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Korshoj LE, Kielian T. Bacterial single-cell RNA sequencing captures biofilm transcriptional heterogeneity and differential responses to immune pressure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.28.601229. [PMID: 38979200 PMCID: PMC11230364 DOI: 10.1101/2024.06.28.601229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Biofilm formation is an important mechanism of survival and persistence for many bacterial pathogens. These multicellular communities contain subpopulations of cells that display vast metabolic and transcriptional diversity along with high recalcitrance to antibiotics and host immune defenses. Investigating the complex heterogeneity within biofilm has been hindered by the lack of a sensitive and high-throughput method to assess stochastic transcriptional activity and regulation between bacterial subpopulations, which requires single-cell resolution. We have developed an optimized bacterial single-cell RNA sequencing method, BaSSSh-seq, to study Staphylococcus aureus diversity during biofilm growth and transcriptional adaptations following immune cell exposure. We validated the ability of BaSSSh-seq to capture extensive transcriptional heterogeneity during biofilm compared to planktonic growth. Application of new computational tools revealed transcriptional regulatory networks across the heterogeneous biofilm subpopulations and identification of gene sets that were associated with a trajectory from planktonic to biofilm growth. BaSSSh-seq also detected alterations in biofilm metabolism, stress response, and virulence that were tailored to distinct immune cell populations. This work provides an innovative platform to explore biofilm dynamics at single-cell resolution, unlocking the potential for identifying biofilm adaptations to environmental signals and immune pressure.
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2
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Wei C, Kesner B, Yin H, Lee JT. Imprinted X chromosome inactivation at the gamete-to-embryo transition. Mol Cell 2024; 84:1442-1459.e7. [PMID: 38458200 PMCID: PMC11031340 DOI: 10.1016/j.molcel.2024.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 12/23/2023] [Accepted: 02/13/2024] [Indexed: 03/10/2024]
Abstract
In mammals, dosage compensation involves two parallel processes: (1) X inactivation, which equalizes X chromosome dosage between males and females, and (2) X hyperactivation, which upregulates the active X for X-autosome balance. The field currently favors models whereby dosage compensation initiates "de novo" during mouse development. Here, we develop "So-Smart-seq" to revisit the question and interrogate a comprehensive transcriptome including noncoding genes and repeats in mice. Intriguingly, de novo silencing pertains only to a subset of Xp genes. Evolutionarily older genes and repetitive elements demonstrate constitutive Xp silencing, adopt distinct signatures, and do not require Xist to initiate silencing. We trace Xp silencing backward in developmental time to meiotic sex chromosome inactivation in the male germ line and observe that Xm hyperactivation is timed to Xp silencing on a gene-by-gene basis. Thus, during the gamete-to-embryo transition, older Xp genes are transmitted in a "pre-inactivated" state. These findings have implications for the evolution of imprinting.
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Affiliation(s)
- Chunyao Wei
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Barry Kesner
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Hao Yin
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA.
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3
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Ohtsubo Y, Kawahara S, Nagata Y. Clamping-mediated incorporation of single-stranded DNA with concomitant DNA synthesis by Taq polymerase involves nick-translation. Sci Rep 2024; 14:2030. [PMID: 38263346 PMCID: PMC10805873 DOI: 10.1038/s41598-024-52095-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/13/2024] [Indexed: 01/25/2024] Open
Abstract
The development and characterization of a new enzyme reaction contribute to advancements in modern biotechnology. Here, we report a novel CIS (clamping-mediated incorporation of single-stranded DNA with concomitant DNA synthesis) reaction catalyzed by Taq polymerase. In the reaction, a single-stranded DNA (ssDNA) with 3' Cs is attached with a preformed 3' G-tail of double-stranded DNA (dsDNA); DNA syntheses starting from both 3' ends result in the incorporation of ssDNA. A 3' G-tail length of 3 nucleotides adequately supports this reaction, indicating that Taq polymerase can clump short Watson-Crick base pairs as short as three pairs and use them to initiate DNA polymerization. The reverse transcriptase from Molony murine leukemia virus catalyzes strand displacement synthesis and produces flapped-end DNA, whereas the reaction by Taq polymerase involves the nick translation. These new reaction properties may be beneficial for the development of new molecular tools applicable in various fields. Apart from its CIS reaction activity, we also report that Taq polymerase has the undesirable characteristic of removing 5' fluorescent labels from dsDNA. This characteristic may have compromised various experiments involving the preparation of fluorescently-labeled dsDNA by PCR for a long time.
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Grants
- 19H02865 Ministry of Education, Culture, Sports, Science and Technology,Japan
- 22H02233 Ministry of Education, Culture, Sports, Science and Technology,Japan
- 22K19124 Ministry of Education, Culture, Sports, Science and Technology,Japan
- K-2016-004 Institute for Fermentation, Osaka,Japan
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Affiliation(s)
- Yoshiyuki Ohtsubo
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai, 980-8577, Japan.
| | - Syoutaro Kawahara
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai, 980-8577, Japan
| | - Yuji Nagata
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai, 980-8577, Japan
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4
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Feng F, Yuen R, Wang Y, Hua A, Kepler TB, Wetzler LM. Characterizing adjuvants' effects at murine immunoglobulin repertoire level. iScience 2024; 27:108749. [PMID: 38269092 PMCID: PMC10805652 DOI: 10.1016/j.isci.2023.108749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 09/29/2023] [Accepted: 12/12/2023] [Indexed: 01/26/2024] Open
Abstract
Generating large-scale, high-fidelity sequencing data is challenging and, furthermore, not much has been done to characterize adjuvants' effects at the repertoire level. Thus, we introduced an IgSeq pipeline that standardized library prep protocols and data analysis functions for accurate repertoire profiling. We then studied systemically effects of CpG and Alum on the Ig heavy chain repertoire using the ovalbumin (OVA) murine model. Ig repertoires of different tissues (spleen and bone marrow) and isotypes (IgG and IgM) were examined and compared in IGHV mutation, gene usage, CDR3 length, clonal diversity, and clonal selection. We found Ig repertoires of different compartments exhibited distinguishable profiles at the non-immunized steady state, and distinctions became more pronounced upon adjuvanted immunizations. Notably, Alum and CpG effects exhibited different tissue- and isotype-preferences. The former led to increased diversity of abundant clones in bone marrow, and the latter promoted the selection of IgG clones in both tissues.
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Affiliation(s)
- Feng Feng
- Department of Microbiology, Boston University, Boston, MA 02118, USA
| | - Rachel Yuen
- Department of Microbiology, Boston University, Boston, MA 02118, USA
| | - Yumei Wang
- Department of Microbiology, Boston University, Boston, MA 02118, USA
| | - Axin Hua
- Department of Microbiology, Boston University, Boston, MA 02118, USA
| | - Thomas B. Kepler
- Department of Microbiology, Boston University, Boston, MA 02118, USA
- Department of Mathematics and Statistics, Boston University, Boston, MA 02118, USA
| | - Lee M. Wetzler
- Department of Microbiology, Boston University, Boston, MA 02118, USA
- Department of Medicine, Boston University School of Medicine, Boston University, Boston, MA 02118, USA
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5
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Liu Y, Lu F, Wang J. Sequencing of Transcriptome-Wide Poly(A) Tails by PAIso-seq. Methods Mol Biol 2024; 2723:215-232. [PMID: 37824073 DOI: 10.1007/978-1-0716-3481-3_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Poly(A) tails are added to most eukaryotic mRNA and have essential regulatory functions. However, due to its homopolymeric nature, the sequence information in poly(A) tails is challenging to obtain in transcriptome measurement studies. In this chapter, we describe the detailed procedures of poly(A) inclusive full-length RNA isoform-sequencing (PAIso-seq), a method that can measure transcriptome-wide poly(A) tails from as low as nanogram level of total RNA based on the PacBio HiFi sequencing platform. The accurate length and base composition of poly(A) tails can be obtained along with the full-length cDNA.
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Affiliation(s)
- Yusheng Liu
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Falong Lu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Jiaqiang Wang
- College of Life Science, Northeast Agricultural University, Harbin, China.
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6
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Schweingruber C, Nijssen J, Benitez JA, Hedlund E. Single-Cell mRNA-Seq of In Vitro-Derived Human Neurons Using Smart-Seq2. Methods Mol Biol 2023; 2594:143-164. [PMID: 36264494 DOI: 10.1007/978-1-0716-2815-7_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Single-cell mRNA sequencing can dissect heterogeneous cell populations as it can identify cell types and cellular states based on their unique transcriptional signatures. We use fluorescence-activated cell sorting (FACS) to isolate individual cultured neurons derived from human-induced pluripotent stem cells (hiPSCs) followed by polyA-based Smart-Seq2 RNA sequencing to analyze the single-cell transcriptional profiles. We provide protocols and guidelines on dissociation, cell selection, and library preparation that can be readily adapted to other cell types or tissue samples.
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Affiliation(s)
- Christoph Schweingruber
- Department for Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jik Nijssen
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | | | - Eva Hedlund
- Department for Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
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7
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Chen W, Guillaume-Gentil O, Rainer PY, Gäbelein CG, Saelens W, Gardeux V, Klaeger A, Dainese R, Zachara M, Zambelli T, Vorholt JA, Deplancke B. Live-seq enables temporal transcriptomic recording of single cells. Nature 2022; 608:733-740. [PMID: 35978187 PMCID: PMC9402441 DOI: 10.1038/s41586-022-05046-9] [Citation(s) in RCA: 84] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/29/2022] [Indexed: 11/26/2022]
Abstract
Single-cell transcriptomics (scRNA-seq) has greatly advanced our ability to characterize cellular heterogeneity1. However, scRNA-seq requires lysing cells, which impedes further molecular or functional analyses on the same cells. Here, we established Live-seq, a single-cell transcriptome profiling approach that preserves cell viability during RNA extraction using fluidic force microscopy2,3, thus allowing to couple a cell's ground-state transcriptome to its downstream molecular or phenotypic behaviour. To benchmark Live-seq, we used cell growth, functional responses and whole-cell transcriptome read-outs to demonstrate that Live-seq can accurately stratify diverse cell types and states without inducing major cellular perturbations. As a proof of concept, we show that Live-seq can be used to directly map a cell's trajectory by sequentially profiling the transcriptomes of individual macrophages before and after lipopolysaccharide (LPS) stimulation, and of adipose stromal cells pre- and post-differentiation. In addition, we demonstrate that Live-seq can function as a transcriptomic recorder by preregistering the transcriptomes of individual macrophages that were subsequently monitored by time-lapse imaging after LPS exposure. This enabled the unsupervised, genome-wide ranking of genes on the basis of their ability to affect macrophage LPS response heterogeneity, revealing basal Nfkbia expression level and cell cycle state as important phenotypic determinants, which we experimentally validated. Thus, Live-seq can address a broad range of biological questions by transforming scRNA-seq from an end-point to a temporal analysis approach.
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Affiliation(s)
- Wanze Chen
- Laboratory of Systems Biology and Genetics, Institute of Bio-engineering and Global Health Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | | | - Pernille Yde Rainer
- Laboratory of Systems Biology and Genetics, Institute of Bio-engineering and Global Health Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Christoph G Gäbelein
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Wouter Saelens
- Laboratory of Systems Biology and Genetics, Institute of Bio-engineering and Global Health Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Vincent Gardeux
- Laboratory of Systems Biology and Genetics, Institute of Bio-engineering and Global Health Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Amanda Klaeger
- Laboratory of Systems Biology and Genetics, Institute of Bio-engineering and Global Health Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Riccardo Dainese
- Laboratory of Systems Biology and Genetics, Institute of Bio-engineering and Global Health Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Magda Zachara
- Laboratory of Systems Biology and Genetics, Institute of Bio-engineering and Global Health Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Tomaso Zambelli
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, Zurich, Switzerland
| | - Julia A Vorholt
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
| | - Bart Deplancke
- Laboratory of Systems Biology and Genetics, Institute of Bio-engineering and Global Health Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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8
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Sztanka-Toth TR, Jens M, Karaiskos N, Rajewsky N. Spacemake: processing and analysis of large-scale spatial transcriptomics data. Gigascience 2022; 11:6646447. [PMID: 35852420 PMCID: PMC9295369 DOI: 10.1093/gigascience/giac064] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/10/2022] [Accepted: 05/31/2022] [Indexed: 01/24/2023] Open
Abstract
Background Spatial sequencing methods increasingly gain popularity within RNA biology studies. State-of-the-art techniques quantify messenger RNA expression levels from tissue sections and at the same time register information about the original locations of the molecules in the tissue. The resulting data sets are processed and analyzed by accompanying software that, however, is incompatible across inputs from different technologies. Findings Here, we present spacemake, a modular, robust, and scalable spatial transcriptomics pipeline built in Snakemake and Python. Spacemake is designed to handle all major spatial transcriptomics data sets and can be readily configured for other technologies. It can process and analyze several samples in parallel, even if they stem from different experimental methods. Spacemake's unified framework enables reproducible data processing from raw sequencing data to automatically generated downstream analysis reports. Spacemake is built with a modular design and offers additional functionality such as sample merging, saturation analysis, and analysis of long reads as separate modules. Moreover, spacemake employs novoSpaRc to integrate spatial and single-cell transcriptomics data, resulting in increased gene counts for the spatial data set. Spacemake is open source and extendable, and it can be seamlessly integrated with existing computational workflows.
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Affiliation(s)
- Tamas Ryszard Sztanka-Toth
- Systems Biology of Gene Regulatory Elements, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), 10115 Berlin, Germany.,Humboldt-Universität zu Berlin, Institut für Biologie, 10099 Berlin, Germany
| | - Marvin Jens
- Systems Biology of Gene Regulatory Elements, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), 10115 Berlin, Germany
| | - Nikos Karaiskos
- Systems Biology of Gene Regulatory Elements, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), 10115 Berlin, Germany
| | - Nikolaus Rajewsky
- Systems Biology of Gene Regulatory Elements, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), 10115 Berlin, Germany.,Humboldt-Universität zu Berlin, Institut für Biologie, 10099 Berlin, Germany.,DZHK (German Center for Cardiovascular Research), Partner Site Berlin, 10117 Berlin, Germany.,Department of Pediatric Oncology, Universitätsmedizin Charité, 13353 Berlin, Germany
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9
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Liu Y, Zhang Y, Wang J, Lu F. Transcriptome-wide measurement of poly(A) tail length and composition at subnanogram total RNA sensitivity by PAIso-seq. Nat Protoc 2022; 17:1980-2007. [PMID: 35831615 DOI: 10.1038/s41596-022-00704-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/23/2022] [Indexed: 12/14/2022]
Abstract
Poly(A) tails are added to the 3' ends of most mRNAs in a non-templated manner and play essential roles in post-transcriptional regulation, including mRNA export, stability and translation. Measuring poly(A) tails is critical for understanding their regulatory roles in almost every aspect of biological and medical studies. Previous methods for analyzing poly(A) tails require large amounts of input RNA (microgram-level total RNA), which limits their application. We recently developed a poly(A) inclusive full-length RNA isoform-sequencing method (PAIso-seq) at single-oocyte-level sensitivity (a single mammalian oocyte contains ~0.5 ng of total RNA) based on PacBio sequencing that enabled accurate measurement of the poly(A) tail length and non-A residues within the body of poly(A) tails along with the full-length cDNA, providing the opportunity to study precious in vivo samples with very limited input material. Here, we describe a detailed protocol for PAIso-seq library preparation from single mouse oocytes or bulk oocyte samples. In addition, we provide a complete bioinformatic pipeline to perform the analysis from the raw data to downstream analysis. The minimum time required is ~14.5 h for PAIso-seq double-stranded cDNA preparation, 2 d for PacBio sequencing in HiFi mode and 8 h for the initial data analysis.
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Affiliation(s)
- Yusheng Liu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.
| | - Yiwei Zhang
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Jiaqiang Wang
- College of Life Science, Northeast Agricultural University, Harbin, China.
| | - Falong Lu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China.
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10
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Gonzales SJ, Clarke KN, Batugedara G, Garza R, Braddom AE, Reyes RA, Ssewanyana I, Garrison KC, Ippolito GC, Greenhouse B, Bol S, Bunnik EM. A Molecular Analysis of Memory B Cell and Antibody Responses Against Plasmodium falciparum Merozoite Surface Protein 1 in Children and Adults From Uganda. Front Immunol 2022; 13:809264. [PMID: 35720313 PMCID: PMC9201334 DOI: 10.3389/fimmu.2022.809264] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 05/05/2022] [Indexed: 01/18/2023] Open
Abstract
Memory B cells (MBCs) and plasma antibodies against Plasmodium falciparum (Pf) merozoite antigens are important components of the protective immune response against malaria. To gain understanding of how responses against Pf develop in these two arms of the humoral immune system, we evaluated MBC and antibody responses against the most abundant merozoite antigen, full-length Pf merozoite surface protein 1 (PfMSP1FL), in individuals from a region in Uganda with high Pf transmission. Our results showed that PfMSP1FL-specific B cells in adults with immunological protection against malaria were predominantly IgG+ classical MBCs, while children with incomplete protection mainly harbored IgM+ PfMSP1FL-specific classical MBCs. In contrast, anti-PfMSP1FL plasma IgM reactivity was minimal in both children and adults. Instead, both groups showed high plasma IgG reactivity against PfMSP1FL, with broadening of the response against non-3D7 strains in adults. The B cell receptors encoded by PfMSP1FL-specific IgG+ MBCs carried high levels of amino acid substitutions and recognized relatively conserved epitopes on the highly variable PfMSP1 protein. Proteomics analysis of PfMSP119-specific IgG in plasma of an adult revealed a limited repertoire of anti-MSP1 antibodies, most of which were IgG1 or IgG3. Similar to B cell receptors of PfMSP1FL-specific MBCs, anti-PfMSP119 IgGs had high levels of amino acid substitutions and their sequences were predominantly found in classical MBCs, not atypical MBCs. Collectively, these results showed evolution of the PfMSP1-specific humoral immune response with cumulative Pf exposure, with a shift from IgM+ to IgG+ B cell memory, diversification of B cells from germline, and stronger recognition of PfMSP1 variants by the plasma IgG repertoire.
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Affiliation(s)
- S. Jake Gonzales
- Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Kathleen N. Clarke
- Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Gayani Batugedara
- Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Rolando Garza
- Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Ashley E. Braddom
- Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Raphael A. Reyes
- Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Isaac Ssewanyana
- Infectious Disease Research Collaboration, Kampala, Uganda
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Kendra C. Garrison
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX, United States
| | - Gregory C. Ippolito
- Department of Molecular Biosciences and Department of Oncology, Dell Medical School, University of Texas at Austin, Austin, TX, United States
| | - Bryan Greenhouse
- Department of Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Sebastiaan Bol
- Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Evelien M. Bunnik
- Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
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11
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Abstract
Transcription start site (TSS) selection influences transcript stability and translation as well as protein sequence. Alternative TSS usage is pervasive in organismal development, is a major contributor to transcript isoform diversity in humans, and is frequently observed in human diseases including cancer. In this review, we discuss the breadth of techniques that have been used to globally profile TSSs and the resulting insights into gene regulation, as well as future prospects in this area of inquiry.
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Affiliation(s)
| | - Gabriel E. Zentner
- Department of Biology, Indiana University, Bloomington, IN 47401, USA
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN 46202, USA
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12
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Hughes TK, Wadsworth MH, Gierahn TM, Do T, Weiss D, Andrade PR, Ma F, de Andrade Silva BJ, Shao S, Tsoi LC, Ordovas-Montanes J, Gudjonsson JE, Modlin RL, Love JC, Shalek AK. Second-Strand Synthesis-Based Massively Parallel scRNA-Seq Reveals Cellular States and Molecular Features of Human Inflammatory Skin Pathologies. Immunity 2020; 53:878-894.e7. [PMID: 33053333 PMCID: PMC7562821 DOI: 10.1016/j.immuni.2020.09.015] [Citation(s) in RCA: 137] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 05/21/2020] [Accepted: 09/18/2020] [Indexed: 01/10/2023]
Abstract
High-throughput single-cell RNA-sequencing (scRNA-seq) methodologies enable characterization of complex biological samples by increasing the number of cells that can be profiled contemporaneously. Nevertheless, these approaches recover less information per cell than low-throughput strategies. To accurately report the expression of key phenotypic features of cells, scRNA-seq platforms are needed that are both high fidelity and high throughput. To address this need, we created Seq-Well S3 ("Second-Strand Synthesis"), a massively parallel scRNA-seq protocol that uses a randomly primed second-strand synthesis to recover complementary DNA (cDNA) molecules that were successfully reverse transcribed but to which a second oligonucleotide handle, necessary for subsequent whole transcriptome amplification, was not appended due to inefficient template switching. Seq-Well S3 increased the efficiency of transcript capture and gene detection compared with that of previous iterations by up to 10- and 5-fold, respectively. We used Seq-Well S3 to chart the transcriptional landscape of five human inflammatory skin diseases, thus providing a resource for the further study of human skin inflammation.
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Affiliation(s)
- Travis K Hughes
- Institute for Medical Engineering & Science (IMES), MIT, Cambridge, Massachusetts, USA; Department of Immunology, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA; Department of Chemistry, MIT, Cambridge, Massachusetts, USA
| | - Marc H Wadsworth
- Institute for Medical Engineering & Science (IMES), MIT, Cambridge, Massachusetts, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA; Department of Chemistry, MIT, Cambridge, Massachusetts, USA
| | - Todd M Gierahn
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA; Department of Chemical Engineering, MIT, Cambridge, MA, USA
| | - Tran Do
- Division of Dermatology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA; Department of Microbiology, Immunology and Molecular Biology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - David Weiss
- Division of Dermatology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA; Department of Microbiology, Immunology and Molecular Biology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Priscila R Andrade
- Division of Dermatology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA; Department of Microbiology, Immunology and Molecular Biology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Feiyang Ma
- Division of Dermatology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA; Department of Microbiology, Immunology and Molecular Biology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Bruno J de Andrade Silva
- Division of Dermatology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA; Department of Microbiology, Immunology and Molecular Biology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Shuai Shao
- Department of Dermatology, University of Michigan, Ann Arbor, MI, USA
| | - Lam C Tsoi
- Department of Dermatology, University of Michigan, Ann Arbor, MI, USA
| | - Jose Ordovas-Montanes
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Gastroenterology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA; Harvard Stem Cell Institute, Cambridge, MA, USA
| | | | - Robert L Modlin
- Division of Gastroenterology, Boston Children's Hospital, Boston, MA, USA
| | - J Christopher Love
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA; Department of Chemical Engineering, MIT, Cambridge, MA, USA.
| | - Alex K Shalek
- Institute for Medical Engineering & Science (IMES), MIT, Cambridge, Massachusetts, USA; Department of Immunology, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Cambridge, MA, USA.
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13
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Gavrilov AA, Zharikova AA, Galitsyna AA, Luzhin A, Rubanova NM, Golov AK, Petrova NV, Logacheva M, Kantidze OL, Ulianov SV, Magnitov MD, Mironov AA, Razin SV. Studying RNA-DNA interactome by Red-C identifies noncoding RNAs associated with various chromatin types and reveals transcription dynamics. Nucleic Acids Res 2020; 48:6699-6714. [PMID: 32479626 PMCID: PMC7337940 DOI: 10.1093/nar/gkaa457] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 05/13/2020] [Accepted: 05/18/2020] [Indexed: 12/15/2022] Open
Abstract
Non-coding RNAs (ncRNAs) participate in various biological processes, including regulating transcription and sustaining genome 3D organization. Here, we present a method termed Red-C that exploits proximity ligation to identify contacts with the genome for all RNA molecules present in the nucleus. Using Red-C, we uncovered the RNA-DNA interactome of human K562 cells and identified hundreds of ncRNAs enriched in active or repressed chromatin, including previously undescribed RNAs. Analysis of the RNA-DNA interactome also allowed us to trace the kinetics of messenger RNA production. Our data support the model of co-transcriptional intron splicing, but not the hypothesis of the circularization of actively transcribed genes.
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Affiliation(s)
- Alexey A Gavrilov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anastasiya A Zharikova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- National Medical Research Center for Preventive Medicine, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Aleksandra A Galitsyna
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Artem V Luzhin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Arkadiy K Golov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Mental Health Research Center, Moscow, Russia
| | | | | | - Omar L Kantidze
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Sergey V Ulianov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Mikhail D Magnitov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Andrey A Mironov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Faculty of Computer Science, Higher School of Economics, Moscow, Russia
| | - Sergey V Razin
- To whom correspondence should be addressed. Tel: +7 499 135 3092; Fax: +7 499 135 4105;
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14
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Onsbring H, Tice AK, Barton BT, Brown MW, Ettema TJG. An efficient single-cell transcriptomics workflow for microbial eukaryotes benchmarked on Giardia intestinalis cells. BMC Genomics 2020; 21:448. [PMID: 32600266 PMCID: PMC7325058 DOI: 10.1186/s12864-020-06858-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 06/22/2020] [Indexed: 01/08/2023] Open
Abstract
Background Most diversity in the eukaryotic tree of life is represented by microbial eukaryotes, which is a polyphyletic group also referred to as protists. Among the protists, currently sequenced genomes and transcriptomes give a biased view of the actual diversity. This biased view is partly caused by the scientific community, which has prioritized certain microbes of biomedical and agricultural importance. Additionally, some protists remain difficult to maintain in cultures, which further influences what has been studied. It is now possible to bypass the time-consuming process of cultivation and directly analyze the gene content of single protist cells. Single-cell genomics was used in the first experiments where individual protists cells were genomically explored. Unfortunately, single-cell genomics for protists is often associated with low genome recovery and the assembly process can be complicated because of repetitive intergenic regions. Sequencing repetitive sequences can be avoided if single-cell transcriptomics is used, which only targets the part of the genome that is transcribed. Results In this study we test different modifications of Smart-seq2, a single-cell RNA sequencing protocol originally developed for mammalian cells, to establish a robust and more cost-efficient workflow for protists. The diplomonad Giardia intestinalis was used in all experiments and the available genome for this species allowed us to benchmark our results. We could observe increased transcript recovery when freeze-thaw cycles were added as an extra step to the Smart-seq2 protocol. Further we reduced the reaction volume and purified the amplified cDNA with alternative beads to test different cost-reducing changes of Smart-seq2. Neither improved the procedure, and reducing the volumes by half led to significantly fewer genes detected. We also added a 5′ biotin modification to our primers and reduced the concentration of oligo-dT, to potentially reduce generation of artifacts. Except adding freeze-thaw cycles and reducing the volume, no other modifications lead to a significant change in gene detection. Therefore, we suggest adding freeze-thaw cycles to Smart-seq2 when working with protists and further consider our other modification described to improve cost and time-efficiency. Conclusions The presented single-cell RNA sequencing workflow represents an efficient method to explore the diversity and cell biology of individual protist cells.
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Affiliation(s)
- Henning Onsbring
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75123, Uppsala, Sweden
| | - Alexander K Tice
- Department of Biological Sciences, Mississippi State University, Starkville, Mississippi State, USA
| | - Brandon T Barton
- Department of Biological Sciences, Mississippi State University, Starkville, Mississippi State, USA
| | - Matthew W Brown
- Department of Biological Sciences, Mississippi State University, Starkville, Mississippi State, USA
| | - Thijs J G Ettema
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75123, Uppsala, Sweden. .,Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, the Netherlands.
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15
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Policastro RA, Raborn RT, Brendel VP, Zentner GE. Simple and efficient profiling of transcription initiation and transcript levels with STRIPE-seq. Genome Res 2020; 30:910-923. [PMID: 32660958 PMCID: PMC7370879 DOI: 10.1101/gr.261545.120] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 06/18/2020] [Indexed: 01/07/2023]
Abstract
Accurate mapping of transcription start sites (TSSs) is key for understanding transcriptional regulation. However, current protocols for genome-wide TSS profiling are laborious and/or expensive. We present Survey of TRanscription Initiation at Promoter Elements with high-throughput sequencing (STRIPE-seq), a simple, rapid, and cost-effective protocol for sequencing capped RNA 5' ends from as little as 50 ng total RNA. Including depletion of uncapped RNA and reaction cleanups, a STRIPE-seq library can be constructed in about 5 h. We show application of STRIPE-seq to TSS profiling in yeast and human cells and show that it can also be effectively used for quantification of transcript levels and analysis of differential gene expression. In conjunction with our ready-to-use computational workflows, STRIPE-seq is a straightforward, efficient means by which to probe the landscape of transcriptional initiation.
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Affiliation(s)
| | | | - Volker P Brendel
- Department of Biology
- Department of Computer Science, Indiana University, Bloomington, Indiana 47405, USA
| | - Gabriel E Zentner
- Department of Biology
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana 46202, USA
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16
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Veeranagouda Y, Remaury A, Guillemot JC, Didier M. RNA Fragmentation and Sequencing (RF-Seq): Cost-Effective, Time-Efficient, and High-Throughput 3' mRNA Sequencing Library Construction in a Single Tube. ACTA ACUST UNITED AC 2019; 129:e109. [PMID: 31763778 DOI: 10.1002/cpmb.109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Over the past decade, transcriptomic studies using next-generation sequencing (NGS)-based RNA sequencing (RNA-Seq) have greatly contributed to characterizing biochemical and physiological changes in cells and tissues across organisms and experimental conditions. Critical steps in RNA-Seq include the preparation of the sequencing library from extracted RNA. Currently, a large panoply of RNA-Seq kits are commercially available. In these kits, conversion of RNA into a sequencing library involves multiple steps, which are labor-intensive, and cost per sample for library preparation may limit routine use of RNA-Seq. Here we describe a simple method for RNA-Seq library construction, referred to as RNA Fragmentation and Sequencing (RF-Seq). RF-Seq requires as little as 10 ng of total RNA and facilitates the sequencing of the 3' end of mRNAs. RF-Seq involves the fragmentation of total RNA followed by reverse transcription in presence of the oligo(dT) primer/template switch oligonucleotide and a sample barcoding/enrichment within a single PCR tube/well. The sample barcoding/enrichment step provides more flexibility for individual sample handling. The use of just twenty orthogonal Illumina TruSeq HT barcoding primers facilitates the preparation of 96 uniquely labeled RF-Seq libraries in a single 96-well PCR plate. Twelve RF-Seq libraries can be prepared within 4 hr, with an approximate cost of $10/sample. We provide an example of using RF-Seq to measure gene expression upon activation of an innate immune pathway using STING activator in human blood cells, highlighting the potential usefulness of the proposed method in routine transcriptomic applications such as high-throughput drug screening and/or preclinical toxicity assays. © 2019 by John Wiley & Sons, Inc. Basic Protocol: RNA fragmentation and sequencing (RF-Seq): Cost-effective, time-efficient, and high-throughput 3' mRNA sequencing library construction in a single tube.
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Affiliation(s)
- Yaligara Veeranagouda
- Molecular Biology and Genomics, Translational Sciences, Sanofi R&D, Chilly-Mazarin, France
| | - Anne Remaury
- Proteomics, Translational Sciences, Sanofi R&D, Chilly-Mazarin, France
| | | | - Michel Didier
- Molecular Biology and Genomics, Translational Sciences, Sanofi R&D, Chilly-Mazarin, France
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17
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Vahrenkamp JM, Szczotka K, Dodson MK, Jarboe EA, Soisson AP, Gertz J. FFPEcap-seq: a method for sequencing capped RNAs in formalin-fixed paraffin-embedded samples. Genome Res 2019; 29:1826-1835. [PMID: 31649055 PMCID: PMC6836741 DOI: 10.1101/gr.249656.119] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 10/03/2019] [Indexed: 12/16/2022]
Abstract
The majority of clinical cancer specimens are preserved as formalin-fixed paraffin-embedded (FFPE) samples. For clinical molecular tests to have wide-reaching impact, they must be applicable to FFPE material. Accurate quantitative measurements of RNA derived from FFPE specimens is challenging because of low yields and high amounts of degradation. Here, we present FFPEcap-seq, a method specifically designed for sequencing capped 5′ ends of RNA derived from FFPE samples. FFPEcap-seq combines enzymatic enrichment of 5′ capped RNAs with template switching to create sequencing libraries. We find that FFPEcap-seq can faithfully capture mRNA expression levels in FFPE specimens while also detecting enhancer RNAs that arise from distal regulatory regions. FFPEcap-seq is a fast and straightforward method for making high-quality 5′ end RNA-seq libraries from FFPE-derived RNA.
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Affiliation(s)
- Jeffery M Vahrenkamp
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - Kathryn Szczotka
- Department of Obstetrics and Gynecology, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - Mark K Dodson
- Department of Obstetrics and Gynecology, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - Elke A Jarboe
- Department of Pathology, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - Andrew P Soisson
- Department of Obstetrics and Gynecology, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - Jason Gertz
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
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18
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Wulf MG, Maguire S, Humbert P, Dai N, Bei Y, Nichols NM, Corrêa IR, Guan S. Non-templated addition and template switching by Moloney murine leukemia virus (MMLV)-based reverse transcriptases co-occur and compete with each other. J Biol Chem 2019; 294:18220-18231. [PMID: 31640989 PMCID: PMC6885630 DOI: 10.1074/jbc.ra119.010676] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 10/17/2019] [Indexed: 11/21/2022] Open
Abstract
Single-cell RNA-Seq (scRNA-Seq) has led to an unprecedented understanding of gene expression and regulation in individual cells. Many scRNA-Seq approaches rely upon the template switching property of Moloney murine leukemia virus (MMLV)-type reverse transcriptases. Template switching is believed to happen in a sequential process involving nontemplated addition of three protruding nucleotides (+CCC) to the 3′-end of the nascent cDNA, which can then anneal to the matching rGrGrG 3′-end of the template-switching oligo (TSO), allowing the reverse transcriptase (RT) to switch templates and continue copying the TSO sequence. In this study, we present a detailed analysis of template switching biases with respect to the RNA template, specifically of the role of the sequence and nature of its 5′-end (capped versus noncapped) in these biases. Our findings confirmed that the presence of a 5′-m7G cap enhances template switching efficiency. We also profiled the composition of the nontemplated addition in the absence of TSO and observed that the 5′-end of RNA template influences the terminal transferase activity of the RT. Furthermore, we found that designing new TSOs that pair with the most common nontemplated additions did little to improve template switching efficiency. Our results provide evidence suggesting that, in contrast to the current understanding of the template switching process, nontemplated addition and template switching are concurrent and competing processes.
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Affiliation(s)
| | - Sean Maguire
- New England Biolabs, Inc., Ipswich, Massachusetts 01938
| | - Paul Humbert
- New England Biolabs, Inc., Ipswich, Massachusetts 01938
| | - Nan Dai
- New England Biolabs, Inc., Ipswich, Massachusetts 01938
| | - Yanxia Bei
- New England Biolabs, Inc., Ipswich, Massachusetts 01938
| | | | - Ivan R Corrêa
- New England Biolabs, Inc., Ipswich, Massachusetts 01938.
| | - Shengxi Guan
- New England Biolabs, Inc., Ipswich, Massachusetts 01938.
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19
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Legnini I, Alles J, Karaiskos N, Ayoub S, Rajewsky N. FLAM-seq: full-length mRNA sequencing reveals principles of poly(A) tail length control. Nat Methods 2019; 16:879-886. [PMID: 31384046 DOI: 10.1101/547034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 06/26/2019] [Indexed: 05/18/2023]
Abstract
Although messenger RNAs are key molecules for understanding life, until now, no method has existed to determine the full-length sequence of endogenous mRNAs including their poly(A) tails. Moreover, although non-A nucleotides can be incorporated in poly(A) tails, there also exists no method to accurately sequence them. Here, we present full-length poly(A) and mRNA sequencing (FLAM-seq), a rapid and simple method for high-quality sequencing of entire mRNAs. We report a complementary DNA library preparation method coupled to single-molecule sequencing to perform FLAM-seq. Using human cell lines, brain organoids and Caenorhabditis elegans we show that FLAM-seq delivers high-quality full-length mRNA sequences for thousands of different genes per sample. We find that 3' untranslated region length is correlated with poly(A) tail length, that alternative polyadenylation sites and alternative promoters for the same gene are linked to different tail lengths, and that tails contain a substantial number of cytosines.
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Affiliation(s)
- Ivano Legnini
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Jonathan Alles
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Nikos Karaiskos
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Salah Ayoub
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Nikolaus Rajewsky
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.
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20
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Legnini I, Alles J, Karaiskos N, Ayoub S, Rajewsky N. FLAM-seq: full-length mRNA sequencing reveals principles of poly(A) tail length control. Nat Methods 2019; 16:879-886. [PMID: 31384046 DOI: 10.1038/s41592-019-0503-y] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 06/26/2019] [Indexed: 12/21/2022]
Abstract
Although messenger RNAs are key molecules for understanding life, until now, no method has existed to determine the full-length sequence of endogenous mRNAs including their poly(A) tails. Moreover, although non-A nucleotides can be incorporated in poly(A) tails, there also exists no method to accurately sequence them. Here, we present full-length poly(A) and mRNA sequencing (FLAM-seq), a rapid and simple method for high-quality sequencing of entire mRNAs. We report a complementary DNA library preparation method coupled to single-molecule sequencing to perform FLAM-seq. Using human cell lines, brain organoids and Caenorhabditis elegans we show that FLAM-seq delivers high-quality full-length mRNA sequences for thousands of different genes per sample. We find that 3' untranslated region length is correlated with poly(A) tail length, that alternative polyadenylation sites and alternative promoters for the same gene are linked to different tail lengths, and that tails contain a substantial number of cytosines.
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Affiliation(s)
- Ivano Legnini
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Jonathan Alles
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Nikos Karaiskos
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Salah Ayoub
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Nikolaus Rajewsky
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.
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21
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Wright C, Rajpurohit A, Burke EE, Williams C, Collado-Torres L, Kimos M, Brandon NJ, Cross AJ, Jaffe AE, Weinberger DR, Shin JH. Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods. BMC Genomics 2019; 20:513. [PMID: 31226924 PMCID: PMC6588940 DOI: 10.1186/s12864-019-5870-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 05/31/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND RNA sequencing offers advantages over other quantification methods for microRNA (miRNA), yet numerous biases make reliable quantification challenging. Previous evaluations of these biases have focused on adapter ligation bias with limited evaluation of reverse transcription bias or amplification bias. Furthermore, evaluations of the quantification of isomiRs (miRNA isoforms) or the influence of starting amount on performance have been very limited. No study had yet evaluated the quantification of isomiRs of altered length or compared the consistency of results derived from multiple moderate starting inputs. We therefore evaluated quantifications of miRNA and isomiRs using four library preparation kits, with various starting amounts, as well as quantifications following removal of duplicate reads using unique molecular identifiers (UMIs) to mitigate reverse transcription and amplification biases. RESULTS All methods resulted in false isomiR detection; however, the adapter-free method tested was especially prone to false isomiR detection. We demonstrate that using UMIs improves accuracy and we provide a guide for input amounts to improve consistency. CONCLUSIONS Our data show differences and limitations of current methods, thus raising concerns about the validity of quantification of miRNA and isomiRs across studies. We advocate for the use of UMIs to improve accuracy and reliability of miRNA quantifications.
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Affiliation(s)
- Carrie Wright
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA.,AstraZeneca Postdoc Program, Innovative Medicines and Early Development Biotech Unit, Cambridge, MA, 01239, USA
| | - Anandita Rajpurohit
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Emily E Burke
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Courtney Williams
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Leonardo Collado-Torres
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Martha Kimos
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Nicholas J Brandon
- AstraZeneca Neuroscience, Innovative Medicines and Early Development Biotech Unit, Cambridge, MA, 01239, USA
| | - Alan J Cross
- AstraZeneca Neuroscience, Innovative Medicines and Early Development Biotech Unit, Cambridge, MA, 01239, USA
| | - Andrew E Jaffe
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA.,Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.,Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21287, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA.,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA.,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA. .,Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21287, USA. .,Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA. .,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA. .,The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA.
| | - Joo Heon Shin
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA. .,Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA.
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22
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Ohtsubo Y, Sasaki H, Nagata Y, Tsuda M. Optimization of single strand DNA incorporation reaction by Moloney murine leukaemia virus reverse transcriptase. DNA Res 2019; 25:477-487. [PMID: 29897438 PMCID: PMC6191310 DOI: 10.1093/dnares/dsy018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 05/10/2018] [Indexed: 11/14/2022] Open
Abstract
In this study, we investigated CIS reaction (clamping-mediated incorporation of single-stranded DNA with concomitant DNA syntheses) of Moloney murine leukaemia virus reverse transcriptase (MMLV-RT), and established a set of conditions with which single-stranded DNA is ligated to a G-tailed model substrate DNA at efficiencies close to 100%. Prior to the CIS reaction, a target blunt-end DNA was 3' G-tailed by MMLV-RT in the presence of a tailing enhancer, deoxycytidine. In the CIS reaction, the G-tail reacted with a single-stranded DNA carrying a stretch of Cs on its 3' end (termed as GAO for guide adaptor oligonucleotide), and MMLV-RT performed DNA polymerization, starting from the 3' overhang, using the GAO as a template. We could append a given nucleotide sequence of as long as 72 nucleotides, which would be sufficient for various NGS-sequencing platforms. The high efficiency and the unique features of this MMLV-RT activity that enables the labelling of each DNA molecule with a unique degenerate sequence as a molecular identifier has many potential uses in biotechnology.
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Affiliation(s)
- Yoshiyuki Ohtsubo
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Haruna Sasaki
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Yuji Nagata
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Masataka Tsuda
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
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23
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Abstract
In the last few years single-cell RNA sequencing (scRNA-seq) has enabled the investigation of cellular heterogeneity at the transcriptional level, the characterization of rare cell types as well as the detailed analysis of the stochastic nature of gene expression. A large number of methods have been developed, varying in their throughput, sensitivity, and scalability. A major distinction is whether they profile only 5'- or 3'-terminal part of the transcripts or allow for the characterization of the entire length of the transcripts. Among the latter, Smart-seq2 is still considered the "gold standard" due to its sensitivity, precision, lower cost, scalability and for being easy to set up on automated platforms. In this chapter I describe how to efficiently generate sequencing-ready libraries, highlight common issues and pitfalls, and offer solutions for generating high-quality data.
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Affiliation(s)
- Simone Picelli
- German Centre for Neurodegenerative Diseases (DZNE), Bonn, Germany.
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24
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Ohtsubo Y, Nagata Y, Tsuda M. Compounds that enhance the tailing activity of Moloney murine leukemia virus reverse transcriptase. Sci Rep 2017; 7:6520. [PMID: 28747695 PMCID: PMC5529421 DOI: 10.1038/s41598-017-04765-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 05/23/2017] [Indexed: 11/30/2022] Open
Abstract
In a previous study, we showed that MMLV-RT has a strong terminal transferase activity, and that the C-, G-, and T-tailing activities are enhanced by dGMP, dCMP, and dAMP, respectively. In this study, to achieve faster reaction and higher tailing efficiency, we screened other compounds for the ability to enhance the tailing activities of MMLV-RT, and determined the corresponding optimal concentrations. The C-, G-, and T-tailing activities were enhanced by guanine, cytosine, and adenine, respectively, and by derivatives thereof, suggesting a transient Watson-Click base pairing between an enhancer molecule and the nucleotide to be incorporated. In the presence of some additives (GMP and GDP for C-tailing and CMP for G-tailing), the tail length increased continuously, resulting in tail lengths of 7 to 15 (GMP and GDP) or 13 to 22 (CMP) nucleotides. Among the compounds that do not induce continuous addition, adenosine, deoxycytidine, and deoxyguanosine mostly enhanced T-, G-, and C-tailings, respectively. The enhancing chemicals described here will improve the feasibility of N-tailing by MMLV-RT in various biotechnological applications.
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Affiliation(s)
- Yoshiyuki Ohtsubo
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai, 980-8577, Japan.
| | - Yuji Nagata
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai, 980-8577, Japan
| | - Masataka Tsuda
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai, 980-8577, Japan
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Svensson V, Natarajan KN, Ly LH, Miragaia RJ, Labalette C, Macaulay IC, Cvejic A, Teichmann SA. Power analysis of single-cell RNA-sequencing experiments. Nat Methods 2017; 14:381-387. [PMID: 28263961 PMCID: PMC5376499 DOI: 10.1038/nmeth.4220] [Citation(s) in RCA: 370] [Impact Index Per Article: 52.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 02/07/2017] [Indexed: 12/19/2022]
Abstract
Single-cell RNA sequencing (scRNA-seq) has become an established and powerful method to investigate transcriptomic cell-to-cell variation, thereby revealing new cell types and providing insights into developmental processes and transcriptional stochasticity. A key question is how the variety of available protocols compare in terms of their ability to detect and accurately quantify gene expression. Here, we assessed the protocol sensitivity and accuracy of many published data sets, on the basis of spike-in standards and uniform data processing. For our workflow, we developed a flexible tool for counting the number of unique molecular identifiers (https://github.com/vals/umis/). We compared 15 protocols computationally and 4 protocols experimentally for batch-matched cell populations, in addition to investigating the effects of spike-in molecular degradation. Our analysis provides an integrated framework for comparing scRNA-seq protocols.
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Affiliation(s)
- Valentine Svensson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Kedar Nath Natarajan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Lam-Ha Ly
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Ricardo J Miragaia
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal
| | - Charlotte Labalette
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Iain C Macaulay
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Ana Cvejic
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Sarah A Teichmann
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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26
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Efficient N-tailing of blunt DNA ends by Moloney murine leukemia virus reverse transcriptase. Sci Rep 2017; 7:41769. [PMID: 28150748 PMCID: PMC5288710 DOI: 10.1038/srep41769] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 12/28/2016] [Indexed: 11/08/2022] Open
Abstract
Moloney murine leukemia virus reverse transcriptase (MMLV-RT) is a widely used enzyme for cDNA synthesis. Here we show that MMLV-RT has a strong template-independent polymerase activity using blunt DNA ends as substrate that generates 3' overhangs of A, C, G, or T. Nucleotides were appended efficiently in the order A > G > T > C, and tail lengths varied from 4 to 5, 2 to 7, 2 to 4, and 2 to 3 for A, C, G, and T, respectively. The activity was so strong that nearly all our test DNA ends were appended with at least one A, C, G, or T. The N-tailing activity of MMLV-RT was enhanced in the presence of Mn2+, and the G-, C-, and T-tailing activities were further enhanced by dCMP, dGMP, and dAMP, respectively. This is the first report of an enzymatic activity that almost thoroughly appends two or more As, or one or more Cs, Gs, or Ts to the 3' end of double-stranded DNA, which would enable exhaustive analysis of DNA samples. The N-tailing activity of MMLV-RT is potentially useful in many biotechnological applications.
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27
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Saliba AE, Li L, Westermann AJ, Appenzeller S, Stapels DAC, Schulte LN, Helaine S, Vogel J. Single-cell RNA-seq ties macrophage polarization to growth rate of intracellular Salmonella. Nat Microbiol 2016; 2:16206. [PMID: 27841856 DOI: 10.1038/nmicrobiol.2016.206] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 09/16/2016] [Indexed: 01/05/2023]
Abstract
Intracellular bacterial pathogens can exhibit large heterogeneity in growth rate inside host cells, with major consequences for the infection outcome. If and how the host responds to this heterogeneity remains poorly understood. Here, we combined a fluorescent reporter of bacterial cell division with single-cell RNA-sequencing analysis to study the macrophage response to different intracellular states of the model pathogen Salmonella enterica serovar Typhimurium. The transcriptomes of individual infected macrophages revealed a spectrum of functional host response states to growing and non-growing bacteria. Intriguingly, macrophages harbouring non-growing Salmonella display hallmarks of the proinflammatory M1 polarization state and differ little from bystander cells, suggesting that non-growing bacteria evade recognition by intracellular immune receptors. By contrast, macrophages containing growing bacteria have turned into an anti-inflammatory, M2-like state, as if fast-growing intracellular Salmonella overcome host defence by reprogramming macrophage polarization. Additionally, our clustering approach reveals intermediate host functional states between these extremes. Altogether, our data suggest that gene expression variability in infected host cells shapes different cellular environments, some of which may favour a growth arrest of Salmonella facilitating immune evasion and the establishment of a long-term niche, while others allow Salmonella to escape intracellular antimicrobial activity and proliferate.
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Affiliation(s)
- Antoine-Emmanuel Saliba
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Straße 2, D-97080 Würzburg, Germany.,Core Unit SysMed, University of Würzburg, Josef-Schneider-Straße 2, D-97080 Würzburg, Germany
| | - Lei Li
- Core Unit SysMed, University of Würzburg, Josef-Schneider-Straße 2, D-97080 Würzburg, Germany
| | - Alexander J Westermann
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Straße 2, D-97080 Würzburg, Germany
| | - Silke Appenzeller
- Core Unit SysMed, University of Würzburg, Josef-Schneider-Straße 2, D-97080 Würzburg, Germany
| | - Daphne A C Stapels
- Section of Microbiology, Medical Research Council (MRC) Centre for Molecular Bacteriology and Infection, Imperial College London, Armstrong Road, London SW7 2AZ, UK
| | - Leon N Schulte
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Straße 2, D-97080 Würzburg, Germany
| | - Sophie Helaine
- Section of Microbiology, Medical Research Council (MRC) Centre for Molecular Bacteriology and Infection, Imperial College London, Armstrong Road, London SW7 2AZ, UK
| | - Jörg Vogel
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Straße 2, D-97080 Würzburg, Germany
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28
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Kitaura K, Shini T, Matsutani T, Suzuki R. A new high-throughput sequencing method for determining diversity and similarity of T cell receptor (TCR) α and β repertoires and identifying potential new invariant TCR α chains. BMC Immunol 2016; 17:38. [PMID: 27729009 PMCID: PMC5059964 DOI: 10.1186/s12865-016-0177-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 09/27/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND High-throughput sequencing of T cell receptor (TCR) genes is a powerful tool for analyses of antigen specificity, clonality and diversity of T lymphocytes. Here, we developed a new TCR repertoire analysis method using 454 DNA sequencing technology in combination with an adaptor-ligation mediated polymerase chain reaction (PCR). This method allows the amplification of all TCR genes without PCR bias. To compare gene usage, diversity and similarity of expressed TCR repertoires among individuals, we conducted next-generation sequencing (NGS) of TRA and TRB genes in peripheral blood mononuclear cells from 20 healthy human individuals. RESULTS From a total of 267,037 sequence reads from 20 individuals, 149,216 unique sequence reads were identified. Preferential usage of several V and J genes were observed while some recombinations of TRAV with TRAJ appeared to be restricted. The extent of TCR diversity was not significantly different between TRA and TRB, while TRA repertoires were more similar between individuals than TRB repertoires were. The interindividual similarity of TRA depended largely on the frequent presence of shared TCRs among two or more individuals. A publicly available TRA had a near-germline TCR with a shorter CDR3. Notably, shared TRA sequences, especially those shared among a large number of individuals', often contained TCRα related with invariant TCRα derived from invariant natural killer T cells and mucosal-associated invariant T cells. CONCLUSION These results suggest that retrieval of shared TCRs by NGS would be useful for the identification of potential new invariant TCRα chains. This NGS method will enable the comprehensive quantitative analysis of TCR repertoires at a clonal level.
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Affiliation(s)
- Kazutaka Kitaura
- Repertoire Genesis Incorporation, 104 Saito-Bioincubator, 7-7-15, Saito-asagi, Ibaraki, Osaka, 567-0085, Japan
| | - Tadasu Shini
- Department of Rheumatology and Clinical Immunology, Clinical Research Center for Rheumatology and Allergy, Sagamihara National Hospital, National Hospital Organization, Sagamihara, Japan.,BITS. Co., Ltd, Tokyo, Japan
| | - Takaji Matsutani
- Repertoire Genesis Incorporation, 104 Saito-Bioincubator, 7-7-15, Saito-asagi, Ibaraki, Osaka, 567-0085, Japan.
| | - Ryuji Suzuki
- Repertoire Genesis Incorporation, 104 Saito-Bioincubator, 7-7-15, Saito-asagi, Ibaraki, Osaka, 567-0085, Japan.,Department of Rheumatology and Clinical Immunology, Clinical Research Center for Rheumatology and Allergy, Sagamihara National Hospital, National Hospital Organization, Sagamihara, Japan
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Abstract
Genome-wide single-cell analysis represents the ultimate frontier of genomics research. In particular, single-cell RNA-sequencing (scRNA-seq) studies have been boosted in the last few years by an explosion of new technologies enabling the study of the transcriptomic landscape of thousands of single cells in complex multicellular organisms. More sensitive and automated methods are being continuously developed and promise to deliver better data quality and higher throughput with less hands-on time. The outstanding amount of knowledge that is going to be gained from present and future studies will have a profound impact in many aspects of our society, from the introduction of truly tailored cancer treatments, to a better understanding of antibiotic resistance and host-pathogen interactions; from the discovery of the mechanisms regulating stem cell differentiation to the characterization of the early event of human embryogenesis.
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Affiliation(s)
- Simone Picelli
- a Eukaryotic Single Cell Genomics Facility , Science for Life Laboratory , Tomtebodavägen , Solna , Sweden
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30
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Machida RJ, Lin YY. Four methods of preparing mRNA 5' end libraries using the Illumina sequencing platform. PLoS One 2014; 9:e101812. [PMID: 25003736 PMCID: PMC4086933 DOI: 10.1371/journal.pone.0101812] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 06/12/2014] [Indexed: 11/18/2022] Open
Abstract
Background The 5′ untranslated regions of mRNA play an important role in their translation. Results Here, we describe the development of four methods of profiling mRNA 5′ ends using the Illumina sequencing platform; the first method utilizes SMART (Switching Mechanism At 5′ end of RNA Transcript) technology, while the second involves replacing the 5′ cap structure with RNA oligomers via ligation. The third and fourth methods are modifications of SMART, and involve enriching mRNA molecules with (nuclear transcripts) and without (mitochondrial transcripts) 5′ end cap structures, respectively. Libraries prepared using SMART technology gave more reproducible results, but the ligation method was advantageous in that it only sequenced mRNAs with a cap structure at the 5′ end. Conclusions These methods are suitable for global mapping of mRNA 5′ ends, both with and without cap structures, at a single molecule resolution. In addition, comparison of the present results obtained using different methods revealed the presence of abundant messenger RNAs without a cap structure.
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Affiliation(s)
- Ryuji J. Machida
- Biodiversity Research Centre, Academia Sinica, Nankang, Taipei, Taiwan
- * E-mail: (RJM); (YYL)
| | - Ya-Ying Lin
- Biodiversity Research Centre, Academia Sinica, Nankang, Taipei, Taiwan
- * E-mail: (RJM); (YYL)
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31
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Turchinovich A, Surowy H, Serva A, Zapatka M, Lichter P, Burwinkel B. Capture and Amplification by Tailing and Switching (CATS). An ultrasensitive ligation-independent method for generation of DNA libraries for deep sequencing from picogram amounts of DNA and RNA. RNA Biol 2014; 11:817-28. [PMID: 24922482 PMCID: PMC4179956 DOI: 10.4161/rna.29304] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Massive parallel sequencing (MPS) technologies have paved the way into new areas of research including individualized medicine. However, sequencing of trace amounts of DNA or RNA still remains a major challenge, especially for degraded nucleic acids like circulating DNA. This together with high cost and time requirements impedes many important applications of MPS in medicine and fundamental science. We have established a fast, cheap and highly efficient protocol called ‘Capture and Amplification by Tailing and Switching’ (CATS) to directly generate ready-to-sequence libraries for MPS from nanogram and picogram quantities of both DNA and RNA. Furthermore, those DNA libraries are strand-specific, can be prepared within 2–3 h and do not require preliminary sample amplification steps. To exemplify the capacity of the technique, we have generated and sequenced DNA libraries from hundred-picogram amounts of circulating nucleic acids isolated from human blood plasma, one nanogram of mRNA-enriched total RNA from cultured cells and few nanograms of bisulfite-converted DNA. The approach for DNA library preparation from minimal and fragmented input described here will find broad application in diverse research areas such as translational medicine including therapy monitoring, prediction, prognosis and early detection of various human disorders and will permit high-throughput DNA sequencing from previously inaccessible material such as minute forensic and archeological samples.
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Affiliation(s)
- Andrey Turchinovich
- Molecular Epidemiology; German Cancer Research Center DKFZ; Heidelberg, Germany; Molecular Biology of Breast Cancer; University Women's Clinic; Heidelberg, Germany
| | - Harald Surowy
- Molecular Epidemiology; German Cancer Research Center DKFZ; Heidelberg, Germany; Molecular Biology of Breast Cancer; University Women's Clinic; Heidelberg, Germany
| | - Andrius Serva
- Molecular Genetics; German Cancer Research Center DKFZ; Heidelberg, Germany
| | - Marc Zapatka
- Molecular Genetics; German Cancer Research Center DKFZ; Heidelberg, Germany
| | - Peter Lichter
- Molecular Genetics; German Cancer Research Center DKFZ; Heidelberg, Germany
| | - Barbara Burwinkel
- Molecular Epidemiology; German Cancer Research Center DKFZ; Heidelberg, Germany; Molecular Biology of Breast Cancer; University Women's Clinic; Heidelberg, Germany
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32
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Zajac P, Islam S, Hochgerner H, Lönnerberg P, Linnarsson S. Base preferences in non-templated nucleotide incorporation by MMLV-derived reverse transcriptases. PLoS One 2013; 8:e85270. [PMID: 24392002 PMCID: PMC3877366 DOI: 10.1371/journal.pone.0085270] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 11/26/2013] [Indexed: 11/21/2022] Open
Abstract
Reverse transcriptases derived from Moloney Murine Leukemia Virus (MMLV) have an intrinsic terminal transferase activity, which causes the addition of a few non-templated nucleotides at the 3´ end of cDNA, with a preference for cytosine. This mechanism can be exploited to make the reverse transcriptase switch template from the RNA molecule to a secondary oligonucleotide during first-strand cDNA synthesis, and thereby to introduce arbitrary barcode or adaptor sequences in the cDNA. Because the mechanism is relatively efficient and occurs in a single reaction, it has recently found use in several protocols for single-cell RNA sequencing. However, the base preference of the terminal transferase activity is not known in detail, which may lead to inefficiencies in template switching when starting from tiny amounts of mRNA. Here, we used fully degenerate oligos to determine the exact base preference at the template switching site up to a distance of ten nucleotides. We found a strong preference for guanosine at the first non-templated nucleotide, with a greatly reduced bias at progressively more distant positions. Based on this result, and a number of careful optimizations, we report conditions for efficient template switching for cDNA amplification from single cells.
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Affiliation(s)
- Pawel Zajac
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Saiful Islam
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Hannah Hochgerner
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Peter Lönnerberg
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Sten Linnarsson
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- *
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33
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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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Fan JB, Chen J, April CS, Fisher JS, Klotzle B, Bibikova M, Kaper F, Ronaghi M, Linnarsson S, Ota T, Chien J, Laurent LC, Loring JF, Nisperos SV, Chen GY, Zhong JF. Highly parallel genome-wide expression analysis of single mammalian cells. PLoS One 2012; 7:e30794. [PMID: 22347404 PMCID: PMC3275609 DOI: 10.1371/journal.pone.0030794] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Accepted: 12/29/2011] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND We have developed a high-throughput amplification method for generating robust gene expression profiles using single cell or low RNA inputs. METHODOLOGY/PRINCIPAL FINDINGS The method uses tagged priming and template-switching, resulting in the incorporation of universal PCR priming sites at both ends of the synthesized cDNA for global PCR amplification. Coupled with a whole-genome gene expression microarray platform, we routinely obtain expression correlation values of R(2)~0.76-0.80 between individual cells and R(2)~0.69 between 50 pg total RNA replicates. Expression profiles generated from single cells or 50 pg total RNA correlate well with that generated with higher input (1 ng total RNA) (R(2)~0.80). Also, the assay is sufficiently sensitive to detect, in a single cell, approximately 63% of the number of genes detected with 1 ng input, with approximately 97% of the genes detected in the single-cell input also detected in the higher input. CONCLUSIONS/SIGNIFICANCE In summary, our method facilitates whole-genome gene expression profiling in contexts where starting material is extremely limiting, particularly in areas such as the study of progenitor cells in early development and tumor stem cell biology.
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Affiliation(s)
- Jian-Bing Fan
- Research and Development, Illumina, Inc, San Diego, California, United States of America.
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35
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He R, Kim MJ, Nelson W, Balbuena TS, Kim R, Kramer R, Crow JA, May GD, Thelen JJ, Soderlund CA, Gang DR. Next-generation sequencing-based transcriptomic and proteomic analysis of the common reed, Phragmites australis (Poaceae), reveals genes involved in invasiveness and rhizome specificity. AMERICAN JOURNAL OF BOTANY 2012; 99:232-47. [PMID: 22301892 DOI: 10.3732/ajb.1100429] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
PREMISE OF THE STUDY The common reed (Phragmites australis), one of the most widely distributed of all angiosperms, uses its rhizomes (underground stems) to invade new territory, making it one of the most successful weedy species worldwide. Characterization of the rhizome transcriptome and proteome is needed to identify candidate genes and proteins involved in rhizome growth, development, metabolism, and invasiveness. METHODS We employed next-generation sequencing technologies including 454 and Illumina platforms to characterize the reed rhizome transcriptome and used quantitative proteomics techniques to identify the rhizome proteome. KEY RESULTS Combining 336514 Roche 454 Titanium reads and 103350802 Illumina paired-end reads in a de novo hybrid assembly yielded 124450 unique transcripts with an average length of 549 bp, of which 54317 were annotated. Rhizome-specific and differentially expressed transcripts were identified between rhizome apical tips (apical meristematic region) and rhizome elongation zones. A total of 1280 nonredundant proteins were identified and quantified using GeLC-MS/MS based label-free proteomics, where 174 and 77 proteins were preferentially expressed in the rhizome elongation zone and apical tip tissues, respectively. Genes involved in allelopathy and in controlling development and potentially invasiveness were identified. CONCLUSIONS In addition to being a valuable sequence and protein data resource for studying plant rhizome species, our results provide useful insights into identifying specific genes and proteins with potential roles in rhizome differentiation, development, and function.
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Affiliation(s)
- Ruifeng He
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, USA
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36
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Kimoto M, Cox RS, Hirao I. Unnatural base pair systems for sensing and diagnostic applications. Expert Rev Mol Diagn 2011; 11:321-31. [PMID: 21463241 DOI: 10.1586/erm.11.5] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Expansion of the genetic alphabet by an unnatural base pair system provides a platform for the site-specific, enzymatic incorporation of extra, functional components into nucleic acids. Recently, several unnatural base pairs that exhibit high fidelity and efficiency in PCR have been developed. Functional groups of interest, such as fluorescent dyes, can be linked to the unnatural bases, and the modified base substrates are site-specifically incorporated into nucleic acids by polymerases. Furthermore, unique unnatural base pairs between fluorophore and quencher base analogs have been developed for imaging PCR amplification and as molecular beacons. Here, we describe the recent progress in the development of unnatural base pairs that function in PCR amplification and their applications as sensing and diagnostic tools.
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Affiliation(s)
- Michiko Kimoto
- RIKEN Systems and Structural Biology Center (SSBC), Yokohama, Japan
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37
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McDowell ET, Kapteyn J, Schmidt A, Li C, Kang JH, Descour A, Shi F, Larson M, Schilmiller A, An L, Jones AD, Pichersky E, Soderlund CA, Gang DR. Comparative functional genomic analysis of Solanum glandular trichome types. PLANT PHYSIOLOGY 2011; 155:524-39. [PMID: 21098679 PMCID: PMC3075747 DOI: 10.1104/pp.110.167114] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Accepted: 11/18/2010] [Indexed: 05/19/2023]
Abstract
Glandular trichomes play important roles in protecting plants from biotic attack by producing defensive compounds. We investigated the metabolic profiles and transcriptomes to characterize the differences between different glandular trichome types in several domesticated and wild Solanum species: Solanum lycopersicum (glandular trichome types 1, 6, and 7), Solanum habrochaites (types 1, 4, and 6), Solanum pennellii (types 4 and 6), Solanum arcanum (type 6), and Solanum pimpinellifolium (type 6). Substantial chemical differences in and between Solanum species and glandular trichome types are likely determined by the regulation of metabolism at several levels. Comparison of S. habrochaites type 1 and 4 glandular trichomes revealed few differences in chemical content or transcript abundance, leading to the conclusion that these two glandular trichome types are the same and differ perhaps only in stalk length. The observation that all of the other species examined here contain either type 1 or 4 trichomes (not both) supports the conclusion that these two trichome types are the same. Most differences in metabolites between type 1 and 4 glands on the one hand and type 6 glands on the other hand are quantitative but not qualitative. Several glandular trichome types express genes associated with photosynthesis and carbon fixation, indicating that some carbon destined for specialized metabolism is likely fixed within the trichome secretory cells. Finally, Solanum type 7 glandular trichomes do not appear to be involved in the biosynthesis and storage of specialized metabolites and thus likely serve another unknown function, perhaps as the site of the synthesis of protease inhibitors.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - David R. Gang
- Bio5 Institute (E.T.M., J.K., A.D., C.A.S., D.R.G.) and Department of Agricultural and Biosystems Engineering (L.A.), University of Arizona, Tucson, Arizona 85721; Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109–1048 (A.S., E.P.); Department of Chemistry (C.L., F.S., A.D.J.), Department of Energy-Plant Research Laboratory (J.-H.K.), and Department of Biochemistry and Molecular Biology (M.L., A.S., A.D.J.), Michigan State University, East Lansing, Michigan 48824–1319; Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164–6340 (D.R.G.)
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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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