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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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2
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Benesova S, Kubista M, Valihrach L. Small RNA-Sequencing: Approaches and Considerations for miRNA Analysis. Diagnostics (Basel) 2021; 11:964. [PMID: 34071824 PMCID: PMC8229417 DOI: 10.3390/diagnostics11060964] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 01/15/2023] Open
Abstract
MicroRNAs (miRNAs) are a class of small RNA molecules that have an important regulatory role in multiple physiological and pathological processes. Their disease-specific profiles and presence in biofluids are properties that enable miRNAs to be employed as non-invasive biomarkers. In the past decades, several methods have been developed for miRNA analysis, including small RNA sequencing (RNA-seq). Small RNA-seq enables genome-wide profiling and analysis of known, as well as novel, miRNA variants. Moreover, its high sensitivity allows for profiling of low input samples such as liquid biopsies, which have now found applications in diagnostics and prognostics. Still, due to technical bias and the limited ability to capture the true miRNA representation, its potential remains unfulfilled. The introduction of many new small RNA-seq approaches that tried to minimize this bias, has led to the existence of the many small RNA-seq protocols seen today. Here, we review all current approaches to cDNA library construction used during the small RNA-seq workflow, with particular focus on their implementation in commercially available protocols. We provide an overview of each protocol and discuss their applicability. We also review recent benchmarking studies comparing each protocol's performance and summarize the major conclusions that can be gathered from their usage. The result documents variable performance of the protocols and highlights their different applications in miRNA research. Taken together, our review provides a comprehensive overview of all the current small RNA-seq approaches, summarizes their strengths and weaknesses, and provides guidelines for their applications in miRNA research.
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Affiliation(s)
- Sarka Benesova
- Laboratory of Gene Expression, Institute of Biotechnology, CAS, BIOCEV, 252 50 Vestec, Czech Republic; (S.B.); (M.K.)
- Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology, 166 28 Prague, Czech Republic
| | - Mikael Kubista
- Laboratory of Gene Expression, Institute of Biotechnology, CAS, BIOCEV, 252 50 Vestec, Czech Republic; (S.B.); (M.K.)
- TATAA Biocenter AB, 411 03 Gothenburg, Sweden
| | - Lukas Valihrach
- Laboratory of Gene Expression, Institute of Biotechnology, CAS, BIOCEV, 252 50 Vestec, Czech Republic; (S.B.); (M.K.)
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3
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Valihrach L, Androvic P, Kubista M. Circulating miRNA analysis for cancer diagnostics and therapy. Mol Aspects Med 2020; 72:100825. [DOI: 10.1016/j.mam.2019.10.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/01/2019] [Accepted: 10/07/2019] [Indexed: 12/12/2022]
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4
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Juzenas S, Lindqvist CM, Ito G, Dolshanskaya Y, Halfvarson J, Franke A, Hemmrich-Stanisak G. Depletion of erythropoietic miR-486-5p and miR-451a improves detectability of rare microRNAs in peripheral blood-derived small RNA sequencing libraries. NAR Genom Bioinform 2020; 2:lqaa008. [PMID: 33575555 PMCID: PMC7671325 DOI: 10.1093/nargab/lqaa008] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 02/07/2020] [Indexed: 12/31/2022] Open
Abstract
Erythroid-specific miR-451a and miR-486-5p are two of the most dominant microRNAs (miRNAs) in human peripheral blood. In small RNA sequencing libraries, their overabundance reduces diversity as well as complexity and consequently causes negative effects such as missing detectability and inaccurate quantification of low abundant miRNAs. Here we present a simple, cost-effective and easy to implement hybridization-based method to deplete these two erythropoietic miRNAs from blood-derived RNA samples. By utilization of blocking oligonucleotides, this method provides a highly efficient and specific depletion of miR-486-5p and miR-451a, which leads to a considerable increase of measured expression as well as detectability of low abundant miRNA species. The blocking oligos are compatible with common 5′ ligation-dependent small RNA library preparation protocols, including commercially available kits, such as Illumina TruSeq and Perkin Elmer NEXTflex. Furthermore, the here described method and oligo design principle can be easily adapted to target many other miRNA molecules, depending on context and research question.
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Affiliation(s)
- Simonas Juzenas
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, DE 24105 Kiel, Germany
| | - Carl M Lindqvist
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, DE 24105 Kiel, Germany.,School of Medical Sciences, Faculty of Medicine and Health, Örebro University, SE 70182 Örebro, Sweden
| | - Go Ito
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, DE 24105 Kiel, Germany
| | - Yewgenia Dolshanskaya
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, DE 24105 Kiel, Germany
| | - Jonas Halfvarson
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, SE 70182 Örebro, Sweden
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, DE 24105 Kiel, Germany
| | - Georg Hemmrich-Stanisak
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, DE 24105 Kiel, Germany
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5
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Hardigan AA, Roberts BS, Moore DE, Ramaker RC, Jones AL, Myers RM. CRISPR/Cas9-targeted removal of unwanted sequences from small-RNA sequencing libraries. Nucleic Acids Res 2019; 47:e84. [PMID: 31165880 PMCID: PMC6698666 DOI: 10.1093/nar/gkz425] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 04/19/2019] [Accepted: 06/03/2019] [Indexed: 02/06/2023] Open
Abstract
In small RNA (smRNA) sequencing studies, highly abundant molecules such as adapter dimer products and tissue-specific microRNAs (miRNAs) inhibit accurate quantification of lowly expressed species. We previously developed a method to selectively deplete highly abundant miRNAs. However, this method does not deplete adapter dimer ligation products that, unless removed by gel-separation, comprise most of the library. Here, we have adapted and modified recently described methods for CRISPR/Cas9-based Depletion of Abundant Species by Hybridization ('DASH') to smRNA-seq, which we have termed miRNA and Adapter Dimer-DASH (MAD-DASH). In MAD-DASH, Cas9 is complexed with single guide RNAs (sgRNAs) targeting adapter dimer ligation products, alongside highly expressed tissue-specific smRNAs, for cleavage in vitro. This process dramatically reduces adapter dimer and targeted smRNA sequences, can be multiplexed, shows minimal off-target effects, improves the quantification of lowly expressed miRNAs from human plasma and tissue derived RNA, and obviates the need for gel-separation, greatly increasing sample throughput. Additionally, the method is fully customizable to other smRNA-seq preparation methods. Like depletion of ribosomal RNA for mRNA-seq and mitochondrial DNA for ATAC-seq, our method allows for greater proportional read-depth of non-targeted sequences.
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Affiliation(s)
- Andrew A Hardigan
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Brian S Roberts
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Dianna E Moore
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Ryne C Ramaker
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Angela L Jones
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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6
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Fishman A, T Lamm A. QsRNA-seq: A protocol for generating libraries for high-throughput sequencing of small RNAs. Bio Protoc 2019; 9:e3179. [PMID: 33654982 DOI: 10.21769/bioprotoc.3179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 01/24/2019] [Accepted: 02/25/2019] [Indexed: 12/15/2022] Open
Abstract
Small RNAs (sRNAs) are 20-30 nt long non-coding RNA molecules that regulate essentially all cellular processes. Besides being an intensively studied topic in academic research, sRNAs also hold a promise as clinical biomarkers. While the need for expressional profiling of sRNAs is growing, preparation of sRNA libraries for high-throughput sequencing (HTS) remains technically challenging, due to their small size. The common PAGE-based protocol is time-consuming and inefficient due to material loss, while gel-free protocols generate libraries of insufficient quality. To overcome these shortcomings, we modified the conditions of size-selection by Solid Phase Reversible Immobilization (SPRI) in a way that allows separation of nucleic acids shorter than 100 nt and differing in length by only 20 nt. Implementing the method for preparation of small RNA libraries for HTS resulted in QsRNA-seq, a gel-free, fast and easy-to-perform protocol, amenable to automation, generating very clean libraries that result in high-depth expression data. The protocol also utilizes Unique Molecular Identifiers (UMI) for reduction of library preparation biases and to quantify expression levels. QsRNA-seq provides an excellent solution to the growing needs for small RNA expression profiling for research clinical use.
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Affiliation(s)
- Alla Fishman
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 32000, Israel
| | - Ayelet T Lamm
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 32000, Israel
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7
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Dard-Dascot C, Naquin D, d'Aubenton-Carafa Y, Alix K, Thermes C, van Dijk E. Systematic comparison of small RNA library preparation protocols for next-generation sequencing. BMC Genomics 2018; 19:118. [PMID: 29402217 PMCID: PMC5799908 DOI: 10.1186/s12864-018-4491-6] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 01/22/2018] [Indexed: 01/19/2023] Open
Abstract
Background Next-generation sequencing technologies have revolutionized the study of small RNAs (sRNAs) on a genome-wide scale. However, classical sRNA library preparation methods introduce serious bias, mainly during adapter ligation steps. Several types of sRNA including plant microRNAs (miRNA), piwi-interacting RNAs (piRNA) in insects, nematodes and mammals, and small interfering RNAs (siRNA) in insects and plants contain a 2’-O-methyl (2’-OMe) modification at their 3′ terminal nucleotide. This inhibits 3′ adapter ligation and makes library preparation particularly challenging. To reduce bias, the NEBNext kit (New England Biolabs) uses polyethylene glycol (PEG), the NEXTflex V2 kit (BIOO Scientific) uses both randomised adapters and PEG, and the novel SMARTer (Clontech) and CATS (Diagenode) kits avoid ligation altogether. Here we compared these methods with Illumina’s classical TruSeq protocol regarding the detection of normal and 2’ OMe RNAs. In addition, we modified the TruSeq and NEXTflex protocols to identify conditions that improve performance. Results Among the five kits tested with their respective standard protocols, the SMARTer and CATS kits had the lowest levels of bias but also had a strong formation of side products, and as a result performed relatively poorly with biological samples; NEXTflex detected the largest numbers of different miRNAs. The use of a novel type of randomised adapters called MidRand-Like (MRL) adapters and PEG improved the detection of 2’ OMe RNAs both in the TruSeq as well as in the NEXTflex protocol. Conclusions While it is commonly accepted that biases in sRNA library preparation protocols are mainly due to adapter ligation steps, the ligation-free protocols were not the best performing methods. Our modified versions of the TruSeq and NEXTflex protocols provide an improved tool for the study of 2’ OMe RNAs. Electronic supplementary material The online version of this article (10.1186/s12864-018-4491-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cloelia Dard-Dascot
- Institute for Integrative Biology of the Cell, UMR9198, CNRS CEA Univ Paris-Sud, Université Paris-Saclay, 9198, Gif sur Yvette Cedex, France
| | - Delphine Naquin
- Institute for Integrative Biology of the Cell, UMR9198, CNRS CEA Univ Paris-Sud, Université Paris-Saclay, 9198, Gif sur Yvette Cedex, France
| | - Yves d'Aubenton-Carafa
- Institute for Integrative Biology of the Cell, UMR9198, CNRS CEA Univ Paris-Sud, Université Paris-Saclay, 9198, Gif sur Yvette Cedex, France
| | - Karine Alix
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Claude Thermes
- Institute for Integrative Biology of the Cell, UMR9198, CNRS CEA Univ Paris-Sud, Université Paris-Saclay, 9198, Gif sur Yvette Cedex, France
| | - Erwin van Dijk
- Institute for Integrative Biology of the Cell, UMR9198, CNRS CEA Univ Paris-Sud, Université Paris-Saclay, 9198, Gif sur Yvette Cedex, France.
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8
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Ghosheh Y, Seridi L, Ryu T, Takahashi H, Orlando V, Carninci P, Ravasi T. Characterization of piRNAs across postnatal development in mouse brain. Sci Rep 2016; 6:25039. [PMID: 27112104 PMCID: PMC4844963 DOI: 10.1038/srep25039] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 04/11/2016] [Indexed: 12/15/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) are responsible for maintaining the genome stability by silencing retrotransposons in germline tissues– where piRNAs were first discovered and thought to be restricted. Recently, novel functions were reported for piRNAs in germline and somatic cells. Using deep sequencing of small RNAs and CAGE of postnatal development of mouse brain, we identified piRNAs only in adult mouse brain. These piRNAs have similar sequence length as those of MILI-bound piRNAs. In addition, we predicted novel candidate regulators and putative targets of adult brain piRNAs.
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Affiliation(s)
- Yanal Ghosheh
- Division of Applied Mathematics and Computer Sciences, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia.,KAUST Environmental Epigenetic Program (KEEP), Division of Biological and Environmental Sciences &Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Loqmane Seridi
- Division of Applied Mathematics and Computer Sciences, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia.,KAUST Environmental Epigenetic Program (KEEP), Division of Biological and Environmental Sciences &Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Taewoo Ryu
- Division of Applied Mathematics and Computer Sciences, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia.,KAUST Environmental Epigenetic Program (KEEP), Division of Biological and Environmental Sciences &Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Hazuki Takahashi
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Valerio Orlando
- KAUST Environmental Epigenetic Program (KEEP), Division of Biological and Environmental Sciences &Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Piero Carninci
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Timothy Ravasi
- Division of Applied Mathematics and Computer Sciences, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia.,KAUST Environmental Epigenetic Program (KEEP), Division of Biological and Environmental Sciences &Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia.,Department of Medicine, Division of Genetic, University of California, San Diego. 9500 Gilman Drive La Jolla, California 92093-0688, USA
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9
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Baran-Gale J, Kurtz CL, Erdos MR, Sison C, Young A, Fannin EE, Chines PS, Sethupathy P. Addressing Bias in Small RNA Library Preparation for Sequencing: A New Protocol Recovers MicroRNAs that Evade Capture by Current Methods. Front Genet 2015; 6:352. [PMID: 26734062 PMCID: PMC4686641 DOI: 10.3389/fgene.2015.00352] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 12/04/2015] [Indexed: 12/31/2022] Open
Abstract
Recent advances in sequencing technology have helped unveil the unexpected complexity and diversity of small RNAs. A critical step in small RNA library preparation for sequencing is the ligation of adapter sequences to both the 5' and 3' ends of small RNAs. Studies have shown that adapter ligation introduces a significant but widely unappreciated bias in the results of high-throughput small RNA sequencing. We show that due to this bias the two widely used Illumina library preparation protocols produce strikingly different microRNA (miRNA) expression profiles in the same batch of cells. There are 102 highly expressed miRNAs that are >5-fold differentially detected and some miRNAs, such as miR-24-3p, are over 30-fold differentially detected. While some level of bias in library preparation is not surprising, the apparent massive differential bias between these two widely used adapter sets is not well appreciated. In an attempt to mitigate this bias, the new Bioo Scientific NEXTflex V2 protocol utilizes a pool of adapters with random nucleotides at the ligation boundary. We show that this protocol is able to detect robustly several miRNAs that evade capture by the Illumina-based methods. While these analyses do not indicate a definitive gold standard for small RNA library preparation, the results of the NEXTflex protocol do correlate best with RT-qPCR. As increasingly more laboratories seek to study small RNAs, researchers should be aware of the extent to which the results may differ with different protocols, and should make an informed decision about the protocol that best fits their study.
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Affiliation(s)
- Jeanette Baran-Gale
- Bioinformatics and Computational Biology Curriculum, School of Medicine, University of North Carolina at Chapel HillChapel Hill, NC, USA; Department of Genetics, School of Medicine, University of North Carolina at Chapel HillChapel Hill, NC, USA
| | - C Lisa Kurtz
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Michael R Erdos
- National Human Genome Research Institute, National Institutes of Health Bethesda, MD, USA
| | - Christina Sison
- NIH Intramural Sequencing Center, National Institutes of Health Rockville, MD, USA
| | - Alice Young
- NIH Intramural Sequencing Center, National Institutes of Health Rockville, MD, USA
| | - Emily E Fannin
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Peter S Chines
- National Human Genome Research Institute, National Institutes of Health Bethesda, MD, USA
| | - Praveen Sethupathy
- Bioinformatics and Computational Biology Curriculum, School of Medicine, University of North Carolina at Chapel HillChapel Hill, NC, USA; Department of Genetics, School of Medicine, University of North Carolina at Chapel HillChapel Hill, NC, USA
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10
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Nielsen BS, Møller T, Holmstrøm K. Chromogen detection of microRNA in frozen clinical tissue samples using LNA™ probe technology. Methods Mol Biol 2015; 1211:77-84. [PMID: 25218378 DOI: 10.1007/978-1-4939-1459-3_7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Specific chromogen- and fluorescence-based detection of microRNA by in situ hybridization (ISH) in formalin-fixed and paraffin-embedded (FFPE) tissue sections has been facilitated by locked nucleic acid (LNA)-based probe technology and can be performed within a single working day. In the current method paper, we present a similar simple 1-day ISH method developed for cryostat sections obtained from clinical cryo-embedded tissue samples. The presented chromogen-based ISH method does not involve proteolytic pretreatment, which is mandatory for FFPE sections, but still retains a sensitivity level similar to that obtained in FFPE sections. The LNA-based ISH method is not only applicable in situations where only access to cryo-embedded material is possible, but it also has a potential use if combining microRNA ISH with immunohistochemistry in double fluorescence staining with antibodies not being compatible with proteolytic predigestion.
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11
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Xu P, Billmeier M, Mohorianu I, Green D, Fraser WD, Dalmay T. An improved protocol for small RNA library construction using High Definition adapters. ACTA ACUST UNITED AC 2015. [DOI: 10.1515/mngs-2015-0001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractNext generation sequencing of small RNA (sRNA) libraries is widely used for studying sRNAs in various biological systems. However, cDNA libraries of sRNAs are biased for molecules that are ligated to adapters more or less efficiently than other molecules. One approach to reduce this ligation bias is to use a pool of adapters instead of a single adapter sequence, which allows many sRNAs to be ligated efficiently. We previously developed High Definition (HD) adapters for the Illumina sequencing platform, which contain degenerate nucleotides at the ligating ends of the adapters. However, the current commercial kits produced a large amount of 5’ adapter – 3’ adapter ligation product without the cDNA insert when HD adapters were used to replace the kit adapters. Here, we report a protocol to generate sRNA libraries using HD adapters with greatly reduced proportion of adapter-adapter products due to the degradation of nonligated 3’ adapters. The libraries can be completed within two days and can be used for various biological and clinical samples. As examples for using this protocol, we constructed sRNA libraries using total RNA extracted from cultured mammalian cells and plant leaf tissue.
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12
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Ninomiya S, Kawano M, Abe T, Ishikawa T, Takahashi M, Tamura M, Takahashi Y, Nashimoto M. Potential small guide RNAs for tRNase ZL from human plasma, peripheral blood mononuclear cells, and cultured cell lines. PLoS One 2015; 10:e0118631. [PMID: 25730316 PMCID: PMC4346264 DOI: 10.1371/journal.pone.0118631] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 01/09/2015] [Indexed: 11/18/2022] Open
Abstract
Several pieces of evidence suggest that small RNA degradation products together with tRNase ZL appear to form another layer of the whole gene regulatory network. The degraded RNA such as a 5'-half-tRNA and an rRNA fragment function as small guide RNA (sgRNA) to guide the enzyme to target RNA. We were curious whether there exist RNAs in plasma that can function as sgRNAs for tRNase ZL, whether these RNAs are working as signaling molecules between cells to fulfill physiological roles, and whether there are any differences in plasma sgRNA species and levels between normal and pathological conditions. Here, we analyzed small plasma RNAs from three healthy persons and three multiple myeloma patients for potential sgRNAs by deep sequencing. We also examined small RNAs from peripheral blood mononuclear cells (PBMC) of three healthy persons and three myeloma patients and from various cultured human cell lines for sgRNAs. We found that read-number distribution patterns of plasma and PBMC RNAs differ between persons in the range of 5-40 nt and that there are many RNA species that exist significantly more or less abundantly in the plasma or PBMC of the myeloma patients than those of the healthy persons. Furthermore, we found that there are many potential sgRNAs in the 5-40-nt RNAs and that, among them, a 31-nt RNA fragment derived from 94-nt Y4-RNA, which can function as a 5'-half-tRNA-type sgRNA, is overwhelmingly abundant in the plasma of 2/3 of the examinees. These observations suggest that the gene regulatory network via tRNase ZL and sgRNA may be extended intercellularly.
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Affiliation(s)
- Sho Ninomiya
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Mitsuoki Kawano
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
- Department of Biochemistry and Molecular Biology, Hokkaido University Graduate School of Dental Medicine, Sapporo, Japan
| | - Takashi Abe
- Department of Information Engineering, Niigata University, Niigata, Japan
| | - Tatsuya Ishikawa
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Masayuki Takahashi
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Masato Tamura
- Department of Biochemistry and Molecular Biology, Hokkaido University Graduate School of Dental Medicine, Sapporo, Japan
| | - Yoshiaki Takahashi
- Laboratory of Biochemistry, Niigata University Graduate School of Health Sciences, Niigata, Japan
| | - Masayuki Nashimoto
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
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13
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Radovich M, Ragoussis J. Methods of quantifying microRNAs for hypoxia research: classic and next generation. Antioxid Redox Signal 2014; 21:1239-48. [PMID: 24328936 DOI: 10.1089/ars.2013.5716] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
SIGNIFICANCE Recent evidence is uncovering the ever-increasing importance of microribonucleic acids (miRNAs) in the hypoxia response. In order to investigate the important roles that these small RNAs play, methods of quantification whether using classic single-gene methods or genome-wide technologies are necessary to obtain a global picture of the differential expression of miRNAs in hypoxia and their interplay with protein coding genes. RECENT ADVANCES Building on the groundwork of classic quantitative polymerase chain reaction (qPCR) and microarrays, the advent of next-generation sequencing technology has revolutionized how small RNAs can be detected and quantified on a genome-wide scale and without a priori knowledge of the small RNA sequence. This method delivers accurate and comprehensive data on the expression and sequence of all expressed small RNAs, and the data can be further combined with other sequencing modalities to better understand miRNAs via integrated genomic analyses. CRITICAL ISSUES Advancing technology has increased the need for better methods of sample and library preparation and for bioinformatics tools. Speed, cost, sample input, and analysis expertise remain the mainstay critical issues of small RNA sequencing. FUTURE DIRECTIONS Future hypoxia research will benefit from the application of genome-wide sequencing technologies. Analyses that combine genomic, transcriptomic, chromosome conformation, DNA/RNA-protein binding, and proteomics will help greatly advance hypoxia miRNA research.
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Affiliation(s)
- Milan Radovich
- 1 Department of Surgery, Indiana University School of Medicine , Indianapolis, Indiana
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14
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Multiplicity of 5' cap structures present on short RNAs. PLoS One 2014; 9:e102895. [PMID: 25079783 PMCID: PMC4117478 DOI: 10.1371/journal.pone.0102895] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 06/24/2014] [Indexed: 12/18/2022] Open
Abstract
Most RNA molecules are co- or post-transcriptionally modified to alter their chemical and functional properties to assist in their ultimate biological function. Among these modifications, the addition of 5′ cap structure has been found to regulate turnover and localization. Here we report a study of the cap structure of human short (<200 nt) RNAs (sRNAs), using sequencing of cDNA libraries prepared by enzymatic pretreatment of the sRNAs with cap sensitive-specificity, thin layer chromatographic (TLC) analyses of isolated cap structures and mass spectrometric analyses for validation of TLC analyses. Processed versions of snoRNAs and tRNAs sequences of less than 50 nt were observed in capped sRNA libraries, indicating additional processing and recapping of these annotated sRNAs biotypes. We report for the first time 2,7 dimethylguanosine in human sRNAs cap structures and surprisingly we find multiple type 0 cap structures (mGpppC, 7mGpppG, GpppG, GpppA, and 7mGpppA) in RNA length fractions shorter than 50 nt. Finally, we find the presence of additional uncharacterized cap structures that wait determination by the creation of needed reference compounds to be used in TLC analyses. These studies suggest the existence of novel biochemical pathways leading to the processing of primary and sRNAs and the modifications of their RNA 5′ ends with a spectrum of chemical modifications.
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15
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Kawaji H, Lizio M, Itoh M, Kanamori-Katayama M, Kaiho A, Nishiyori-Sueki H, Shin JW, Kojima-Ishiyama M, Kawano M, Murata M, Ninomiya-Fukuda N, Ishikawa-Kato S, Nagao-Sato S, Noma S, Hayashizaki Y, Forrest AR, Carninci P. Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing. Genome Res 2014; 24:708-17. [PMID: 24676093 PMCID: PMC3975069 DOI: 10.1101/gr.156232.113] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Accepted: 12/10/2013] [Indexed: 01/11/2023]
Abstract
CAGE (cap analysis gene expression) and RNA-seq are two major technologies used to identify transcript abundances as well as structures. They measure expression by sequencing from either the 5' end of capped molecules (CAGE) or tags randomly distributed along the length of a transcript (RNA-seq). Library protocols for clonally amplified (Illumina, SOLiD, 454 Life Sciences [Roche], Ion Torrent), second-generation sequencing platforms typically employ PCR preamplification prior to clonal amplification, while third-generation, single-molecule sequencers can sequence unamplified libraries. Although these transcriptome profiling platforms have been demonstrated to be individually reproducible, no systematic comparison has been carried out between them. Here we compare CAGE, using both second- and third-generation sequencers, and RNA-seq, using a second-generation sequencer based on a panel of RNA mixtures from two human cell lines to examine power in the discrimination of biological states, detection of differentially expressed genes, linearity of measurements, and quantification reproducibility. We found that the quantified levels of gene expression are largely comparable across platforms and conclude that CAGE and RNA-seq are complementary technologies that can be used to improve incomplete gene models. We also found systematic bias in the second- and third-generation platforms, which is likely due to steps such as linker ligation, cleavage by restriction enzymes, and PCR amplification. This study provides a perspective on the performance of these platforms, which will be a baseline in the design of further experiments to tackle complex transcriptomes uncovered in a wide range of cell types.
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Affiliation(s)
- Hideya Kawaji
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Saitama 351-0198, Japan
- RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, 230-0045, Japan;4
- RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies (DGT), Kanagawa, 230-0045, Japan
| | - Marina Lizio
- RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, 230-0045, Japan;4
- RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies (DGT), Kanagawa, 230-0045, Japan
| | - Masayoshi Itoh
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Saitama 351-0198, Japan
- RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, 230-0045, Japan;4
- RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies (DGT), Kanagawa, 230-0045, Japan
| | | | - Ai Kaiho
- RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, 230-0045, Japan;4
| | - Hiromi Nishiyori-Sueki
- RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, 230-0045, Japan;4
- RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies (DGT), Kanagawa, 230-0045, Japan
| | - Jay W. Shin
- RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, 230-0045, Japan;4
- RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies (DGT), Kanagawa, 230-0045, Japan
| | - Miki Kojima-Ishiyama
- RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, 230-0045, Japan;4
- RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies (DGT), Kanagawa, 230-0045, Japan
| | - Mitsuoki Kawano
- RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, 230-0045, Japan;4
| | - Mitsuyoshi Murata
- RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, 230-0045, Japan;4
- RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies (DGT), Kanagawa, 230-0045, Japan
| | - Noriko Ninomiya-Fukuda
- RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, 230-0045, Japan;4
| | - Sachi Ishikawa-Kato
- RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, 230-0045, Japan;4
- RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies (DGT), Kanagawa, 230-0045, Japan
| | - Sayaka Nagao-Sato
- RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, 230-0045, Japan;4
| | - Shohei Noma
- RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, 230-0045, Japan;4
- RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies (DGT), Kanagawa, 230-0045, Japan
| | - Yoshihide Hayashizaki
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Saitama 351-0198, Japan
- RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, 230-0045, Japan;4
| | - Alistair R.R. Forrest
- RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, 230-0045, Japan;4
- RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies (DGT), Kanagawa, 230-0045, Japan
| | - Piero Carninci
- RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, 230-0045, Japan;4
- RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies (DGT), Kanagawa, 230-0045, Japan
| | - The FANTOM Consortium
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Saitama 351-0198, Japan
- RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, 230-0045, Japan;4
- RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies (DGT), Kanagawa, 230-0045, Japan
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16
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Raabe CA, Tang TH, Brosius J, Rozhdestvensky TS. Biases in small RNA deep sequencing data. Nucleic Acids Res 2013; 42:1414-26. [PMID: 24198247 PMCID: PMC3919602 DOI: 10.1093/nar/gkt1021] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
High-throughput RNA sequencing (RNA-seq) is considered a powerful tool for novel gene discovery and fine-tuned transcriptional profiling. The digital nature of RNA-seq is also believed to simplify meta-analysis and to reduce background noise associated with hybridization-based approaches. The development of multiplex sequencing enables efficient and economic parallel analysis of gene expression. In addition, RNA-seq is of particular value when low RNA expression or modest changes between samples are monitored. However, recent data uncovered severe bias in the sequencing of small non-protein coding RNA (small RNA-seq or sRNA-seq), such that the expression levels of some RNAs appeared to be artificially enhanced and others diminished or even undetectable. The use of different adapters and barcodes during ligation as well as complex RNA structures and modifications drastically influence cDNA synthesis efficacies and exemplify sources of bias in deep sequencing. In addition, variable specific RNA G/C-content is associated with unequal polymerase chain reaction amplification efficiencies. Given the central importance of RNA-seq to molecular biology and personalized medicine, we review recent findings that challenge small non-protein coding RNA-seq data and suggest approaches and precautions to overcome or minimize bias.
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Affiliation(s)
- Carsten A Raabe
- Institute of Experimental Pathology (ZMBE), University of Muenster, Von-Esmarch-Strasse 56, 48149 Muenster, Germany and Advanced Medical and Dental Institute (AMDI), Universiti Sains Malaysia, 13200 Penang, Malaysia
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17
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Tang DTP, Plessy C, Salimullah M, Suzuki AM, Calligaris R, Gustincich S, Carninci P. Suppression of artifacts and barcode bias in high-throughput transcriptome analyses utilizing template switching. Nucleic Acids Res 2012. [PMID: 23180801 PMCID: PMC3562004 DOI: 10.1093/nar/gks1128] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Template switching (TS) has been an inherent mechanism of reverse transcriptase, which
has been exploited in several transcriptome analysis methods, such as CAGE, RNA-Seq and
short RNA sequencing. TS is an attractive option, given the simplicity of the protocol,
which does not require an adaptor mediated step and thus minimizes sample loss. As such,
it has been used in several studies that deal with limited amounts of RNA, such as in
single cell studies. Additionally, TS has also been used to introduce DNA barcodes or
indexes into different samples, cells or molecules. This labeling allows one to pool
several samples into one sequencing flow cell, increasing the data throughput of
sequencing and takes advantage of the increasing throughput of current sequences. Here, we
report TS artifacts that form owing to a process called strand invasion. Due to the way in
which barcodes/indexes are introduced by TS, strand invasion becomes more problematic by
introducing unsystematic biases. We describe a strategy that eliminates these artifacts
in silico and propose an experimental solution that suppresses biases
from TS.
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Affiliation(s)
- Dave T P Tang
- Omics Science Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Yokohama, Kanagawa 230-0045, Japan
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18
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Site-specific DICER and DROSHA RNA products control the DNA-damage response. Nature 2012; 488:231-5. [PMID: 22722852 PMCID: PMC3442236 DOI: 10.1038/nature11179] [Citation(s) in RCA: 405] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2010] [Accepted: 05/04/2012] [Indexed: 01/07/2023]
Abstract
Non-coding RNAs (ncRNAs) are involved in an increasing number of cellular events1. Some ncRNAs are processed by DICER and DROSHA ribonucleases to give rise to small double-stranded RNAs involved in RNA interference (RNAi)2. The DNA-damage response (DDR) is a signaling pathway that originates from the DNA lesion and arrests cell proliferation3. So far, DICER or DROSHA RNA products have not been reported to control DDR activation. Here we show that DICER and DROSHA, but not downstream elements of the RNAi pathway, are necessary to activate DDR upon oncogene-induced genotoxic stress and exogenous DNA damage, as studied also by DDR foci formation in mammalian cells and zebrafish and by checkpoint assays. DDR foci are sensitive to RNase A treatment, and DICER- and DROSHA-dependent RNA products are required to restore DDR foci in treated cells. Through RNA deep sequencing and studies of DDR activation at an inducible unique DNA double-strand break (DSB), we demonstrate that DDR foci formation requires site-specific DICER- and DROSHA-dependent small RNAs, named DDRNAs, which act in a MRE11-RAD50-NBS1 (MRN) complex-dependent manner. Chemically synthesized or in vitro-generated by DICER cleavage, DDRNAs are sufficient to restore DDR in RNase A-treated cells, also in the absence of other cellular RNAs. Our results describe an unanticipated direct role of a novel class of ncRNAs in the control of DDR activation at sites of DNA damage.
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19
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Vigneault F, Ter-Ovanesyan D, Alon S, Eminaga S, Christodoulou DC, Seidman JG, Eisenberg E, Church GM. High-throughput multiplex sequencing of miRNA. CURRENT PROTOCOLS IN HUMAN GENETICS 2012; Chapter 11:11.12.1-11.12.10. [PMID: 22470142 PMCID: PMC3673877 DOI: 10.1002/0471142905.hg1112s73] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Next-generation sequencing offers many advantages over other methods of microRNA (miRNA) expression profiling, such as sample throughput and the capability to discover novel miRNAs. As the sequencing depth of current sequencing platforms exceeds what is necessary to quantify miRNAs, multiplexing several samples in one sequencing run offers a significant cost advantage. Although previous studies have achieved this goal by adding bar codes to miRNA libraries at the ligation step, this was recently shown to introduce significant bias into the miRNA expression data. This bias can be avoided, however, by bar coding the miRNA libraries at the PCR step instead. Here, we describe a user-friendly PCR bar-coding method of preparing multiplexed microRNA libraries for Illumina-based sequencing. The method also prevents the production of adapter dimers and can be completed in one day.
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Affiliation(s)
- Francois Vigneault
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Wyss Institute for Biologically Inspired Engineering, Boston, MA 02115, USA,Ragon Institute of MGH, MIT and Harvard, Massachusetts, MA 02129, USA
| | - Dmitry Ter-Ovanesyan
- Wyss Institute for Biologically Inspired Engineering, Boston, MA 02115, USA,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02139, USA
| | - Shahar Alon
- Department of Neurobiology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Israel,Raymond and Beverly Sackler School of Physics and Astronomy, Tel-Aviv University, Israel
| | - Seda Eminaga
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | | | - J. G. Seidman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Eli Eisenberg
- Department of Neurobiology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Israel,Raymond and Beverly Sackler School of Physics and Astronomy, Tel-Aviv University, Israel
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Wyss Institute for Biologically Inspired Engineering, Boston, MA 02115, USA
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20
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Loakes D. Nucleotides and nucleic acids; oligo- and polynucleotides. ORGANOPHOSPHORUS CHEMISTRY 2012. [DOI: 10.1039/9781849734875-00169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- David Loakes
- Medical Research Council Laboratory of Molecular Biology, Hills Road Cambridge CB2 2QH UK
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21
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Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila. Nature 2011; 480:391-5. [PMID: 22056986 PMCID: PMC4082306 DOI: 10.1038/nature10492] [Citation(s) in RCA: 172] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2009] [Accepted: 08/17/2011] [Indexed: 12/22/2022]
Abstract
RNAi pathways have evolved as important modulators of gene expression that act in the cytoplasm by degrading RNA target molecules via the activity of short (21-30nt) RNAs1-6 RNAi components have been reported to play a role in the nucleus as they are involved in epigenetic regulation and heterochromatin formation7-10. However, although RNAi-mediated post-transcriptional silencing (PTGS) is well documented, mechanisms of RNAi-mediated transcriptional gene silencing (TGS) and in particular the role of RNAi components in chromatin, especially in higher eukaryotes, are still elusive. Here we show that key RNAi components Dicer-2 (Dcr2) and and Argonaute-2 (AGO2) AGO2 associate with chromatin, with strong preference for euchromatic, transcriptionally active loci and interact with core transcription machinery. Notably Dcr2 and AGO2 loss of function show that transcriptional defects are accompanied by perturbation of Pol II positioning on promoters. Further, both Dcr2 and Ago2 null mutations as well as missense mutations compromising the RNAi activity impair global Pol II dynamics upon heat shock. Finally, AGO2 RIP-seq experiments reveal that, AGO2 is strongly enriched in small-RNAs encompassing promoter as well as other parts of heat shock and other gene loci on both sense and antisense, with a strong bias for antisense, particularly after heat shock. Taken together our results reveal a new scenario in which Dcr2 and AGO2 are globally associated with transcriptionally active loci and may play a pivotal role in shaping the transcriptome by controlling RNA Pol II processivity.
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Burroughs AM, Kawano M, Ando Y, Daub CO, Hayashizaki Y. pre-miRNA profiles obtained through application of locked nucleic acids and deep sequencing reveals complex 5'/3' arm variation including concomitant cleavage and polyuridylation patterns. Nucleic Acids Res 2011; 40:1424-37. [PMID: 22058130 PMCID: PMC3287202 DOI: 10.1093/nar/gkr903] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Recent research hints at an underappreciated complexity in pre-miRNA processing and regulation. Global profiling of pre-miRNA and its potential to increase understanding of the pre-miRNA landscape is impeded by overlap with highly expressed classes of other non coding (nc) RNA. Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3′- and 5′-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Additionally, examination of nuclear-enriched flanking sequences of pre-miRNA, particularly those derived from polycistronic miRNA transcripts, provides insight into miRNA and miRNA-offset (moRNA) production, specifically identifying novel classes of RNA potentially functioning as moRNA precursors. Our findings point to particularly intricate regulation of the let-7 family in many ways reminiscent of DICER1-independent, pre-mir-451-like processing, introduce novel and unify known forms of pre-miRNA regulation and processing, and shed new light on overlooked products of miRNA processing pathways.
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Affiliation(s)
- A Maxwell Burroughs
- Omics Science Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama-shi, Kanagawa 230-0045, Japan.
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Shinohara Y, Yahagi K, Kawano M, Nishiyori H, Kawazu C, Suzuki N, Manabe RI, Hirase H. miRNA profiling of bilateral rat hippocampal CA3 by deep sequencing. Biochem Biophys Res Commun 2011; 409:293-8. [PMID: 21575607 DOI: 10.1016/j.bbrc.2011.05.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Accepted: 05/02/2011] [Indexed: 12/21/2022]
Abstract
MicroRNAs (miRNAs) have been demonstrated to be potent post-trascriptional modulators of protein expression. miRNA expression was profiled in the left and right dorsal hippocampal CA3 of mature rats by high-throughput deep sequencing. Among the sequenced and cross-mapped small RNAs, 88% belonged to the miRNAs annotated in the miRBase 15 database. Nearly half of the small RNAs belonged to the let-7 family miRNA. Seven percent of the sequenced small RNAs were not annotated in miRBase 15. Bioinformatic analysis of the unannotated small RNA sequences suggested seventeen novel miRNA candidates with relatively high expression levels (>100 tags per million). The left:right expression ratios were similar for all highly expressed miRNAs with less than 10% differences. These results provide a basic idea of the relative expression strengths of known and unknown miRNAs in the dorsal hippocampal CA3.
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Saxena A, Carninci P. Whole transcriptome analysis: what are we still missing? WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2010; 3:527-43. [PMID: 21197667 DOI: 10.1002/wsbm.135] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
New technologies such as tag-based sequencing and tiling arrays have provided unique insights into the transcriptional output of cells. Many new RNA classes have been uncovered in the past decade, despite limitations in current technologies. Even as the repertoire of known functional elements of the transcriptome increases and contemporary technologies become mainstream, inadequacies in conventional protocols for library preparation, sequencing and mapping continue to hamper revelation of the entire transcriptome of cells. In this article, we review current protocols and outline their deficiencies. We also provide our view on what we may be overlooking in the transcriptome, despite exhaustive investigations, and indicate future areas of technological development and research.
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Affiliation(s)
- Alka Saxena
- Omics Science Center, RIKEN Yokohama Institute, Tsurumi, Japan
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