Center for Reproduction and Genetics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Jianqiang Bao
- Department of Obstetrics and Gynecology, Center for Reproduction and Genetics, The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Hefei, Anhui, China
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12
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Iosub IA, Wilkins OG, Ule J. Riboseq-flow: A streamlined, reliable pipeline for ribosome profiling data analysis and quality control. Wellcome Open Res 2024; 9:179. [PMID: 38846930 PMCID: PMC11153996 DOI: 10.12688/wellcomeopenres.21000.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2024] [Indexed: 06/09/2024] Open
Abstract
Ribosome profiling is a powerful technique to study translation at a transcriptome-wide level. However, ensuring good data quality is paramount for accurate interpretation, as is ensuring that the analyses are reproducible. We introduce a new Nextflow DSL2 pipeline, riboseq-flow, designed for processing and comprehensive quality control of ribosome profiling experiments. Riboseq-flow is user-friendly, versatile and upholds high standards in reproducibility, scalability, portability, version control and continuous integration. It enables users to efficiently analyse multiple samples in parallel and helps them evaluate the quality and utility of their data based on the detailed metrics and visualisations that are automatically generated. Riboseq-flow is available at https://github.com/iraiosub/riboseq-flow.
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Affiliation(s)
- Ira A. Iosub
- The Francis Crick Institute, London, England, UK
- UK Dementia Research Institute at King's College London, London, UK
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Oscar G. Wilkins
- The Francis Crick Institute, London, England, UK
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Jernej Ule
- The Francis Crick Institute, London, England, UK
- UK Dementia Research Institute at King's College London, London, UK
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
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13
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Cabrelle C, Giorgi FM, Mercatelli D. Quantitative and qualitative detection of tRNAs, tRNA halves and tRFs in human cancer samples: Molecular grounds for biomarker development and clinical perspectives. Gene 2024; 898:148097. [PMID: 38128792 DOI: 10.1016/j.gene.2023.148097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 12/04/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
Transfer RNAs (tRNAs) are small non-coding RNAs playing a central role during protein synthesis. Besides translation, growing evidence suggests that in many contexts, precursor or mature tRNAs can also be processed into smaller fragments playing many non-canonical regulatory roles in different biological pathways with oncogenic relevance. Depending on the source, these molecules can be classified as tRNA halves (also known as tiRNAs) or tRNA-derived fragments (tRFs), and furtherly divided into 5'-tRNA and 3'-tRNA halves, or tRF-1, tRF-2, tRF-3, tRF-5, and i-tRF, respectively. Unlike DNA and mRNA, high-throughput sequencing of tRNAs is challenging, because of technical limitations of currently developed sequencing methods. In recent years, different sequencing approaches have been proposed allowing the quantification and identification of an increasing number of tRNA fragments with critical functions in distinct physiological and pathophysiological processes. In the present review, we discussed pros and cons of recent advances in different sequencing methods, also introducing the expanding repertoire of bioinformatics tool and resources specifically focused on tRNA research and discussing current issues in the study of these small RNA molecules. Furthermore, we discussed the potential value of tRNA fragments as diagnostic and prognostic biomarkers for different types of cancers.
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Affiliation(s)
- Chiara Cabrelle
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy.
| | | | - Daniele Mercatelli
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy.
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14
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Tosar JP, Castellano M, Costa B, Cayota A. Small RNA structural biochemistry in a post-sequencing era. Nat Protoc 2024; 19:595-602. [PMID: 38057624 DOI: 10.1038/s41596-023-00936-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/25/2023] [Indexed: 12/08/2023]
Abstract
High-throughput sequencing has had an enormous impact on small RNA research during the past decade. However, sequencing only offers a one-dimensional view of the transcriptome and is often highly biased. Additionally, the 'sequence, map and annotate' approach, used widely in small RNA research, can lead to flawed interpretations of the data, lacking biological plausibility, due in part to database issues. Even in the absence of technical biases, the loss of three-dimensional information is a major limitation to understanding RNA stability, turnover and function. For example, noncoding RNA-derived fragments seem to exist mainly as dimers, tetramers or as nicked forms of their parental RNAs, contrary to widespread assumptions. In this perspective, we will discuss main sources of bias during small RNA-sequencing, present several useful bias-reducing strategies and provide guidance on the interpretation of small RNA-sequencing results, with emphasis on RNA fragmentomics. As sequencing offers a one-dimensional projection of a four-dimensional reality, prior structure-level knowledge is often needed to make sense of the data. Consequently, while less-biased sequencing methods are welcomed, integration of orthologous experimental techniques is also strongly recommended.
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Affiliation(s)
- Juan Pablo Tosar
- Functional Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay.
- Analytical Biochemistry Unit, Center for Nuclear Research, School of Science, Universidad de la República, Montevideo, Uruguay.
| | - Mauricio Castellano
- Functional Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Biochemistry Department, School of Science, Universidad de la República, Montevideo, Uruguay
| | - Bruno Costa
- Functional Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Analytical Biochemistry Unit, Center for Nuclear Research, School of Science, Universidad de la República, Montevideo, Uruguay
| | - Alfonso Cayota
- Functional Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Hospital de Clínicas, Universidad de la República, Montevideo, Uruguay
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15
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Zhang X, Van Treeck B, Horton CA, McIntyre JJR, Palm SM, Shumate JL, Collins K. Harnessing eukaryotic retroelement proteins for transgene insertion into human safe-harbor loci. Nat Biotechnol 2024:10.1038/s41587-024-02137-y. [PMID: 38379101 PMCID: PMC11371274 DOI: 10.1038/s41587-024-02137-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/10/2024] [Indexed: 02/22/2024]
Abstract
Current approaches for inserting autonomous transgenes into the genome, such as CRISPR-Cas9 or virus-based strategies, have limitations including low efficiency and high risk of untargeted genome mutagenesis. Here, we describe precise RNA-mediated insertion of transgenes (PRINT), an approach for site-specifically primed reverse transcription that directs transgene synthesis directly into the genome at a multicopy safe-harbor locus. PRINT uses delivery of two in vitro transcribed RNAs: messenger RNA encoding avian R2 retroelement-protein and template RNA encoding a transgene of length validated up to 4 kb. The R2 protein coordinately recognizes the target site, nicks one strand at a precise location and primes complementary DNA synthesis for stable transgene insertion. With a cultured human primary cell line, over 50% of cells can gain several 2 kb transgenes, of which more than 50% are full-length. PRINT advantages include no extragenomic DNA, limiting risk of deleterious mutagenesis and innate immune responses, and the relatively low cost, rapid production and scalability of RNA-only delivery.
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Affiliation(s)
- Xiaozhu Zhang
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Briana Van Treeck
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Connor A Horton
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Jeremy J R McIntyre
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Sarah M Palm
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Justin L Shumate
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Kathleen Collins
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA.
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16
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Manning AC, Bashir MM, Jimenez AR, Upton HE, Collins K, Lowe TM, Tucker JM. Gammaherpesvirus infection alters transfer RNA splicing and triggers tRNA cleavage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.16.580780. [PMID: 38405876 PMCID: PMC10888928 DOI: 10.1101/2024.02.16.580780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Transfer RNAs (tRNAs) are fundamental for both cellular and viral gene expression during viral infection. Moreover, mounting evidence supports a noncanonical role for tRNA cleavage products in the control of gene expression during diverse conditions of stress and infection. We previously reported that infection with the model murine gammaherpesvirus, MHV68, leads to altered tRNA transcription, suggesting that tRNA regulation may play an important role in mediating viral replication or the host response. To better understand how viral infection alters tRNA expression, we combined Ordered Two Template Relay (OTTR) with tRNA-specific bioinformatic software called tRAX to profile full-length tRNAs and fragmented tRNA-derived RNAs (tDRs) during infection with MHV68. We find that OTTR-tRAX is a powerful sequencing strategy for combined tRNA/tDR profiling and reveals that MHV68 infection triggers pre-tRNA and mature tRNA cleavage, resulting in the accumulation of specific tDRs. Fragments of virally-encoded tRNAs (virtRNAs), as well as virtRNA base modification signatures are also detectable during infection. We present evidence that tRNA splicing factors are involved in the biogenesis of MHV68-induced cleavage products from pre-tRNAs and, in the case of CLP1 kinase, impact infectious virus production. Our data offers new insights into the importance of tRNA processing during gammaherpesvirus infection.
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Affiliation(s)
- Aidan C Manning
- Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Mahmoud M Bashir
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Ariana R Jimenez
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
- Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA, 52242, USA
| | - Heather E Upton
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Kathleen Collins
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Todd M Lowe
- Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Jessica M Tucker
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
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17
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Davey-Young J, Hasan F, Tennakoon R, Rozik P, Moore H, Hall P, Cozma E, Genereaux J, Hoffman KS, Chan PP, Lowe TM, Brandl CJ, O’Donoghue P. Mistranslating the genetic code with leucine in yeast and mammalian cells. RNA Biol 2024; 21:1-23. [PMID: 38629491 PMCID: PMC11028032 DOI: 10.1080/15476286.2024.2340297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2024] [Indexed: 04/19/2024] Open
Abstract
Translation fidelity relies on accurate aminoacylation of transfer RNAs (tRNAs) by aminoacyl-tRNA synthetases (AARSs). AARSs specific for alanine (Ala), leucine (Leu), serine, and pyrrolysine do not recognize the anticodon bases. Single nucleotide anticodon variants in their cognate tRNAs can lead to mistranslation. Human genomes include both rare and more common mistranslating tRNA variants. We investigated three rare human tRNALeu variants that mis-incorporate Leu at phenylalanine or tryptophan codons. Expression of each tRNALeu anticodon variant in neuroblastoma cells caused defects in fluorescent protein production without significantly increased cytotoxicity under normal conditions or in the context of proteasome inhibition. Using tRNA sequencing and mass spectrometry we confirmed that each tRNALeu variant was expressed and generated mistranslation with Leu. To probe the flexibility of the entire genetic code towards Leu mis-incorporation, we created 64 yeast strains to express all possible tRNALeu anticodon variants in a doxycycline-inducible system. While some variants showed mild or no growth defects, many anticodon variants, enriched with G/C at positions 35 and 36, including those replacing Leu for proline, arginine, alanine, or glycine, caused dramatic reductions in growth. Differential phenotypic defects were observed for tRNALeu mutants with synonymous anticodons and for different tRNALeu isoacceptors with the same anticodon. A comparison to tRNAAla anticodon variants demonstrates that Ala mis-incorporation is more tolerable than Leu at nearly every codon. The data show that the nature of the amino acid substitution, the tRNA gene, and the anticodon are each important factors that influence the ability of cells to tolerate mistranslating tRNAs.
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Affiliation(s)
- Josephine Davey-Young
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Farah Hasan
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Rasangi Tennakoon
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Peter Rozik
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Henry Moore
- Department of Biomolecular Engineering, Baskin School of Engineering & UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Peter Hall
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Ecaterina Cozma
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Julie Genereaux
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | | | - Patricia P. Chan
- Department of Biomolecular Engineering, Baskin School of Engineering & UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Todd M. Lowe
- Department of Biomolecular Engineering, Baskin School of Engineering & UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Christopher J. Brandl
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Patrick O’Donoghue
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada
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18
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Ngo JM, Williams JK, Lehman IM, Schekman R. Biochemical Reconstitution of Ca 2+-Dependent Exosome Secretion in Permeabilized Mammalian Cells. Bio Protoc 2023; 13:e4890. [PMID: 38094256 PMCID: PMC10714152 DOI: 10.21769/bioprotoc.4890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/12/2023] [Accepted: 10/19/2023] [Indexed: 02/01/2024] Open
Abstract
Exosomes are a subpopulation of the heterogenous pool of extracellular vesicles that are secreted to the extracellular space. Exosomes have been purported to play a role in intercellular communication and have demonstrated utility as biomarkers for a variety of diseases. Despite broad interest in exosome biology, the conditions that regulate their secretion are incompletely understood. The goal of this procedure is to biochemically reconstitute exosome secretion in Streptolysin O (SLO)-permeabilized mammalian cells. This protocol describes the reconstitution of lyophilized SLO, preparation of cytosol and SLO-permeabilized cells, assembly of the biochemical reconstitution reaction, and quantification of exosome secretion using a sensitive luminescence-based assay. This biochemical reconstitution reaction can be utilized to characterize the molecular mechanisms by which different gene products regulate exosome secretion. Key features This protocol establishes a functional in vitro system to reconstitute exosome secretion in permeabilized mammalian cells upon addition of cytosol, ATP, GTP, and calcium (Ca2+).
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Affiliation(s)
- Jordan M. Ngo
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, USA
| | - Justin K. Williams
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, USA
| | - Isabelle M. Lehman
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, USA
| | - Randy Schekman
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, USA
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19
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Kuhle B, Chen Q, Schimmel P. tRNA renovatio: Rebirth through fragmentation. Mol Cell 2023; 83:3953-3971. [PMID: 37802077 PMCID: PMC10841463 DOI: 10.1016/j.molcel.2023.09.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/15/2023] [Accepted: 09/12/2023] [Indexed: 10/08/2023]
Abstract
tRNA function is based on unique structures that enable mRNA decoding using anticodon trinucleotides. These structures interact with specific aminoacyl-tRNA synthetases and ribosomes using 3D shape and sequence signatures. Beyond translation, tRNAs serve as versatile signaling molecules interacting with other RNAs and proteins. Through evolutionary processes, tRNA fragmentation emerges as not merely random degradation but an act of recreation, generating specific shorter molecules called tRNA-derived small RNAs (tsRNAs). These tsRNAs exploit their linear sequences and newly arranged 3D structures for unexpected biological functions, epitomizing the tRNA "renovatio" (from Latin, meaning renewal, renovation, and rebirth). Emerging methods to uncover full tRNA/tsRNA sequences and modifications, combined with techniques to study RNA structures and to integrate AI-powered predictions, will enable comprehensive investigations of tRNA fragmentation products and new interaction potentials in relation to their biological functions. We anticipate that these directions will herald a new era for understanding biological complexity and advancing pharmaceutical engineering.
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Affiliation(s)
- Bernhard Kuhle
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA; Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Qi Chen
- Molecular Medicine Program, Department of Human Genetics, and Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Paul Schimmel
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.
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20
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Ferguson L, Upton HE, Pimentel SC, Mok A, Lareau LF, Collins K, Ingolia NT. Streamlined and sensitive mono- and di-ribosome profiling in yeast and human cells. Nat Methods 2023; 20:1704-1715. [PMID: 37783882 PMCID: PMC11276118 DOI: 10.1038/s41592-023-02028-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 08/23/2023] [Indexed: 10/04/2023]
Abstract
Ribosome profiling has unveiled diverse regulation and perturbations of translation through a transcriptome-wide survey of ribosome occupancy, read out by sequencing of ribosome-protected messenger RNA fragments. Generation of ribosome footprints and their conversion into sequencing libraries is technically demanding and sensitive to biases that distort the representation of physiological ribosome occupancy. We address these challenges by producing ribosome footprints with P1 nuclease rather than RNase I and replacing RNA ligation with ordered two-template relay, a single-tube protocol for sequencing library preparation that incorporates adaptors by reverse transcription. Our streamlined approach reduced sequence bias and enhanced enrichment of ribosome footprints relative to ribosomal RNA. Furthermore, P1 nuclease preserved distinct juxtaposed ribosome complexes informative about yeast and human ribosome fates during translation initiation, stalling and termination. Our optimized methods for mRNA footprint generation and capture provide a richer translatome profile with low input and fewer technical challenges.
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Affiliation(s)
- Lucas Ferguson
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- Center for Computational Biology, University of California, Berkeley, CA, USA.
| | - Heather E Upton
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Sydney C Pimentel
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Amanda Mok
- Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Liana F Lareau
- Center for Computational Biology, University of California, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
| | - Kathleen Collins
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA.
| | - Nicholas T Ingolia
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA.
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21
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Shaw A, Craig JM, Amiri H, Kim J, Upton HE, Pimentel SC, Huang JR, Marqusee S, Collins K, Gundlach JH, Bustamante CJ. Nanopore molecular trajectories of a eukaryotic reverse transcriptase reveal a long-range RNA structure sensing mechanism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.05.535757. [PMID: 37066208 PMCID: PMC10104057 DOI: 10.1101/2023.04.05.535757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Eukaryotic reverse transcriptases (RTs) can have essential or deleterious roles in normal human physiology and disease. Compared to well-studied helicases, it remains unclear how RTs overcome the ubiquitous RNA structural barriers during reverse transcription. Herein, we describe the development of a Mycobacterium smegmatis porin A (MspA) nanopore technique to sequence RNA to quantify the single-molecule kinetics of an RT from Bombyx mori with single-nucleotide resolution. By establishing a quadromer map that correlates RNA sequence and MspA ion current, we were able to quantify the RT's dwell time at every single nucleotide step along its RNA template. By challenging the enzyme with various RNA structures, we found that during cDNA synthesis the RT can sense and actively destabilize RNA structures 11-12 nt downstream of its front boundary. The ability to sequence single molecules of RNA with nanopores paves the way to investigate the single-nucleotide activity of other processive RNA translocases.
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Affiliation(s)
- Alan Shaw
- Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720
| | | | - Hossein Amiri
- Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720
| | - Jeonghoon Kim
- Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720
- Biophysics Graduate Group, University of California, Berkeley, CA, 94720
- Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, CA 94720
| | - Heather E. Upton
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720
- Bakar Fellows Program, University of California, Berkeley, CA, 94720
| | - Sydney C. Pimentel
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720
- Present address: NYU Grossman School of Medicine 550 First Avenue New York, NY 10016
| | - Jesse R. Huang
- Department of Physics, University of Washington, Seattle, WA, 98195
| | - Susan Marqusee
- Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720
- Biophysics Graduate Group, University of California, Berkeley, CA, 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Kathleen Collins
- Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720
- Bakar Fellows Program, University of California, Berkeley, CA, 94720
| | - Jens H. Gundlach
- Department of Physics, University of Washington, Seattle, WA, 98195
| | - Carlos J. Bustamante
- Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720
- Biophysics Graduate Group, University of California, Berkeley, CA, 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720
- Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, CA 94720
- Department of Chemistry, University of California, Berkeley, CA 94720
- Department of Physics, University of California, Berkeley, CA 94720
- Kavli Energy Nanoscience Institute, University of California, Berkeley, CA 94720
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720
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22
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Chen Q, Zhou T. Emerging functional principles of tRNA-derived small RNAs and other regulatory small RNAs. J Biol Chem 2023; 299:105225. [PMID: 37673341 PMCID: PMC10562873 DOI: 10.1016/j.jbc.2023.105225] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 08/22/2023] [Accepted: 08/28/2023] [Indexed: 09/08/2023] Open
Abstract
Recent advancements in small RNA sequencing have unveiled a previously hidden world of regulatory small noncoding RNAs (sncRNAs) that extend beyond the well-studied small interfering RNAs, microRNAs, and piwi-interacting RNAs. This exploration, starting with tRNA-derived small RNAs, has led to the discovery of a diverse universe of sncRNAs derived from various longer structured RNAs such as rRNAs, small nucleolar RNAs, small nuclear RNAs, Y RNAs, and vault RNAs, with exciting uncharted functional possibilities. In this perspective, we discuss the emerging functional principles of sncRNAs beyond the well-known RNAi-like mechanisms, focusing on those that operate independent of linear sequence complementarity but rather function in an aptamer-like fashion. Aptamers use 3D structure for specific interactions with ligands and are modulated by RNA modifications and subcellular environments. Given that aptamer-like sncRNA functions are widespread and present in species lacking RNAi, they may represent an ancient functional principle that predates RNAi. We propose a rethinking of the origin of RNAi and its relationship with these aptamer-like functions in sncRNAs and how these complementary mechanisms shape biological processes. Lastly, the aptamer-like function of sncRNAs highlights the need for caution in using small RNA mimics in research and therapeutics, as their specificity is not restricted solely to linear sequence.
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Affiliation(s)
- Qi Chen
- Molecular Medicine Program, University of Utah School of Medicine, Salt Lake City, Utah, USA; Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, Utah, USA; Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, USA.
| | - Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, Nevada, USA.
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23
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Dremel SE, Jimenez AR, Tucker JM. "Transfer" of power: The intersection of DNA virus infection and tRNA biology. Semin Cell Dev Biol 2023; 146:31-39. [PMID: 36682929 PMCID: PMC10101907 DOI: 10.1016/j.semcdb.2023.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/17/2023] [Accepted: 01/17/2023] [Indexed: 01/21/2023]
Abstract
Transfer RNAs (tRNAs) are at the heart of the molecular biology central dogma, functioning to decode messenger RNAs into proteins. As obligate intracellular parasites, viruses depend on the host translation machinery, including host tRNAs. Thus, the ability of a virus to fine-tune tRNA expression elicits the power to impact the outcome of infection. DNA viruses commonly upregulate the output of RNA polymerase III (Pol III)-dependent transcripts, including tRNAs. Decades after these initial discoveries we know very little about how mature tRNA pools change during viral infection, as tRNA sequencing methodology has only recently reached proficiency. Here, we review perturbation of tRNA biogenesis by DNA virus infection, including an emerging player called tRNA-derived fragments (tRFs). We discuss how tRNA dysregulation shifts the power landscape between the host and virus, highlighting the potential for tRNA-based antivirals as a future therapeutic.
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Affiliation(s)
- Sarah E Dremel
- HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ariana R Jimenez
- Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA, USA
| | - Jessica M Tucker
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA.
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24
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Silveira d'Almeida G, Casius A, Henderson JC, Knuesel S, Aphasizhev R, Aphasizheva I, Manning AC, Lowe TM, Alfonzo JD. tRNA Tyr has an unusually short half-life in Trypanosoma brucei. RNA (NEW YORK, N.Y.) 2023; 29:1243-1254. [PMID: 37197826 PMCID: PMC10351884 DOI: 10.1261/rna.079674.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 04/28/2023] [Indexed: 05/19/2023]
Abstract
Following transcription, tRNAs undergo a series of processing and modification events to become functional adaptors in protein synthesis. Eukaryotes have also evolved intracellular transport systems whereby nucleus-encoded tRNAs may travel out and into the nucleus. In trypanosomes, nearly all tRNAs are also imported from the cytoplasm into the mitochondrion, which lacks tRNA genes. Differential subcellular localization of the cytoplasmic splicing machinery and a nuclear enzyme responsible for queuosine modification at the anticodon "wobble" position appear to be important quality control mechanisms for tRNATyr, the only intron-containing tRNA in T. brucei Since tRNA-guanine transglycosylase (TGT), the enzyme responsible for Q formation, cannot act on an intron-containing tRNA, retrograde nuclear transport is an essential step in maturation. Unlike maturation/processing pathways, the general mechanisms of tRNA stabilization and degradation in T. brucei are poorly understood. Using a combination of cellular and molecular approaches, we show that tRNATyr has an unusually short half-life. tRNATyr, and in addition tRNAAsp, also show the presence of slow-migrating bands during electrophoresis; we term these conformers: alt-tRNATyr and alt-tRNAAsp, respectively. Although we do not know the chemical or structural nature of these conformers, alt-tRNATyr has a short half-life resembling that of tRNATyr; the same is not true for alt-tRNAAsp We also show that RRP44, which is usually an exosome subunit in other organisms, is involved in tRNA degradation of the only intron-containing tRNA in T. brucei and is partly responsible for its unusually short half-life.
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Affiliation(s)
- Gabriel Silveira d'Almeida
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
- The Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Ananth Casius
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
- The Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Jeremy C Henderson
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
- The Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Sebastian Knuesel
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, Boston 02118, USA
| | - Ruslan Aphasizhev
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, Boston 02118, USA
| | - Inna Aphasizheva
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, Boston 02118, USA
| | - Aidan C Manning
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California 95064, USA
| | - Todd M Lowe
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California 95064, USA
| | - Juan D Alfonzo
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
- The Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, USA
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25
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Scacchetti A, Shields EJ, Trigg NA, Wilusz JE, Conine CC, Bonasio R. A ligation-independent sequencing method reveals tRNA-derived RNAs with blocked 3' termini. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.06.543899. [PMID: 37333231 PMCID: PMC10274639 DOI: 10.1101/2023.06.06.543899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Despite the numerous sequencing methods available, the vast diversity in size and chemical modifications of RNA molecules makes the capture of the full spectrum of cellular RNAs a difficult task. By combining quasi-random hexamer priming with a custom template switching strategy, we developed a method to construct sequencing libraries from RNA molecules of any length and with any type of 3' terminal modification, allowing the sequencing and analysis of virtually all RNA species. Ligation-independent detection of all types of RNA (LIDAR) is a simple, effective tool to comprehensively characterize changes in small non-coding RNAs and mRNAs simultaneously, with performance comparable to separate dedicated methods. With LIDAR, we comprehensively characterized the coding and non-coding transcriptome of mouse embryonic stem cells, neural progenitor cells, and sperm. LIDAR detected a much larger variety of tRNA-derived RNAs (tDRs) compared to traditional ligation-dependent sequencing methods, and uncovered the presence of tDRs with blocked 3' ends that had previously escaped detection. Our findings highlight the potential of LIDAR to systematically detect all RNAs in a sample and uncover new RNA species with potential regulatory functions.
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Affiliation(s)
- Alessandro Scacchetti
- Epigenetics Institute and Department of Cell and Developmental Biology; University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Emily J. Shields
- Epigenetics Institute and Department of Cell and Developmental Biology; University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Department of Urology and Institute of Neuropathology, Medical Center–University of Freiburg, 79106 Freiburg, Germany
| | - Natalie A. Trigg
- Departments of Genetics and Pediatrics - Penn Epigenetics Institute, Institute of Regenerative Medicine, and Center for Research on Reproduction and Women’s Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Division of Neonatology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jeremy E. Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Colin C. Conine
- Departments of Genetics and Pediatrics - Penn Epigenetics Institute, Institute of Regenerative Medicine, and Center for Research on Reproduction and Women’s Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Division of Neonatology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Roberto Bonasio
- Epigenetics Institute and Department of Cell and Developmental Biology; University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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26
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Wang H, Wang Z, Zhou T, Morris D, Chen S, Li M, Wang Y, Zheng H, Fu W, Yan W. Small RNA shuffling between murine sperm and their cytoplasmic droplets during epididymal maturation. Dev Cell 2023; 58:779-790.e4. [PMID: 37023748 PMCID: PMC10627525 DOI: 10.1016/j.devcel.2023.03.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 12/18/2022] [Accepted: 03/10/2023] [Indexed: 04/08/2023]
Abstract
Reports that mouse sperm gain small RNAs from the epididymosomes secreted by epididymal epithelial cells and that these "foreign" small RNAs act as an epigenetic information carrier mediating the transmission of acquired paternal traits have drawn great attention because the findings suggest that heritable information can flow from soma to germ line, thus invalidating the long-standing Weismann's barrier theory on heritable information flow. Using small RNA sequencing (sRNA-seq), northern blots, sRNA in situ hybridization, and immunofluorescence, we detected substantial changes in the small RNA profile in murine caput epididymal sperm (sperm in the head of the epididymis), and we further determined that the changes resulted from sperm exchanging small RNAs, mainly tsRNAs and rsRNAs, with cytoplasmic droplets rather than the epididymosomes. Moreover, the murine sperm-borne small RNAs were mainly derived from the nuclear small RNAs in late spermatids. Thus, caution is needed regarding sperm gaining foreign small RNAs as an underlying mechanism of epigenetic inheritance.
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Affiliation(s)
- Hetan Wang
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA, Torrance, CA 90502, USA; Department of Medical Genetics, China Medical University, Shenyang 110122, China
| | - Zhuqing Wang
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA, Torrance, CA 90502, USA
| | - Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | - Dayton Morris
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA, Torrance, CA 90502, USA
| | - Sheng Chen
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA, Torrance, CA 90502, USA
| | - Musheng Li
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | - Yue Wang
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA, Torrance, CA 90502, USA
| | - Huili Zheng
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA, Torrance, CA 90502, USA
| | - Weineng Fu
- Department of Medical Genetics, China Medical University, Shenyang 110122, China
| | - Wei Yan
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA, Torrance, CA 90502, USA; Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA.
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27
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Chen X, Wolin SL. Transfer RNA halves are found as nicked tRNAs in cells: evidence that nicked tRNAs regulate expression of an RNA repair operon. RNA (NEW YORK, N.Y.) 2023; 29:620-629. [PMID: 36781286 PMCID: PMC10159003 DOI: 10.1261/rna.079575.122] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 02/01/2023] [Indexed: 05/06/2023]
Abstract
Transfer RNA fragments are proposed to regulate numerous processes in eukaryotes, including translation inhibition, epigenetic inheritance, and cancer. In the bacterium Salmonella enterica serovar Typhimurium, 5' tRNA halves ending in 2',3' cyclic phosphate are proposed to bind the RtcR transcriptional activator, resulting in transcription of an RNA repair operon. However, since 5' and 3' tRNA halves can remain base paired after cleavage, the 5' tRNA halves could potentially bind RtcR as nicked tRNAs. Here we report that nicked tRNAs are ligands for RtcR. By isolating RNA from bacteria under conditions that preserve base pairing, we show that many tRNA halves are in the form of nicked tRNAs. Using a circularly permuted tRNA that mimics a nicked tRNA, we show that nicked tRNA ending in 2',3' cyclic phosphate is a better ligand for RtcR than the corresponding 5' tRNA half. In human cells, we show that some tRNA halves similarly remain base paired as nicked tRNAs following cleavage by anticodon nucleases. Our work supports a role for the RNA repair operon in repairing nicked tRNAs and has implications for the functions proposed for tRNA fragments in eukaryotes.
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Affiliation(s)
- Xinguo Chen
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
| | - Sandra L Wolin
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
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28
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Liu S, Sharma U. Sperm RNA Payload: Implications for Intergenerational Epigenetic Inheritance. Int J Mol Sci 2023; 24:5889. [PMID: 36982962 PMCID: PMC10052761 DOI: 10.3390/ijms24065889] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 03/03/2023] [Accepted: 03/14/2023] [Indexed: 03/30/2023] Open
Abstract
There is mounting evidence that ancestral life experiences and environment can influence phenotypes in descendants. The parental environment regulates offspring phenotypes potentially via modulating epigenetic marks in the gametes. Here, we review examples of across-generational inheritance of paternal environmental effects and the current understanding of the role of small RNAs in such inheritance. We discuss recent advances in revealing the small RNA payload of sperm and how environmental conditions modulate sperm small RNAs. Further, we discuss the potential mechanism of inheritance of paternal environmental effects by focusing on sperm small RNA-mediated regulation of early embryonic gene expression and its role in influencing offspring phenotypes.
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Affiliation(s)
| | - Upasna Sharma
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
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29
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Experimental and computational workflow for the analysis of tRNA pools from eukaryotic cells by mim-tRNAseq. STAR Protoc 2022; 3:101579. [PMID: 35942339 PMCID: PMC9356165 DOI: 10.1016/j.xpro.2022.101579] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Quantifying tRNAs is crucial for understanding how they regulate mRNA translation but is hampered by their extensive sequence similarity and premature termination of reverse transcription at multiple modified nucleotides. Here, we describe the use of modification-induced misincorporation tRNA sequencing (mim-tRNAseq), which overcomes these limitations with optimized library construction and a comprehensive toolkit for data analysis and visualization. We outline algorithm improvements that enhance the efficiency and accuracy of read alignment and provide details on data analysis outputs using example datasets. For complete details on the use and execution of this protocol, please refer to Behrens et al. (2021). mim-tRNAseq enables efficient quantitation and analysis of eukaryotic tRNA pools Combined library generation and computational package ensures user-friendly workflow Improved multiplexing enables more cost-effective sample analysis Novel deconvolution algorithm enhances read alignment accuracy and sensitivity
Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
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30
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Abstract
Small RNAs are ubiquitous regulators of gene expression that participate in nearly all aspects of physiology in a wide range of organisms. There are many different classes of eukaryotic small RNAs that play regulatory roles at every level of gene expression, including transcription, RNA stability, and translation. While eukaryotic small RNAs display diverse functions across and within classes, they are generally grouped functionally based on the machinery required for their biogenesis, the effector proteins they associate with, and their molecular characteristics. The development of techniques to clone and sequence small RNAs has been critical for their identification, yet the ligation-dependent addition of RNA adapters and the use of reverse transcriptase to generate cDNA in traditional library preparation protocols can be unsuitable to detect certain small RNA subtypes. In particular, 3' or 5' chemical modifications that are characteristic of specific types of small RNAs can impede the ligation-dependent addition of RNA adapters, while internal RNA modifications can interfere with accurate reverse transcription. The inability to clone certain small RNA subtypes with traditional protocols results in an inaccurate assessment of small RNA abundance and diversity, where some RNAs appear over-represented and others are not detected. This overview aims to guide users on how to design small RNA cloning workflows in eukaryotes to more accurately capture specific small RNAs of interest. Hence, we discuss the molecular biology underlying the identification and quantitation of small RNAs, explore the limitations of commonly used protocols, and detail the alternative approaches that can be used to enrich specific small RNA classes. © 2022 Wiley Periodicals LLC.
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Affiliation(s)
- Olivia J Crocker
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Departments of Genetics and Pediatrics - Penn Epigenetics Institute, Institute of Regenerative Medicine, and Center for Research on Reproduction and Women's Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Natalie A Trigg
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Departments of Genetics and Pediatrics - Penn Epigenetics Institute, Institute of Regenerative Medicine, and Center for Research on Reproduction and Women's Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Colin C Conine
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Departments of Genetics and Pediatrics - Penn Epigenetics Institute, Institute of Regenerative Medicine, and Center for Research on Reproduction and Women's Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
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31
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Shi J, Zhou T, Chen Q. Exploring the expanding universe of small RNAs. Nat Cell Biol 2022; 24:415-423. [PMID: 35414016 PMCID: PMC9035129 DOI: 10.1038/s41556-022-00880-5] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 03/02/2022] [Indexed: 12/11/2022]
Abstract
The world of small noncoding RNAs (sncRNAs) is ever-expanding, from small interfering RNA, microRNA and Piwi-interacting RNA to the recently emerging non-canonical sncRNAs derived from longer structured RNAs (for example, transfer, ribosomal, Y, small nucleolar, small nuclear and vault RNAs), showing distinct biogenesis and functional principles. Here we discuss recent tools for sncRNA identification, caveats in sncRNA expression analysis and emerging methods for direct sequencing of sncRNAs and systematic mapping of RNA modifications that are integral to their function.
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Affiliation(s)
- Junchao Shi
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, USA
| | - Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA.
| | - Qi Chen
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, USA.
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32
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Pimentel SC, Upton HE, Collins K. Separable structural requirements for cDNA synthesis, nontemplated extension, and template jumping by a non-LTR retroelement reverse transcriptase. J Biol Chem 2022; 298:101624. [PMID: 35065960 PMCID: PMC8857657 DOI: 10.1016/j.jbc.2022.101624] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 11/16/2022] Open
Abstract
Broad evolutionary expansion of polymerase families has enabled specialization of their activities for distinct cellular roles. In addition to template-complementary synthesis, many polymerases extend their duplex products by nontemplated nucleotide addition (NTA). This activity is exploited for laboratory strategies of cloning and sequencing nucleic acids and could have important biological function, although the latter has been challenging to test without separation-of-function mutations. Several retroelement and retroviral reverse transcriptases (RTs) support NTA and also template jumping, by which the RT performs continuous complementary DNA (cDNA) synthesis using physically separate templates. Previous studies that aimed to dissect the relationship between NTA and template jumping leave open questions about structural requirements for each activity and their interdependence. Here, we characterize the structural requirements for cDNA synthesis, NTA, template jumping, and the unique terminal transferase activity of Bombyx mori R2 non-long terminal repeat retroelement RT. With sequence alignments and structure modeling to guide mutagenesis, we generated enzyme variants across motifs generally conserved or specific to RT subgroups. Enzyme variants had diverse NTA profiles not correlated with other changes in cDNA synthesis activity or template jumping. Using these enzyme variants and panels of activity assay conditions, we show that template jumping requires NTA. However, template jumping by NTA-deficient enzymes can be rescued using primer duplex with a specific length of 3′ overhang. Our findings clarify the relationship between NTA and template jumping as well as additional activities of non-long terminal repeat RTs, with implications for the specialization of RT biological functions and laboratory applications.
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Affiliation(s)
- Sydney C Pimentel
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California, USA
| | - Heather E Upton
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California, USA
| | - Kathleen Collins
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California, USA.
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