1
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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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2
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Kolberg T, von Löhneysen S, Ozerova I, Wellner K, Hartmann R, Stadler P, Mörl M. Led-Seq: ligation-enhanced double-end sequence-based structure analysis of RNA. Nucleic Acids Res 2023; 51:e63. [PMID: 37114986 PMCID: PMC10287922 DOI: 10.1093/nar/gkad312] [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: 01/24/2023] [Revised: 03/21/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Structural analysis of RNA is an important and versatile tool to investigate the function of this type of molecules in the cell as well as in vitro. Several robust and reliable procedures are available, relying on chemical modification inducing RT stops or nucleotide misincorporations during reverse transcription. Others are based on cleavage reactions and RT stop signals. However, these methods address only one side of the RT stop or misincorporation position. Here, we describe Led-Seq, a new approach based on lead-induced cleavage of unpaired RNA positions, where both resulting cleavage products are investigated. The RNA fragments carrying 2', 3'-cyclic phosphate or 5'-OH ends are selectively ligated to oligonucleotide adapters by specific RNA ligases. In a deep sequencing analysis, the cleavage sites are identified as ligation positions, avoiding possible false positive signals based on premature RT stops. With a benchmark set of transcripts in Escherichia coli, we show that Led-Seq is an improved and reliable approach based on metal ion-induced phosphodiester hydrolysis to investigate RNA structures in vivo.
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Affiliation(s)
- Tim Kolberg
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Sarah von Löhneysen
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstr. 16–18, 04107 Leipzig, Germany
| | - Iuliia Ozerova
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstr. 16–18, 04107 Leipzig, Germany
| | - Karolin Wellner
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Roland K Hartmann
- Institute for Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35037 Marburg, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstr. 16–18, 04107 Leipzig, Germany
- Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany
- Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria
- Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
- Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
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3
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Chin S, Goyon A, Zhang K, Kurita KL. Middle-out sequence confirmation of CRISPR/Cas9 single guide RNA (sgRNA) using DNA primers and ribonuclease T1 digestion. Anal Bioanal Chem 2023; 415:2809-2818. [PMID: 37093234 DOI: 10.1007/s00216-023-04693-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/29/2023] [Accepted: 04/06/2023] [Indexed: 04/25/2023]
Abstract
Accurate sequencing of single guide RNAs (sgRNAs) for CRISPR/Cas9 genome editing is critical for patient safety, as the sgRNA guides the Cas9 nuclease to target site-specific cleavages in DNA. An approach to fully sequence sgRNA using protective DNA primers followed by ribonuclease (RNase) T1 digestion was developed to facilitate the analysis of these larger molecules by hydrophilic interaction liquid chromatography coupled with high-resolution mass spectrometry (HILIC-HRMS). Without RNase digestion, top-down mass spectrometry alone struggles to properly fragment precursor ions in large RNA oligonucleotides to provide confidence in sequence coverage. With RNase T1 digestion of these larger oligonucleotides, however, bottom-up analysis cannot confirm full sequence coverage due to the presence of short, redundant digestion products. By combining primer protection with RNase T1 digestion, digestion products are large enough to prevent redundancy and small enough to provide base resolution by tandem mass spectrometry to allow for full sgRNA sequence coverage. An investigation into the general requirements for adequate primer protection of specific regions of the RNA was conducted, followed by the development of a generic protection and digestion strategy that may be applied to different sgRNA sequences. This middle-out technique has the potential to expedite accurate sequence confirmation of chemically modified sgRNA oligonucleotides.
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Affiliation(s)
- Steven Chin
- Department of Small Molecule Analytical Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Alexandre Goyon
- Department of Small Molecule Analytical Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Kelly Zhang
- Department of Small Molecule Analytical Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Kenji L Kurita
- Department of Small Molecule Analytical Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA.
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4
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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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5
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Shigematsu M, Kirino Y. Making Invisible RNA Visible: Discriminative Sequencing Methods for RNA Molecules with Specific Terminal Formations. Biomolecules 2022; 12:611. [PMID: 35625540 PMCID: PMC9138997 DOI: 10.3390/biom12050611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/15/2022] [Accepted: 04/15/2022] [Indexed: 12/18/2022] Open
Abstract
Next generation sequencing of RNA molecules (RNA-seq) has become a common tool to characterize the expression profiles of RNAs and their regulations in normal physiological processes and diseases. Although increasingly accumulating RNA-seq data are widely available through publicly accessible sites, most of the data for short non-coding RNAs (sncRNAs) have been obtained for microRNA (miRNA) analyses by standard RNA-seq, which only capture the sncRNAs with 5'-phosphate (5'-P) and 3'-hydroxyl (3'-OH) ends. The sncRNAs with other terminal formations such as those with a 5'-hydroxyl end (5'-OH), a 3'-phosphate (3'-P) end, or a 2',3'-cyclic phosphate end (2',3'-cP) cannot be efficiently amplified and sequenced by standard RNA-seq. Due to the invisibility in standard RNA-seq data, these non-miRNA-sncRNAs have been a hidden component in the transcriptome. However, as the functional significances of these sncRNAs have become increasingly apparent, specific RNA-seq methods compatible with various terminal formations of sncRNAs have been developed and started shedding light on the previously unrecognized sncRNAs that lack 5'-P/3'-OH ends. In this review, we summarize the expanding world of sncRNAs with various terminal formations and the strategic approaches of specific RNA-seq methods to distinctively characterize their expression profiles.
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Affiliation(s)
| | - Yohei Kirino
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA;
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6
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Olzog VJ, Gärtner C, Stadler PF, Fallmann J, Weinberg CE. cyPhyRNA-seq: a genome-scale RNA-seq method to detect active self-cleaving ribozymes by capturing RNAs with 2',3' cyclic phosphates and 5' hydroxyl ends. RNA Biol 2021; 18:818-831. [PMID: 34906034 PMCID: PMC8782182 DOI: 10.1080/15476286.2021.1999105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Self-cleaving ribozymes are catalytically active RNAs that cleave themselves into a 5′-fragment with a 2′,3′-cyclic phosphate and a 3′-fragment with a 5′-hydroxyl. They are widely applied for the construction of synthetic RNA devices and RNA-based therapeutics. However, the targeted discovery of self-cleaving ribozymes remains a major challenge. We developed a transcriptome-wide method, called cyPhyRNA-seq, to screen for ribozyme cleavage fragments in total RNA extract. This approach employs the specific ligation-based capture of ribozyme 5′-fragments using a variant of the Arabidopsis thaliana tRNA ligase we engineered. To capture ribozyme 3′-fragments, they are enriched from total RNA by enzymatic treatments. We optimized and enhanced the individual steps of cyPhyRNA-seq in vitro and in spike-in experiments. Then, we applied cyPhyRNA-seq to total RNA isolated from the bacterium Desulfovibrio vulgaris and detected self-cleavage of the three predicted type II hammerhead ribozymes, whose activity had not been examined to date. cyPhyRNA-seq can be used for the global analysis of active self-cleaving ribozymes with the advantage to capture both ribozyme cleavage fragments from total RNA. Especially in organisms harbouring many self-cleaving RNAs, cyPhyRNA-seq facilitates the investigation of cleavage activity. Moreover, this method has the potential to be used to discover novel self-cleaving ribozymes in different organisms.
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Affiliation(s)
- V Janett Olzog
- Department of Life Science, Institute for Biochemistry, Leipzig, Germany
| | - Christiane Gärtner
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany.,Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.,Department of Theoretical Chemistry, Vienna, Austria.,Facultad de Ciencias, Universidad National de Colombia, Sede Bogotá, Colombia.,Santa Fe Institute, University of Vienna, Santa Fe, New Mexico, USA
| | - Jörg Fallmann
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany
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7
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Yip MCJ, Savickas S, Gygi SP, Shao S. ELAC1 Repairs tRNAs Cleaved during Ribosome-Associated Quality Control. Cell Rep 2021; 30:2106-2114.e5. [PMID: 32075755 DOI: 10.1016/j.celrep.2020.01.082] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 12/30/2019] [Accepted: 01/22/2020] [Indexed: 12/31/2022] Open
Abstract
Ribosome-associated quality control (RQC) disassembles aberrantly stalled translation complexes to recycle or degrade the constituent parts. A key step of RQC is the cleavage of P-site tRNA by the endonuclease ANKZF1 (Vms1 in yeast) to release incompletely synthesized polypeptides from ribosomes for degradation. Re-use of the cleaved tRNA for translation requires re-addition of the universal 3'CCA nucleotides removed by ANKZF1. Here, we show that ELAC1 is both necessary and sufficient to remove the 2',3'-cyclic phosphate on ANKZF1-cleaved tRNAs to permit CCA re-addition by TRNT1. ELAC1 activity is optimized for tRNA recycling, whereas ELAC2, the essential RNase Z isoform in eukaryotes, is required to remove 3' trailers during tRNA biogenesis. Cells lacking ELAC1 specifically accumulate unrepaired tRNA intermediates upon the induction of ribosome stalling. Thus, optimal recycling of ANKZF1-cleaved tRNAs in vertebrates is achieved through the duplication and specialization of a conserved tRNA biosynthesis enzyme.
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Affiliation(s)
- Matthew C J Yip
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Simonas Savickas
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Steven P Gygi
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Sichen Shao
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
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8
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Ancar R, Li Y, Kindler E, Cooper DA, Ransom M, Thiel V, Weiss SR, Hesselberth JR, Barton DJ. Physiologic RNA targets and refined sequence specificity of coronavirus EndoU. RNA (NEW YORK, N.Y.) 2020; 26:1976-1999. [PMID: 32989044 PMCID: PMC7668261 DOI: 10.1261/rna.076604.120] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 09/12/2020] [Indexed: 05/15/2023]
Abstract
Coronavirus EndoU inhibits dsRNA-activated antiviral responses; however, the physiologic RNA substrates of EndoU are unknown. In this study, we used mouse hepatitis virus (MHV)-infected bone marrow-derived macrophage (BMM) and cyclic phosphate cDNA sequencing to identify the RNA targets of EndoU. EndoU targeted viral RNA, cleaving the 3' side of pyrimidines with a strong preference for U ↓ A and C ↓ A sequences (endoY ↓ A). EndoU-dependent cleavage was detected in every region of MHV RNA, from the 5' NTR to the 3' NTR, including transcriptional regulatory sequences (TRS). Cleavage at two CA dinucleotides immediately adjacent to the MHV poly(A) tail suggests a mechanism to suppress negative-strand RNA synthesis and the accumulation of viral dsRNA. MHV with EndoU (EndoUmut) or 2'-5' phosphodiesterase (PDEmut) mutations provoked the activation of RNase L in BMM, with corresponding cleavage of RNAs by RNase L. The physiologic targets of EndoU are viral RNA templates required for negative-strand RNA synthesis and dsRNA accumulation. Coronavirus EndoU cleaves U ↓ A and C ↓ A sequences (endoY ↓ A) within viral (+) strand RNA to evade dsRNA-activated host responses.
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Affiliation(s)
- Rachel Ancar
- Department of Biochemistry and Molecular Genetics, Program in Molecular Biology, School of Medicine, University of Colorado, Aurora 80045, Colorado, USA
| | - Yize Li
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Eveline Kindler
- Institute of Virology and Immunology IVI, 3001 Bern and 3147 Mittelhausern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - Daphne A Cooper
- Department of Immunology and Microbiology, School of Medicine, University of Colorado, Aurora, Colorado 80045, USA
| | - Monica Ransom
- Department of Biochemistry and Molecular Genetics, Program in Molecular Biology, School of Medicine, University of Colorado, Aurora 80045, Colorado, USA
| | - Volker Thiel
- Institute of Virology and Immunology IVI, 3001 Bern and 3147 Mittelhausern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - Susan R Weiss
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Jay R Hesselberth
- Department of Biochemistry and Molecular Genetics, Program in Molecular Biology, School of Medicine, University of Colorado, Aurora 80045, Colorado, USA
| | - David J Barton
- Department of Immunology and Microbiology, Program in Molecular Biology, School of Medicine, University of Colorado, Aurora, Colorado 80045, USA
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9
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Berk C, Wang Y, Laski A, Tsagkris S, Hall J. Ligation of 2', 3'-cyclic phosphate RNAs for the identification of microRNA binding sites. FEBS Lett 2020; 595:230-240. [PMID: 33113149 PMCID: PMC7894349 DOI: 10.1002/1873-3468.13976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/27/2020] [Accepted: 10/08/2020] [Indexed: 11/21/2022]
Abstract
Identifying the targetome of a microRNA is key for understanding its functions. Cross‐linking and immunoprecipitation (CLIP) methods capture native miRNA‐mRNA interactions in cells. Some of these methods yield small amounts of chimeric miRNA‐mRNA sequences via ligation of 5′‐phosphorylated RNAs produced during the protocol. Here, we introduce chemically synthesized microRNAs (miRNAs) bearing 2′‐, 3′‐cyclic phosphate groups, as part of a new CLIP method that does not require 5′‐phosphorylation for ligation. We show in a system that models miRNAs bound to their targets, that addition of recombinant bacterial ligase RtcB increases ligation efficiency, and that the transformation proceeds via a 3′‐phosphate intermediate. By optimizing the chemistry underlying ligation, we provide the basis for an improved method to identify miRNA targetomes.
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Affiliation(s)
- Christian Berk
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Switzerland
| | - Yuluan Wang
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Switzerland
| | - Artur Laski
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Switzerland
| | - Stylianos Tsagkris
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Switzerland
| | - Jonathan Hall
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Switzerland
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10
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Shigematsu M, Morichika K, Kawamura T, Honda S, Kirino Y. Genome-wide identification of short 2',3'-cyclic phosphate-containing RNAs and their regulation in aging. PLoS Genet 2019; 15:e1008469. [PMID: 31721758 PMCID: PMC6853296 DOI: 10.1371/journal.pgen.1008469] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 10/10/2019] [Indexed: 12/19/2022] Open
Abstract
RNA molecules generated by ribonuclease cleavage sometimes harbor a 2′,3′-cyclic phosphate (cP) at their 3′-ends. Those cP-containing RNAs (cP-RNAs) form a hidden layer of transcriptome because standard RNA-seq cannot capture them as a result of cP’s prevention of an adapter ligation reaction. Here we provide genome-wide analyses of short cP-RNA transcriptome across multiple mouse tissues. Using cP-RNA-seq that can exclusively sequence cP-RNAs, we identified numerous novel cP-RNA species which are mainly derived from cytoplasmic tRNAs, mRNAs, and rRNAs. Determination of the processing sites of substrate RNAs for cP-RNA generation revealed highly-specific RNA cleavage events between cytidine and adenosine in cP-RNA biogenesis. cP-RNAs were not evenly derived from the overall region of substrate RNAs but rather from specific sites, implying that cP-RNAs are not from random degradation but are produced through a regulated biogenesis pathway. The identified cP-RNAs were abundantly accumulated in mouse tissues, and the expression levels of cP-RNAs showed age-dependent reduction. These analyses of cP-RNA transcriptome unravel a novel, abundant class of non-coding RNAs whose expression could have physiological roles. With the advent and evolution of next-generation sequencing technology, efforts to identify and catalog the expressed RNA molecules have greatly advanced our understanding of RNA biology. However, the current standard RNA-seq methods, particularly those targeting short ncRNAs, do not fully capture all of the RNAs expressed but allow for some “escapers” to slip. RNAs generated by ribonuclease cleavage sometimes harbor a 2′,3′-cyclic phosphate (cP) at their 3′-ends, and those cP-containing RNAs (cP-RNAs) are one such escaper that are not ligated to a 3′-adapter and thus uncaptured by standard RNA-seq. Although an increasing number of studies has been suggesting their functional significances, cP-RNAs remained a hidden component in the transcriptome, infrequently recognized and characterized. In this study, we provide the first genome-wide analyses of short cP-RNA transcriptome across multiple mouse tissues. By using cP-RNA-seq technique that can specifically sequence cP-RNAs, we identified numerous novel cP-RNA species which are mainly derived from tRNAs, mRNAs, and rRNAs. cP-RNAs are generated by previously-uncharacterized, highly-specific RNA cleavage events between cytidine and adenosine, which is regulated through aging. These analyses of cP-RNA transcriptome unravel a novel, abundant class of non-coding RNAs whose expression could have physiological roles.
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Affiliation(s)
- Megumi Shigematsu
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Keisuke Morichika
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Takuya Kawamura
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Shozo Honda
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Yohei Kirino
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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11
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Kirsch R, Olzog VJ, Bonin S, Weinberg CE, Betat H, Stadler PF, Mörl M. A streamlined protocol for the detection of mRNA-sRNA interactions using AMT-crosslinking in vitro. Biotechniques 2019; 67:178-183. [PMID: 31462065 DOI: 10.2144/btn-2019-0047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Until recently, RNA-RNA interactions were mainly identified by crosslinking RNAs with interacting proteins, RNA proximity ligation and deep sequencing. Recently, AMT-based direct RNA crosslinking was established. Yet, several steps of these procedures are rather inefficient, reducing the output of identified interaction partners. To increase the local concentration of RNA ends, interacting RNAs are often fragmented. However, the resulting 2',3'-cyclic phosphate and 5'-OH ends are not accepted by T4 RNA ligase and have to be converted to 3'-OH and 5'-phosphate ends. Using an artificial mRNA/sRNA pair, we optimized the workflow downstream of the crosslinking reaction in vitro. The use of a tRNA ligase allows direct fusion of 2',3'-cyclic phosphate and 5'-OH RNA ends.
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Affiliation(s)
- Rebecca Kirsch
- Institute for Biochemistry, Brüderstraße 34, 04103 Leipzig, Germany.,Center for Non-Coding RNA in Technology & Health, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark
| | - V Janett Olzog
- Institute for Biochemistry, Brüderstraße 34, 04103 Leipzig, Germany
| | - Sonja Bonin
- Institute for Biochemistry, Brüderstraße 34, 04103 Leipzig, Germany
| | | | - Heike Betat
- Institute for Biochemistry, Brüderstraße 34, 04103 Leipzig, Germany
| | - Peter F Stadler
- Center for Non-Coding RNA in Technology & Health, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark.,Bioinformatics Group, Department of Computer Science & Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany.,Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, 04103 Leipzig, Germany.,Department of Theoretical Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria.,Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
| | - Mario Mörl
- Institute for Biochemistry, Brüderstraße 34, 04103 Leipzig, Germany
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12
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Rigoutsos I, Londin E, Kirino Y. Short RNA regulators: the past, the present, the future, and implications for precision medicine and health disparities. Curr Opin Biotechnol 2019; 58:202-210. [PMID: 31323485 DOI: 10.1016/j.copbio.2019.05.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 05/09/2019] [Accepted: 05/27/2019] [Indexed: 01/03/2023]
Abstract
We herein provide a brief review of the trajectory that the field of short RNA research followed in the last 25 years. We place emphasis on the unexpected discoveries and the ramifications of these discoveries for the field, as well as offer some thoughts about what the next 25 years may bring. Arguably, the uncovered dependence of different types of short RNAs on individual attributes such as a person's sex, population origin, race, and on tissue type, tissue state, and disease was most unexpected. This dependence has important ramifications in that it will provide a boost to our understanding of the molecular mechanisms of health disparities as well as pave the way for novel approaches to designing improved and personalized diagnostics and therapeutics.
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Affiliation(s)
- Isidore Rigoutsos
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, United States.
| | - Eric Londin
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, United States.
| | - Yohei Kirino
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, United States.
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13
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Krogh N, Nielsen H. Sequencing-based methods for detection and quantitation of ribose methylations in RNA. Methods 2018; 156:5-15. [PMID: 30503826 DOI: 10.1016/j.ymeth.2018.11.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 11/23/2018] [Accepted: 11/27/2018] [Indexed: 10/27/2022] Open
Abstract
Ribose methylation is one of the most abundant RNA modifications and is found in all domains of life and all major classes of RNA (rRNA, tRNA, and mRNA). Ribose methylations are introduced by stand-alone enzymes or by generic enzymes guided to the target by small RNA guides. Recent years have seen the development of several sequencing-based methods for RNA modifications relying on different principles. In this review, we compare mapping and quantitation studies of ribose methylations from yeast and human culture cells. The emphasis is on ribosomal RNA for which the results can be compared to results from RNA fingerprinting and mass spectrometry. One sequencing approach is consistent with these methods and paints a conservative picture of rRNA modifications. Other approaches detect many more sites. Similar discrepancies are found in measurements of modification stoichiometry. The results are discussed in relation to the more challenging task of mapping ribose methylations in mRNA.
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Affiliation(s)
- Nicolai Krogh
- Department of Cellular and Molecular Medicine, University of Copenhagen, Denmark
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Denmark.
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14
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Shigematsu M, Kawamura T, Kirino Y. Generation of 2',3'-Cyclic Phosphate-Containing RNAs as a Hidden Layer of the Transcriptome. Front Genet 2018; 9:562. [PMID: 30538719 PMCID: PMC6277466 DOI: 10.3389/fgene.2018.00562] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 11/06/2018] [Indexed: 01/03/2023] Open
Abstract
Cellular RNA molecules contain phosphate or hydroxyl ends. A 2′,3′-cyclic phosphate (cP) is one of the 3′-terminal forms of RNAs mainly generated from RNA cleavage by ribonucleases. Although transcriptome profiling using RNA-seq has become a ubiquitous tool in biological and medical research, cP-containing RNAs (cP-RNAs) form a hidden transcriptome layer, which is infrequently recognized and characterized, because standard RNA-seq is unable to capture them. Despite cP-RNAs’ invisibility in RNA-seq data, increasing evidence indicates that they are not accumulated simply as non-functional degradation products; rather, they have physiological roles in various biological processes, designating them as noteworthy functional molecules. This review summarizes our current knowledge of cP-RNA biogenesis pathways and their catalytic enzymatic activities, discusses how the cP-RNA generation affects biological processes, and explores future directions to further investigate cP-RNA biology.
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Affiliation(s)
- Megumi Shigematsu
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, United States
| | - Takuya Kawamura
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, United States
| | - Yohei Kirino
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, United States
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15
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Lyons SM, Fay MM, Ivanov P. The role of RNA modifications in the regulation of tRNA cleavage. FEBS Lett 2018; 592:2828-2844. [PMID: 30058219 DOI: 10.1002/1873-3468.13205] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 06/28/2018] [Accepted: 07/18/2018] [Indexed: 12/21/2022]
Abstract
Transfer RNA (tRNA) have been harbingers of many paradigms in RNA biology. They are among the first recognized noncoding RNA (ncRNA) playing fundamental roles in RNA metabolism. Although mainly recognized for their role in decoding mRNA and delivering amino acids to the growing polypeptide chain, tRNA also serve as an abundant source of small ncRNA named tRNA fragments. The functional significance of these fragments is only beginning to be uncovered. Early on, tRNA were recognized as heavily post-transcriptionally modified, which aids in proper folding and modulates the tRNA:mRNA anticodon-codon interactions. Emerging data suggest that these modifications play critical roles in the generation and activity of tRNA fragments. Modifications can both protect tRNA from cleavage or promote their cleavage. Modifications to individual fragments may be required for their activity. Recent work has shown that some modifications are critical for stem cell development and that failure to deposit certain modifications has profound effects on disease. This review will discuss how tRNA modifications regulate the generation and activity of tRNA fragments.
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Affiliation(s)
- Shawn M Lyons
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Marta M Fay
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Pavel Ivanov
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA.,The Broad Institute of Harvard and M.I.T., Cambridge, MA, USA
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16
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Cherry PD, White LK, York K, Hesselberth JR. Genetic bypass of essential RNA repair enzymes in budding yeast. RNA (NEW YORK, N.Y.) 2018; 24:313-323. [PMID: 29212664 PMCID: PMC5824351 DOI: 10.1261/rna.061788.117] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 12/04/2017] [Indexed: 05/15/2023]
Abstract
RNA repair enzymes catalyze rejoining of an RNA molecule after cleavage of phosphodiester linkages. RNA repair in budding yeast is catalyzed by two separate enzymes that process tRNA exons during their splicing and HAC1 mRNA exons during activation of the unfolded protein response (UPR). The RNA ligase Trl1 joins 2',3'-cyclic phosphate and 5'-hydroxyl RNA fragments, creating a phosphodiester linkage with a 2'-phosphate at the junction. The 2'-phosphate is removed by the 2'-phosphotransferase Tpt1. We bypassed the essential functions of TRL1 and TPT1 in budding yeast by expressing "prespliced," intronless versions of the 10 normally intron-containing tRNAs, indicating this repair pathway does not have additional essential functions. Consistent with previous studies, expression of intronless tRNAs failed to rescue the growth of cells with deletions in components of the SEN complex, implying an additional essential role for the splicing endonuclease. The trl1Δ and tpt1Δ mutants accumulate tRNA and HAC1 splicing intermediates indicative of RNA repair defects and are hypersensitive to drugs that inhibit translation. Failure to induce the unfolded protein response in trl1Δ cells grown with tunicamycin is lethal owing to their inability to ligate HAC1 after its cleavage by Ire1. In contrast, tpt1Δ mutants grow in the presence of tunicamycin despite reduced accumulation of spliced HAC1 mRNA. We optimized a PCR-based method to detect RNA 2'-phosphate modifications and show they are present on ligated HAC1 mRNA. These RNA repair mutants enable new studies of the role of RNA repair in cellular physiology.
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Affiliation(s)
- Patrick D Cherry
- Department of Biochemistry and Molecular Genetics, Program in Molecular Biology, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Laura K White
- Department of Biochemistry and Molecular Genetics, Program in Molecular Biology, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Kerri York
- Department of Biochemistry and Molecular Genetics, Program in Molecular Biology, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Jay R Hesselberth
- Department of Biochemistry and Molecular Genetics, Program in Molecular Biology, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
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17
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Ikeda Y, Okada Y, Sato A, Kanai T, Tomita M, Atomi H, Kanai A. An archaeal RNA binding protein, FAU-1, is a novel ribonuclease related to rRNA stability in Pyrococcus and Thermococcus. Sci Rep 2017; 7:12674. [PMID: 28978920 PMCID: PMC5627344 DOI: 10.1038/s41598-017-13062-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 09/12/2017] [Indexed: 12/28/2022] Open
Abstract
Ribosome biogenesis and turnover are processes necessary for cell viability and proliferation, and many kinds of proteins are known to regulate these processes. However, many questions still remain, especially in the Archaea. Generally, several ribonucleases are required to process precursor rRNAs to their mature forms, and to degrade rRNAs for quality control. Here, we found that FAU-1, which is known to be an RNA binding protein, possesses an RNase activity against precursor 5S rRNA derived from P. furiosus and T. kodakarensis in the order Thermococcales in vitro. An in vitro analysis revealed that UA sequences in the upstream of 5S rRNA were preferentially degraded by addition of FAU-1. Moreover, a fau-1 gene deletion mutant of T. kodakarensis showed a delay of exponential phase, reduction of maximum cell number and significant changes in the nucleotide sequence lengths of its 5S, 16S, and 23S rRNAs in early exponential phase. Our results suggest that FAU-1 is a potential RNase involved in rRNA stability through maturation and/or degradation processes.
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Affiliation(s)
- Yoshiki Ikeda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, 997-0017, Japan.
| | - Yasuhiro Okada
- Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan
| | - Asako Sato
- Institute for Advanced Biosciences, Keio University, Tsuruoka, 997-0017, Japan
| | - Tamotsu Kanai
- Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, 997-0017, Japan
| | - Haruyuki Atomi
- Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan
| | - Akio Kanai
- Institute for Advanced Biosciences, Keio University, Tsuruoka, 997-0017, Japan
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18
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Yoshinari S, Liu Y, Gollnick P, Ho CK. Cleavage of 3'-terminal adenosine by archaeal ATP-dependent RNA ligase. Sci Rep 2017; 7:11662. [PMID: 28912583 PMCID: PMC5599603 DOI: 10.1038/s41598-017-11693-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 08/29/2017] [Indexed: 01/15/2023] Open
Abstract
Methanothermobacter thermoautotrophicus RNA ligase (MthRnl) catalyzes formation of phosphodiester bonds between the 5′-phosphate and 3′-hydroxyl termini of single-stranded RNAs. It can also react with RNA with a 3′-phosphate end to generate a 2′,3′-cyclic phosphate. Here, we show that MthRnl can additionally remove adenosine from the 3′-terminus of the RNA to produce 3′-deadenylated RNA, RNA(3′-rA). This 3′-deadenylation activity is metal-dependent and requires a 2′-hydroxyl at both the terminal adenosine and the penultimate nucleoside. Residues that contact the ATP/AMP in the MthRnl crystal structures are essential for the 3′-deadenylation activity, suggesting that 3′-adenosine may occupy the ATP-binding pocket. The 3′-end of cleaved RNA(3′-rA) consists of 2′,3′-cyclic phosphate which protects RNA(3′-rA) from ligation and further deadenylation. These findings suggest that ATP-dependent RNA ligase may act on a specific set of 3′-adenylated RNAs to regulate their processing and downstream biological events.
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Affiliation(s)
- Shigeo Yoshinari
- Department of Biological Sciences, State University of New York, Buffalo, NY, 14260, United States of America
| | - Yancheng Liu
- Human Biology Program, School of Integrative and Global Majors, University of Tsukuba, Ibaraki, 305-8575, Japan
| | - Paul Gollnick
- Department of Biological Sciences, State University of New York, Buffalo, NY, 14260, United States of America
| | - C Kiong Ho
- Department of Biological Sciences, State University of New York, Buffalo, NY, 14260, United States of America. .,Human Biology Program, School of Integrative and Global Majors, University of Tsukuba, Ibaraki, 305-8575, Japan. .,Department of Infection Biology, Faculty of Medicine, University of Tsukuba, Ibaraki, 305-8575, Japan.
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19
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Zinder JC, Lima CD. Targeting RNA for processing or destruction by the eukaryotic RNA exosome and its cofactors. Genes Dev 2017; 31:88-100. [PMID: 28202538 PMCID: PMC5322736 DOI: 10.1101/gad.294769.116] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In this review, Zinder and Lima highlight recent advances that have illuminated roles for the RNA exosome and its cofactors in specific biological pathways, alongside studies that attempted to dissect these activities through structural and biochemical characterization of nuclear and cytoplasmic RNA exosome complexes. The eukaryotic RNA exosome is an essential and conserved protein complex that can degrade or process RNA substrates in the 3′-to-5′ direction. Since its discovery nearly two decades ago, studies have focused on determining how the exosome, along with associated cofactors, achieves the demanding task of targeting particular RNAs for degradation and/or processing in both the nucleus and cytoplasm. In this review, we highlight recent advances that have illuminated roles for the RNA exosome and its cofactors in specific biological pathways, alongside studies that attempted to dissect these activities through structural and biochemical characterization of nuclear and cytoplasmic RNA exosome complexes.
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Affiliation(s)
- John C Zinder
- Tri-Institutional Training Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Structural Biology Program, Sloan Kettering Institute, New York, New York, 10065, USA
| | - Christopher D Lima
- Structural Biology Program, Sloan Kettering Institute, New York, New York, 10065, USA.,Howard Hughes Medical Institute, New York, New York, 10065 USA
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20
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Abstract
RiboMeth-seq is a sequencing-based method for mapping and quantitation of one of the most abundant RNA modifications, ribose methylation. It is based on a simple chemical principle, namely the several orders of magnitude difference in nucleophilicity of a 2'-OH and a 2'-O-Me. Thus, the method combines alkaline fragmentation and a specialized library construction protocol based on 5'-OH and 2',3' cyclic phosphate ends to prepare RNA for sequencing. The read-ends of library fragments are used for mapping with nucleotide resolution and calculation of the fraction of molecules methylated at the 2'-O-Me sites.
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Affiliation(s)
- Nicolai Krogh
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, 3 Blegdamsvej, 18.2.22, DK-2200N, Copenhagen, Denmark
| | - Ulf Birkedal
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, 3 Blegdamsvej, 18.2.22, DK-2200N, Copenhagen, Denmark
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, 3 Blegdamsvej, 18.2.22, DK-2200N, Copenhagen, Denmark.
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21
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Selective amplification and sequencing of cyclic phosphate-containing RNAs by the cP-RNA-seq method. Nat Protoc 2016; 11:476-89. [PMID: 26866791 DOI: 10.1038/nprot.2016.025] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
RNA digestions catalyzed by many ribonucleases generate RNA fragments that contain a 2',3'-cyclic phosphate (cP) at their 3' termini. However, standard RNA-seq methods are unable to accurately capture cP-containing RNAs because the cP inhibits the adapter ligation reaction. We recently developed a method named cP-RNA-seq that is able to selectively amplify and sequence cP-containing RNAs. Here we describe the cP-RNA-seq protocol in which the 3' termini of all RNAs, except those containing a cP, are cleaved through a periodate treatment after phosphatase treatment; hence, subsequent adapter ligation and cDNA amplification steps are exclusively applied to cP-containing RNAs. cP-RNA-seq takes ∼6 d, excluding the time required for sequencing and bioinformatics analyses, which are not covered in detail in this protocol. Biochemical validation of the existence of cP in the identified RNAs takes ∼3 d. Even though the cP-RNA-seq method was developed to identify angiogenin-generating 5'-tRNA halves as a proof of principle, the method should be applicable to global identification of cP-containing RNA repertoires in various transcriptomes.
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22
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Arabidopsis tRNA ligase completes the cytoplasmic splicing of bZIP60 mRNA in the unfolded protein response. Biochem Biophys Res Commun 2016; 470:941-6. [DOI: 10.1016/j.bbrc.2016.01.145] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 01/22/2016] [Indexed: 01/20/2023]
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23
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Kaito C. Understanding of bacterial virulence using the silkworm infection model. Drug Discov Ther 2016; 10:30-3. [DOI: 10.5582/ddt.2016.01020] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Chikara Kaito
- Laboratory of Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo
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24
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Uzilov AV, Underwood JG. High-Throughput Nuclease Probing of RNA Structures Using FragSeq. Methods Mol Biol 2016; 1490:105-34. [PMID: 27665596 DOI: 10.1007/978-1-4939-6433-8_8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
High-throughput sequencing of cDNA (RNA-Seq) can be used to generate nuclease accessibility data for many distinct transcripts in the same mixture simultaneously. Such assays accelerate RNA structure analysis and provide researchers with new technologies to tackle biological questions on a transcriptome-wide scale. FragSeq is an experimental assay for transcriptome-wide RNA structure probing using RNA-Seq, coupled with data analysis tools that allow quantitative determination of nuclease accessibility at single-base resolution. We provide a practical guide to designing and carrying out FragSeq experiments and data analysis.
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Affiliation(s)
- Andrew V Uzilov
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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25
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Shchepachev V, Wischnewski H, Soneson C, Arnold AW, Azzalin CM. Human Mpn1 promotes post-transcriptional processing and stability of U6atac. FEBS Lett 2015. [PMID: 26213367 DOI: 10.1016/j.febslet.2015.06.046] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Mpn1 is an exoribonuclease that modifies the spliceosomal small nuclear RNA (snRNA) U6 by trimming its oligouridine tail and introducing a cyclic phosphate group (>p). Mpn1 deficiency induces U6 3' end misprocessing, accelerated U6 decay and pre-mRNA splicing defects. Mutations in the human MPN1 gene are associated with the genodermatosis Clericuzio-type poikiloderma with neutropenia (PN). Here we present the deep sequencing of the >p-containing transcriptomes of mpn1Δ fission yeast and PN cells. While in yeast U6 seems to be the only substrate of Mpn1, human Mpn1 also processes U6atac snRNA. PN cells bear unstable U6atac species with aberrantly long and oligoadenylated 3' ends. Our data corroborate the link between Mpn1 and snRNA stability suggesting that PN could derive from pre-mRNA splicing aberrations.
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Affiliation(s)
- Vadim Shchepachev
- Institute of Biochemistry (IBC), Eidgenössische Technische Hochschule Zürich (ETHZ), Zürich CH-8093, Switzerland
| | - Harry Wischnewski
- Institute of Biochemistry (IBC), Eidgenössische Technische Hochschule Zürich (ETHZ), Zürich CH-8093, Switzerland
| | - Charlotte Soneson
- Bioinformatics Core Facility, SIB Swiss Institute of Bioinformatics, Lausanne CH-1015, Switzerland
| | - Andreas W Arnold
- Dermatologische Universitätsklinik, Universitätsspital Basel, Basel CH-4031, Switzerland
| | - Claus M Azzalin
- Institute of Biochemistry (IBC), Eidgenössische Technische Hochschule Zürich (ETHZ), Zürich CH-8093, Switzerland.
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26
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Sex hormone-dependent tRNA halves enhance cell proliferation in breast and prostate cancers. Proc Natl Acad Sci U S A 2015; 112:E3816-25. [PMID: 26124144 DOI: 10.1073/pnas.1510077112] [Citation(s) in RCA: 251] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Sex hormones and their receptors play critical roles in the development and progression of the breast and prostate cancers. Here we report that a novel type of transfer RNA (tRNA)-derived small RNA, termed Sex HOrmone-dependent TRNA-derived RNAs (SHOT-RNAs), are specifically and abundantly expressed in estrogen receptor (ER)-positive breast cancer and androgen receptor (AR)-positive prostate cancer cell lines. SHOT-RNAs are not abundantly present in ER(-) breast cancer, AR(-) prostate cancer, or other examined cancer cell lines from other tissues. ER-dependent accumulation of SHOT-RNAs is not limited to a cell culture system, but it also occurs in luminal-type breast cancer patient tissues. SHOT-RNAs are produced from aminoacylated mature tRNAs by angiogenin-mediated anticodon cleavage, which is promoted by sex hormones and their receptors. Resultant 5'- and 3'-SHOT-RNAs, corresponding to 5'- and 3'-tRNA halves, bear a cyclic phosphate (cP) and an amino acid at the 3'-end, respectively. By devising a "cP-RNA-seq" method that is able to exclusively amplify and sequence cP-containing RNAs, we identified the complete repertoire of 5'-SHOT-RNAs. Furthermore, 5'-SHOT-RNA, but not 3'-SHOT-RNA, has significant functional involvement in cell proliferation. These results have unveiled a novel tRNA-engaged pathway in tumorigenesis of hormone-dependent cancers and implicate SHOT-RNAs as potential candidates for biomarkers and therapeutic targets.
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27
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Jinks-Robertson S, Klein HL. Ribonucleotides in DNA: hidden in plain sight. Nat Struct Mol Biol 2015; 22:176-8. [PMID: 25736085 DOI: 10.1038/nsmb.2981] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Sue Jinks-Robertson
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Hannah L Klein
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, USA
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28
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Peach SE, York K, Hesselberth JR. Global analysis of RNA cleavage by 5'-hydroxyl RNA sequencing. Nucleic Acids Res 2015; 43:e108. [PMID: 26001965 PMCID: PMC4787814 DOI: 10.1093/nar/gkv536] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 05/10/2015] [Indexed: 11/12/2022] Open
Abstract
RNA cleavage by some endoribonucleases and self-cleaving ribozymes produces RNA fragments with 5′-hydroxyl (5′-OH) and 2′,3′-cyclic phosphate termini. To identify 5′-OH RNA fragments produced by these cleavage events, we exploited the unique ligation mechanism of Escherichia coli RtcB RNA ligase to attach an oligonucleotide linker to RNAs with 5′-OH termini, followed by steps for library construction and analysis by massively parallel DNA sequencing. We applied the method to RNA from budding yeast and captured known 5′-OH fragments produced by tRNA Splicing Endonuclease (SEN) during processing of intron-containing pre-tRNAs and by Ire1 cleavage of HAC1 mRNA following induction of the unfolded protein response (UPR). We identified numerous novel 5′-OH fragments derived from mRNAs: some 5′-OH mRNA fragments were derived from single, localized cleavages, while others were likely produced by multiple, distributed cleavages. Many 5′-OH fragments derived from mRNAs were produced upstream of codons for highly electrostatic peptides, suggesting that the fragments may be generated by co-translational mRNA decay. Several 5′-OH RNA fragments accumulated during the induction of the UPR, some of which share a common sequence motif that may direct cleavage of these mRNAs. This method enables specific capture of 5′-OH termini and complements existing methods for identifying RNAs with 2′,3′-cyclic phosphate termini.
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Affiliation(s)
- Sally E Peach
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA Program in Molecular Biology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Kerri York
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Jay R Hesselberth
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA Program in Molecular Biology, University of Colorado School of Medicine, Aurora, CO 80045, USA
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29
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Dhahbi JM. 5' tRNA Halves: The Next Generation of Immune Signaling Molecules. Front Immunol 2015; 6:74. [PMID: 25745425 PMCID: PMC4333838 DOI: 10.3389/fimmu.2015.00074] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Accepted: 02/05/2015] [Indexed: 01/01/2023] Open
Affiliation(s)
- Joseph Mohsen Dhahbi
- Biochemistry Department, University of California Riverside , Riverside, CA , USA ; Center for Genetics, Children's Hospital Oakland Research Institute , Oakland, CA , USA
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30
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Koh KD, Balachander S, Hesselberth JR, Storici F. Ribose-seq: global mapping of ribonucleotides embedded in genomic DNA. Nat Methods 2015; 12:251-7, 3 p following 257. [PMID: 25622106 DOI: 10.1038/nmeth.3259] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 12/22/2014] [Indexed: 02/06/2023]
Abstract
Abundant ribonucleotide incorporation in DNA during replication and repair has profound consequences for genome stability, but the global distribution of ribonucleotide incorporation is unknown. We developed ribose-seq, a method for capturing unique products generated by alkaline cleavage of DNA at embedded ribonucleotides. High-throughput sequencing of these fragments in DNA from the yeast Saccharomyces cerevisiae revealed widespread ribonucleotide distribution, with a strong preference for cytidine and guanosine, and identified hotspots of ribonucleotide incorporation in nuclear and mitochondrial DNA. Ribonucleotides were primarily incorporated on the newly synthesized leading strand of nuclear DNA and were present upstream of (G+C)-rich tracts in the mitochondrial genome. Ribose-seq is a powerful tool for the systematic profiling of ribonucleotide incorporation in genomic DNA.
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Affiliation(s)
- Kyung Duk Koh
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Sathya Balachander
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Jay R Hesselberth
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora, Colorado, USA
| | - Francesca Storici
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA
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31
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Abstract
UNLABELLED Influenza A virus (IAV) infections are influenced by type 1 interferon-mediated antiviral defenses and by viral countermeasures to these defenses. When IAV NS1 protein is disabled, RNase L restricts virus replication; however, the RNAs targeted for cleavage by RNase L under these conditions have not been defined. In this study, we used deep-sequencing methods to identify RNase L cleavage sites within host and viral RNAs from IAV PR8ΔNS1-infected A549 cells. Short hairpin RNA knockdown of RNase L allowed us to distinguish between RNase L-dependent and RNase L-independent cleavage sites. RNase L-dependent cleavage sites were evident at discrete locations in IAV RNA segments (both positive and negative strands). Cleavage in PB2, PB1, and PA genomic RNAs suggests that viral RNPs are susceptible to cleavage by RNase L. Prominent amounts of cleavage mapped to specific regions within IAV RNAs, including some areas of increased synonymous-site conservation. Among cellular RNAs, RNase L-dependent cleavage was most frequent at precise locations in rRNAs. Our data show that RNase L targets specific sites in both host and viral RNAs to restrict influenza virus replication when NS1 protein is disabled. IMPORTANCE RNase L is a critical component of interferon-regulated and double-stranded-RNA-activated antiviral host responses. We sought to determine how RNase L exerts its antiviral activity during influenza virus infection. We enhanced the antiviral activity of RNase L by disabling a viral protein, NS1, that inhibits the activation of RNase L. Then, using deep-sequencing methods, we identified the host and viral RNAs targeted by RNase L. We found that RNase L cleaved viral RNAs and rRNAs at very precise locations. The direct cleavage of IAV RNAs by RNase L highlights an intimate battle between viral RNAs and an antiviral endonuclease.
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Anderson P, Ivanov P. tRNA fragments in human health and disease. FEBS Lett 2014; 588:4297-304. [PMID: 25220675 PMCID: PMC4339185 DOI: 10.1016/j.febslet.2014.09.001] [Citation(s) in RCA: 271] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 09/03/2014] [Accepted: 09/04/2014] [Indexed: 01/07/2023]
Abstract
Transfer RNA (tRNA) is traditionally considered to be an adaptor molecule that helps ribosomes to decode messenger RNA (mRNA) and synthesize protein. Recent studies have demonstrated that tRNAs also serve as a major source of small non-coding RNAs that possess distinct and varied functions. These tRNA fragments are heterogeneous in size, nucleotide composition, biogenesis and function. Here we describe multiple roles that tRNA fragments play in cell physiology and discuss their relevance to human health and disease.
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Affiliation(s)
- Paul Anderson
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
| | - Pavel Ivanov
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
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Riccitelli N, Lupták A. HDV family of self-cleaving ribozymes. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2014; 120:123-71. [PMID: 24156943 DOI: 10.1016/b978-0-12-381286-5.00004-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The hepatitis delta virus (HDV) ribozymes are catalytic RNAs capable of cleaving their own sugar-phosphate backbone. The HDV virus possesses the ribozymes in both sense and antisense genomic transcripts, where they are essential for processing during replication. These ribozymes have been the subject of intense biochemical scrutiny and have yielded a wealth of mechanistic insights. In recent years, many HDV-like ribozymes have been identified in nearly all branches of life. The ribozymes are implicated in a variety of biological events, including episodic memory in mammals and retrotransposition in many eukaryotes. Detailed analysis of additional HDV-like ribozyme isolates will likely reveal many more biological functions and provide information about the evolution of this unique RNA.
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Affiliation(s)
- Nathan Riccitelli
- Department of Chemistry, University of California, Irvine, California, USA
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Remus BS, Shuman S. Distinctive kinetics and substrate specificities of plant and fungal tRNA ligases. RNA (NEW YORK, N.Y.) 2014; 20:462-73. [PMID: 24554441 PMCID: PMC3964908 DOI: 10.1261/rna.043752.113] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 01/07/2014] [Indexed: 05/23/2023]
Abstract
Plant and fungal tRNA ligases are trifunctional enzymes that repair RNA breaks with 2',3'-cyclic-PO4 and 5'-OH ends. They are composed of cyclic phosphodiesterase (CPDase) and polynucleotide kinase domains that heal the broken ends to generate the 3'-OH, 2'-PO4, and 5'-PO4 required for sealing by a ligase domain. Here, we use short HORNA>p substrates to determine, in a one-pot assay format under single-turnover conditions, the order and rates of the CPDase, kinase and ligase steps. The observed reaction sequence for the plant tRNA ligase AtRNL, independent of RNA length, is that the CPDase engages first, converting HORNA>p to HORNA2'p, which is then phosphorylated to pRNA2'p by the kinase. Whereas the rates of the AtRNL CPDase and kinase reactions are insensitive to RNA length, the rate of the ligase reaction is slowed by a factor of 16 in the transition from 10-mer RNA to 8-mer and further by eightfold in the transition from 8-mer RNA to 6-mer. We report that a single ribonucleoside-2',3'-cyclic-PO4 moiety enables AtRNL to efficiently splice an otherwise all-DNA strand. Our characterization of a fungal tRNA ligase (KlaTrl1) highlights important functional distinctions vis à vis the plant homolog. We find that (1) the KlaTrl1 kinase is 300-fold faster than the AtRNL kinase; and (2) the KlaTrl1 kinase is highly specific for GTP or dGTP as the phosphate donor. Our findings recommend tRNA ligase as a tool to map ribonucleotides embedded in DNA and as a target for antifungal drug discovery.
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Cooper DA, Jha BK, Silverman RH, Hesselberth JR, Barton DJ. Ribonuclease L and metal-ion-independent endoribonuclease cleavage sites in host and viral RNAs. Nucleic Acids Res 2014; 42:5202-16. [PMID: 24500209 PMCID: PMC4005677 DOI: 10.1093/nar/gku118] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Ribonuclease L (RNase L) is a metal-ion–independent endoribonuclease associated with antiviral and antibacterial defense, cancer and lifespan. Despite the biological significance of RNase L, the RNAs cleaved by this enzyme are poorly defined. In this study, we used deep sequencing methods to reveal the frequency and location of RNase L cleavage sites within host and viral RNAs. To make cDNA libraries, we exploited the 2′, 3′-cyclic phosphate at the end of RNA fragments produced by RNase L and other metal-ion–independent endoribonucleases. We optimized and validated 2′, 3′-cyclic phosphate cDNA synthesis and Illumina sequencing methods using viral RNAs cleaved with purified RNase L, viral RNAs cleaved with purified RNase A and RNA from uninfected and poliovirus-infected HeLa cells. Using these methods, we identified (i) discrete regions of hepatitis C virus and poliovirus RNA genomes that were profoundly susceptible to RNase L and other single-strand specific endoribonucleases, (ii) RNase L-dependent and RNase L-independent cleavage sites within ribosomal RNAs (rRNAs) and (iii) 2′, 3′-cyclic phosphates at the ends of 5S rRNA and U6 snRNA. Monitoring the frequency and location of metal-ion–independent endoribonuclease cleavage sites within host and viral RNAs reveals, in part, how these enzymes contribute to health and disease.
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Affiliation(s)
- Daphne A Cooper
- Department of Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA, Department of Cancer Biology, Lerner Research Institute, The Cleveland Clinic, Cleveland, OH 44195, USA, Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA and Program in Molecular Biology, University of Colorado School of Medicine, Aurora, CO 80045, USA
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Mroczek S, Dziembowski A. U6 RNA biogenesis and disease association. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 4:581-92. [PMID: 23776162 DOI: 10.1002/wrna.1181] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 05/14/2013] [Accepted: 05/15/2013] [Indexed: 12/15/2022]
Abstract
U6 snRNA is one of five uridine-rich noncoding RNAs that form the major spliceosome complex. Unlike other U-snRNAs, it reveals many distinctive aspects of biogenesis such as transcription by RNA polymerase III, transcript nuclear retention and particular features of transcript ends: monomethylated 5'-guanosine triphosphate as cap structure and a 2',3'-cyclic phosphate moiety (>P) at the 3' termini. U6-snRNA plays a central role in splicing and thus its transcription, maturation, snRNP formation, and recycling are essential for cellular homeostasis. U6 snRNA enters the splicing cycle as part of the tri-U4/U6.U5snRNP complex, and after significant structural arrangements forms the catalytic site of the spliceosome together with U2 snRNA and Prp8. U6 snRNA also contributes to the splicing reaction by coordinating metal cations required for catalysis. Many human diseases are associated with altered splicing processes. Disruptions of the basal splicing machinery can be lethal or lead to severe diseases such as spinal muscular atrophy, amyotrophic lateral sclerosis, or retinitis pigmentosa. Recent studies have identified a new U6 snRNA biogenesis factor Usb1, the absence of which leads to poikiloderma with neutropenia (PN) (OMIM 604173), an autosomal recessive skin disease. Usb1 is an evolutionarily conserved 3'→5' exoribonuclease that is responsible for removing 3'-terminal uridines from U6 snRNA transcripts, which leads to the formation of a 2',3' cyclic phosphate moiety (>P). This maturation step is fundamental for U6 snRNP assembly and recycling. Usb1 represents the first example of a direct association between a spliceosomal U6 snRNA biogenesis factor and human genetic disease.
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Affiliation(s)
- Seweryn Mroczek
- Department of Biophysics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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37
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Shchepachev V, Azzalin CM. The Mpn1 RNA exonuclease: Cellular functions and implication in disease. FEBS Lett 2013; 587:1858-62. [DOI: 10.1016/j.febslet.2013.05.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 05/06/2013] [Accepted: 05/06/2013] [Indexed: 01/23/2023]
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Abstract
The recessive disorder poikiloderma with neutropenia (PN) is caused by mutations in the C16orf57 gene that encodes the highly conserved USB1 protein. Here, we present the 1.1 Å resolution crystal structure of human USB1, defining it as a member of the LigT-like superfamily of 2H phosphoesterases. We show that human USB1 is a distributive 3'-5' exoribonuclease that posttranscriptionally removes uridine and adenosine nucleosides from the 3' end of spliceosomal U6 small nuclear RNA (snRNA), directly catalyzing terminal 2', 3' cyclic phosphate formation. USB1 measures the appropriate length of the U6 oligo(U) tail by reading the position of a key adenine nucleotide (A102) and pausing 5 uridine residues downstream.We show that the 3' ends of U6 snRNA in PN patient lymphoblasts are elongated and unexpectedly carry nontemplated 3' oligo(A) tails that are characteristic of nuclear RNA surveillance targets. Thus, our study reveals a novel quality control pathway in which posttranscriptional 3'-end processing by USB1 protects U6 snRNA from targeting and destruction by the nuclear exosome. Our data implicate aberrant oligoadenylation of U6 snRNA in the pathogenesis of the leukemia predisposition disorder PN.
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39
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Kimmig P, Diaz M, Zheng J, Williams CC, Lang A, Aragón T, Li H, Walter P. The unfolded protein response in fission yeast modulates stability of select mRNAs to maintain protein homeostasis. eLife 2012; 1:e00048. [PMID: 23066505 PMCID: PMC3470409 DOI: 10.7554/elife.00048] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 07/23/2012] [Indexed: 01/19/2023] Open
Abstract
The unfolded protein response (UPR) monitors the protein folding capacity of the endoplasmic reticulum (ER). In all organisms analyzed to date, the UPR drives transcriptional programs that allow cells to cope with ER stress. The non-conventional splicing of Hac1 (yeasts) and XBP1 (metazoans) mRNA, encoding orthologous UPR transcription activators, is conserved and dependent on Ire1, an ER membrane-resident kinase/endoribonuclease. We found that the fission yeast Schizosaccharomyces pombe lacks both a Hac1/XBP1 ortholog and a UPR-dependent-transcriptional-program. Instead, Ire1 initiates the selective decay of a subset of ER-localized-mRNAs that is required to survive ER stress. We identified Bip1 mRNA, encoding a major ER-chaperone, as the sole mRNA cleaved upon Ire1 activation that escapes decay. Instead, truncation of its 3' UTR, including loss of its polyA tail, stabilized Bip1 mRNA, resulting in increased Bip1 translation. Thus, S. pombe uses a universally conserved stress-sensing machinery in novel ways to maintain homeostasis in the ER.DOI:http://dx.doi.org/10.7554/eLife.00048.001.
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Affiliation(s)
- Philipp Kimmig
- Department of Biochemistry and Biophysics , University of California, San Francisco , San Francisco , United States
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40
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Mroczek S, Krwawicz J, Kutner J, Lazniewski M, Kuciński I, Ginalski K, Dziembowski A. C16orf57, a gene mutated in poikiloderma with neutropenia, encodes a putative phosphodiesterase responsible for the U6 snRNA 3' end modification. Genes Dev 2012; 26:1911-25. [PMID: 22899009 DOI: 10.1101/gad.193169.112] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
C16orf57 encodes a human protein of unknown function, and mutations in the gene occur in poikiloderma with neutropenia (PN), which is a rare, autosomal recessive disease. Interestingly, mutations in C16orf57 were also observed among patients diagnosed with Rothmund-Thomson syndrome (RTS) and dyskeratosis congenita (DC), which are caused by mutations in genes involved in DNA repair and telomere maintenance. A genetic screen in Saccharomyces cerevisiae revealed that the yeast ortholog of C16orf57, USB1 (YLR132C), is essential for U6 small nuclear RNA (snRNA) biogenesis and cell viability. Usb1 depletion destabilized U6 snRNA, leading to splicing defects and cell growth defects, which was suppressed by the presence of multiple copies of the U6 snRNA gene SNR6. Moreover, Usb1 is essential for the generation of a unique feature of U6 snRNA; namely, the 3'-terminal phosphate. RNAi experiments in human cells followed by biochemical and functional analyses confirmed that, similar to yeast, C16orf57 encodes a protein involved in the 2',3'-cyclic phosphate formation at the 3' end of U6 snRNA. Advanced bioinformatics predicted that C16orf57 encodes a phosphodiesterase whose putative catalytic activity is essential for its function in vivo. Our results predict an unexpected molecular basis for PN, DC, and RTS and provide insight into U6 snRNA 3' end formation.
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Affiliation(s)
- Seweryn Mroczek
- Department of Biophysics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
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41
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Dhungel N, Hopper AK. Beyond tRNA cleavage: novel essential function for yeast tRNA splicing endonuclease unrelated to tRNA processing. Genes Dev 2012; 26:503-14. [PMID: 22391451 DOI: 10.1101/gad.183004.111] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Pre-tRNA splicing is an essential process in all eukaryotes. In yeast and vertebrates, the enzyme catalyzing intron removal from pre-tRNA is a heterotetrameric complex (splicing endonuclease [SEN] complex). Although the SEN complex is conserved, the subcellular location where pre-tRNA splicing occurs is not. In yeast, the SEN complex is located at the cytoplasmic surface of mitochondria, whereas in vertebrates, pre-tRNA splicing is nuclear. We engineered yeast to mimic the vertebrate cell biology and demonstrate that all three steps of pre-tRNA splicing, as well as tRNA nuclear export and aminoacylation, occur efficiently when the SEN complex is nuclear. However, nuclear pre-tRNA splicing fails to complement growth defects of cells with defective mitochondrial-located splicing, suggesting that the yeast SEN complex surprisingly serves a novel and essential function in the cytoplasm that is unrelated to tRNA splicing. The novel function requires all four SEN complex subunits and the catalytic core. A subset of pre-rRNAs accumulates when the SEN complex is restricted to the nucleus, indicating that the SEN complex moonlights in rRNA processing. Thus, findings suggest that selection for the subcellular distribution of the SEN complex may reside not in its canonical, but rather in a novel, activity.
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Affiliation(s)
- Nripesh Dhungel
- Department of Molecular Genetics, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
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Popow J, Schleiffer A, Martinez J. Diversity and roles of (t)RNA ligases. Cell Mol Life Sci 2012; 69:2657-70. [PMID: 22426497 PMCID: PMC3400036 DOI: 10.1007/s00018-012-0944-2] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 02/01/2012] [Accepted: 02/13/2012] [Indexed: 12/29/2022]
Abstract
The discovery of discontiguous tRNA genes triggered studies dissecting the process of tRNA splicing. As a result, we have gained detailed mechanistic knowledge on enzymatic removal of tRNA introns catalyzed by endonuclease and ligase proteins. In addition to the elucidation of tRNA processing, these studies facilitated the discovery of additional functions of RNA ligases such as RNA repair and non-conventional mRNA splicing events. Recently, the identification of a new type of RNA ligases in bacteria, archaea, and humans closed a long-standing gap in the field of tRNA processing. This review summarizes past and recent findings in the field of tRNA splicing with a focus on RNA ligation as it preferentially occurs in archaea and humans. In addition to providing an integrated view of the types and phyletic distribution of RNA ligase proteins known to date, this survey also aims at highlighting known and potential accessory biological functions of RNA ligases.
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Affiliation(s)
- Johannes Popow
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Dr. Bohrgasse 3, 1030 Vienna, Austria
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Integrative deep sequencing of the mouse lung transcriptome reveals differential expression of diverse classes of small RNAs in response to respiratory virus infection. mBio 2011; 2:mBio.00198-11. [PMID: 22086488 PMCID: PMC3221602 DOI: 10.1128/mbio.00198-11] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
UNLABELLED We previously reported widespread differential expression of long non-protein-coding RNAs (ncRNAs) in response to virus infection. Here, we expanded the study through small RNA transcriptome sequencing analysis of the host response to both severe acute respiratory syndrome coronavirus (SARS-CoV) and influenza virus infections across four founder mouse strains of the Collaborative Cross, a recombinant inbred mouse resource for mapping complex traits. We observed differential expression of over 200 small RNAs of diverse classes during infection. A majority of identified microRNAs (miRNAs) showed divergent changes in expression across mouse strains with respect to SARS-CoV and influenza virus infections and responded differently to a highly pathogenic reconstructed 1918 virus compared to a minimally pathogenic seasonal influenza virus isolate. Novel insights into miRNA expression changes, including the association with pathogenic outcomes and large differences between in vivo and in vitro experimental systems, were further elucidated by a survey of selected miRNAs across diverse virus infections. The small RNAs identified also included many non-miRNA small RNAs, such as small nucleolar RNAs (snoRNAs), in addition to nonannotated small RNAs. An integrative sequencing analysis of both small RNAs and long transcripts from the same samples showed that the results revealing differential expression of miRNAs during infection were largely due to transcriptional regulation and that the predicted miRNA-mRNA network could modulate global host responses to virus infection in a combinatorial fashion. These findings represent the first integrated sequencing analysis of the response of host small RNAs to virus infection and show that small RNAs are an integrated component of complex networks involved in regulating the host response to infection. IMPORTANCE Most studies examining the host transcriptional response to infection focus only on protein-coding genes. However, mammalian genomes transcribe many short and long non-protein-coding RNAs (ncRNAs). With the advent of deep-sequencing technologies, systematic transcriptome analysis of the host response, including analysis of ncRNAs of different sizes, is now possible. Using this approach, we recently discovered widespread differential expression of host long (>200 nucleotide [nt]) ncRNAs in response to virus infection. Here, the samples described in the previous report were again used, but we sequenced another fraction of the transcriptome to study very short (about 20 to 30 nt) ncRNAs. We demonstrated that virus infection also altered expression of many short ncRNAs of diverse classes. Putting the results of the two studies together, we show that small RNAs may also play an important role in regulating the host response to virus infection.
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Abstract
Eukaryotic genomes accommodate numerous types of information within diverse DNA and RNA sequence elements. At many loci, these elements overlap and the same sequence is read multiple times during the production, processing, localization, function and turnover of a single transcript. Moreover, two or more transcripts from the same locus might use a common sequence in different ways, to perform distinct biological roles. Recent results show that many transcripts also undergo post-transcriptional cleavage to release specific fragments, which can then function independently. This phenomenon appears remarkably widespread, with even well-documented transcript classes such as messenger RNAs yielding fragments. RNA fragmentation significantly expands the already extraordinary spectrum of transcripts present within eukaryotic cells, and also calls into question how the 'gene' should be defined.
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Jain R, Shuman S. Active site mapping and substrate specificity of bacterial Hen1, a manganese-dependent 3' terminal RNA ribose 2'O-methyltransferase. RNA (NEW YORK, N.Y.) 2011; 17:429-38. [PMID: 21205839 PMCID: PMC3039143 DOI: 10.1261/rna.2500711] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The RNA methyltransferase Hen1 and the RNA end-healing/sealing enzyme Pnkp comprise an RNA repair system encoded by an operon-like cassette present in bacteria from eight different phyla. Clostridium thermocellum Hen1 (CthHen1) is a manganese-dependent RNA ribose 2'O-methyltransferase that marks the 3' terminal nucleoside of broken RNAs and protects repair junctions from iterative damage by transesterifying endonucleases. Here we used the crystal structure of the homologous plant Hen1 to guide a mutational analysis of CthHen1, the results of which provide new insights to RNA end recognition and catalysis. We illuminated structure-activity relations at eight essential constituents of the active site implicated in binding the 3' dinucleotide of the RNA methyl acceptor (Arg273, Arg414), the manganese cofactor (Glu366, Glu369, His370, His418), and the AdoMet methyl donor (Asp291, Asp316). We investigated the effects of varying the terminal nucleobase, RNA size, RNA content, and RNA secondary structure on methyl acceptor activity. Key findings are as follows. CthHen1 displayed a fourfold preference for guanosine as the terminal nucleoside. RNA size had little impact in the range of 12-24 nucleotides, but activity declined sharply with a 9-mer. CthHen1 was adept at methylating a polynucleotide composed of 23 deoxyribonucleotides and one 3' terminal ribonucleotide, signifying that it has no strict RNA specificity beyond the 3' nucleoside. CthHen1 methylated RNA ends in the context of duplex secondary structures. These properties distinguish bacterial Hen1 from plant and metazoan homologs.
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Affiliation(s)
- Ruchi Jain
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA
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Kumar P, Johnston BH, Kazakov SA. miR-ID: a novel, circularization-based platform for detection of microRNAs. RNA (NEW YORK, N.Y.) 2011; 17:365-80. [PMID: 21169480 PMCID: PMC3022285 DOI: 10.1261/rna.2490111] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Accepted: 11/10/2010] [Indexed: 05/08/2023]
Abstract
MicroRNAs (miRNAs) are important regulators of gene expression and have great potential as biomarkers, prognostic indicators, and therapeutic targets. Determining the expression patterns of these molecules is essential for elucidating their biogenesis, regulation, relation to disease, and response to therapy. Although PCR-based assays are commonly used for expression profiling of miRNAs, the small size, sequence heterogeneity, and (in some cases) end modifications of miRNAs constrain the performance of existing PCR methods. Here we introduce miR-ID, a novel method that avoids these constraints while providing superior sensitivity and sequence specificity at a lower cost. It also has the unique ability to differentiate unmodified small RNAs from those carrying 2'-OMe groups at their 3'-ends while detecting both forms. miR-ID is comprised of the following steps: (1) circularization of the miRNA by a ligase; (2) reverse transcription of the circularized miRNA (RTC), producing tandem repeats of a DNA sequence complementary to the miRNA; and (3) qPCR amplification of segments of this multimeric cDNA using 5'-overlapping primers and a nonspecific dye such as SYBR Green. No chemically modified probes (e.g., TaqMan) or primers (e.g., LNA) are required. The circular RNA and multimeric cDNA templates provide unmatched flexibility in the positioning of primers, which may include straddling the boundaries between these repetitive miRNA sequences. miR-ID is based on new findings that are themselves of general interest, including reverse transcription of small RNA circles and the use of 5'-overlapping primers for detection of repetitive sequences by qPCR.
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Affiliation(s)
- Pavan Kumar
- Somagenics, Inc., Santa Cruz, California 95060, USA
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Makino SI, Sawasaki T, Endo Y, Takai K. Use of domain enzymes from wheat RNA ligase for in vitro preparation of RNA molecules. Biochem Biophys Res Commun 2010; 404:1050-4. [PMID: 21187077 DOI: 10.1016/j.bbrc.2010.12.108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Accepted: 12/21/2010] [Indexed: 10/18/2022]
Abstract
Wheat RNA ligase can be dissected into three isolated domain enzymes that are responsible for its core ligase, 5'-kinase, and 2',3'-cyclic phosphate 3'-phosphodiesterase activities, respectively. In the present study, we pursued a practical strategy using the domain enzymes for in vitro step-by-step ligation of RNA molecules. As a part of it, we demonstrated that a novel side reaction on 5'-tri/diphosphate RNAs is dependent on ATP, a 2'-phosphate-3'-hydroxyl end, and the ligase domain. Mass spectroscopy and RNA cleavage analyses strongly suggested that it is an adenylylation on the 5' terminus. The ligase domain enzyme showed a high productivity for any of the possible 16 combinations of terminal bases and a high selectivity for the 5'-phosphate and 2'-phosphate-3'-hydroxyl ends. Two RNA molecules having 5'-hydroxyl and 2',3'-cyclic monophosphate groups were ligated almost stoichiometrically after separate conversion of respective terminal phosphate states into reactive ones. As the product has the same terminal state as the starting material, the next rounds of ligation are also possible in principle. Thus, we propose a flexible method for in vitro RNA ligation.
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Affiliation(s)
- Shin-ichi Makino
- Cell-free Science and Technology Research Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
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