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Nadal-Ribelles M, Solé C, de Nadal E, Posas F. The rise of single-cell transcriptomics in yeast. Yeast 2024; 41:158-170. [PMID: 38403881 DOI: 10.1002/yea.3934] [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: 09/29/2023] [Revised: 01/24/2024] [Accepted: 02/15/2024] [Indexed: 02/27/2024] Open
Abstract
The field of single-cell omics has transformed our understanding of biological processes and is constantly advancing both experimentally and computationally. One of the most significant developments is the ability to measure the transcriptome of individual cells by single-cell RNA-seq (scRNA-seq), which was pioneered in higher eukaryotes. While yeast has served as a powerful model organism in which to test and develop transcriptomic technologies, the implementation of scRNA-seq has been significantly delayed in this organism, mainly because of technical constraints associated with its intrinsic characteristics, namely the presence of a cell wall, a small cell size and little amounts of RNA. In this review, we examine the current technologies for scRNA-seq in yeast and highlight their strengths and weaknesses. Additionally, we explore opportunities for developing novel technologies and the potential outcomes of implementing single-cell transcriptomics and extension to other modalities. Undoubtedly, scRNA-seq will be invaluable for both basic and applied yeast research, providing unique insights into fundamental biological processes.
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Affiliation(s)
- Mariona Nadal-Ribelles
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Carme Solé
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Eulalia de Nadal
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Francesc Posas
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
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Nugraha Y, Laksmi FA, Nuryana I, Helbert, Khasna FN. Production of reverse transcriptase from Moloney murine Leukemia virus in Escherichia coli expression system. Prep Biochem Biotechnol 2024:1-9. [PMID: 38411149 DOI: 10.1080/10826068.2024.2317311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Reverse transcriptase (RT) is one of the most important enzymes used in molecular biology applications, enabling the conversion of RNA into complementary DNA (cDNA) that is used in reverse transcription-polymerase chain reaction (RT-PCR). The high demand of RT enzymes in biotechnological applications making the production optimization of RT is crucial for meeting the growing demand in industrial settings. Conventionally, the expression of recombinant RT is T7-induced promoter using IPTG in Escherichia coli expression systems, which is not cost-efficient. Here, we successfully made an alternative procedure for RT expression from Moloney murine leukemia virus (M-MLV) using autoinduction method in chemically defined medium. The optimization of carbon source composition (glucose, lactose, and glycerol) was analyzed using Response Surface Methodology (RSM). M-MLV RT was purified for further investigation on its activity. A total of 32.8 mg/L purified M-MLV RT was successfully obtained when glucose, glycerol, and lactose were present at concentration of 0.06%, 0.9%, and 0.5% respectively, making a 3.9-fold improvement in protein yield. In addition, the protein was produced in its active form by displaying 7462.50 U/mg of specific activity. This study provides the first step of small-scale procedures of M-MLV RT production that make it a cost-effective and industrially applicable strategy.
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Affiliation(s)
- Yudhi Nugraha
- Research Center for Molecular Biology Eijkman, National Research and Innovation Agency, Cibinong, Bogor, West Java, Indonesia
| | - Fina Amreta Laksmi
- Research Center for Applied Microbiology, National Research and Innovation Agency, Cibinong, Bogor, West Java, Indonesia
| | - Isa Nuryana
- Research Center for Applied Microbiology, National Research and Innovation Agency, Cibinong, Bogor, West Java, Indonesia
| | - Helbert
- Research Center for Ecology and Ethnobiology, National Research and Innovation Agency, Cibinong, Bogor, West Java, Indonesia
| | - Firyal Nida Khasna
- Research Center for Applied Microbiology, National Research and Innovation Agency, Cibinong, Bogor, West Java, Indonesia
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Hong CH, Pyo HS, Baek IC, Kim TG. Rapid identification of CMV-specific TCRs via reverse TCR cloning system based on bulk TCR repertoire data. Front Immunol 2022; 13:1021067. [PMID: 36466875 PMCID: PMC9716090 DOI: 10.3389/fimmu.2022.1021067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 10/31/2022] [Indexed: 08/11/2023] Open
Abstract
Advances in next-generation sequencing (NGS) have improved the resolution of T-cell receptor (TCR) repertoire analysis, and recent single-cell sequencing has made it possible to obtain information about TCR pairs. In our previous study, cytomegalovirus (CMV) pp65-specific T-cell response restricted by a single human leukocyte antigen (HLA) class I allotype was observed in an individual. Therefore, to effectively clone an antigen-specific TCR from these T cells, we developed a TCR cloning system that does not require a single cell level. First, we established the improved Jurkat reporter cell line, which was TCRαβ double knock-out and expressed CD8αβ molecules. Furthermore, functional TCRs were directly obtained by reverse TCR cloning using unique CDR3-specific PCR primers after bulk TCR sequencing of activation marker-positive CD8 T cells by NGS. A total of 15 TCRα and 14 TCRβ strands were successfully amplified by PCR from cDNA of 4-1BB-positive CD8 T cells restricted by HLA-A*02:01, HLA-A*02:06, HLA-B*07:02, and HLA-B*40:06. The panels with combinations of TCRα and TCRβ genes were investigated using Jurkat reporter cell line and artificial antigen-presenting cells (APCs). In two TCR pairs restricted by HLA-A*02:01, one TCR pair by HLA-A*02:06, four TCR pairs by HLA-B*07:02, and one TCR pair by HLA-B*40:06, their specificity and affinity were confirmed. The TCR pair of A*02:01/1-1 showed alloreactivity to HLA-A*02:06. The one TCR pair showed a higher response to the naturally processed antigen than that of the peptide pool. This reverse TCR cloning system will not only provide functional information to TCR repertoire analysis by NGS but also help in the development of TCR-T therapy.
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Affiliation(s)
- Cheol-Hwa Hong
- Department of Biomedicine and Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, South Korea
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea
- Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Hong-Seon Pyo
- Department of Biomedicine and Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, South Korea
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - In-Cheol Baek
- Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Tai-Gyu Kim
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea
- Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea
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Expression of Codon-Optimized Gene Encoding Murine Moloney Leukemia Virus Reverse Transcriptase in Escherichia coli. Protein J 2022; 41:515-526. [PMID: 35933571 PMCID: PMC9362449 DOI: 10.1007/s10930-022-10066-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2022] [Indexed: 10/27/2022]
Abstract
Moloney murine leukemia virus reverse transcriptase (MMLV-RT) is the most frequently used enzyme in molecular biology for cDNA synthesis. To date, reverse transcription coupled with Polymerase Chain Reaction, known as RT-PCR, has been popular as an excellent approach for the detection of SARS-CoV-2 during the COVID-19 pandemic. In this study, we aimed to improve the enzymatic production and performance of MMLV-RT by optimizing both codon and culture conditions in E. coli expression system. By applying the optimized codon and culture conditions, the enzyme was successfully overexpressed and increased at high level based on the result of SDS-PAGE and Western blotting. The total amount of MMLV-RT has improved 85-fold from 0.002 g L-1 to 0.175 g L-1 of culture. One-step purification by nickel affinity chromatography has been performed to generate the purified enzyme for further analysis of qualitative and quantitative RT activity. Overall, our investigation provides useful strategies to enhance the recombinant enzyme of MMLV-RT in both production and performance. More importantly, the enzyme has shown promising activity to be used for RT-PCR assay.
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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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6
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Molecular spikes: a gold standard for single-cell RNA counting. Nat Methods 2022; 19:560-566. [PMID: 35468967 PMCID: PMC9119855 DOI: 10.1038/s41592-022-01446-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 03/06/2022] [Indexed: 12/25/2022]
Abstract
Single-cell sequencing methods rely on molecule-counting strategies to account for amplification biases, yet no experimental strategy to evaluate counting performance exists. Here, we introduce molecular spikes—RNA spike-ins containing built-in unique molecular identifiers (UMIs) that we use to identify critical experimental and computational conditions for accurate RNA counting in single-cell RNA-sequencing (scRNA-seq). Using molecular spikes, we uncovered impaired RNA counting in methods that were not informative for cellular RNA abundances due to inflated UMI counts. We further leverage molecular spikes to improve estimates of total endogenous RNA amounts in cells, and introduce a strategy to correct experiments with impaired RNA counting. The molecular spikes and the accompanying R package UMIcountR (https://github.com/cziegenhain/UMIcountR) will improve the validation of new methods, better estimate and adjust for cellular mRNA amounts and enable more indepth characterization of RNA counting in scRNA-seq. This work presents an RNA spike-in that can be used to improve RNA counting in single-cell RNA-sequencing (scRNA-seq) analysis, as well as to report the performance of scRNA-seq methods.
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7
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Bradshaw WJ, Poeschla M, Placzek A, Kean S, Valenzano DR. Extensive age-dependent loss of antibody diversity in naturally short-lived turquoise killifish. eLife 2022; 11:65117. [PMID: 35129436 PMCID: PMC8880994 DOI: 10.7554/elife.65117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 02/05/2022] [Indexed: 11/13/2022] Open
Abstract
Aging individuals exhibit a pervasive decline in adaptive immune function, with important implications for health and lifespan. Previous studies have found a pervasive loss of immune-repertoire diversity in human peripheral blood during aging; however, little is known about repertoire aging in other immune compartments, or in species other than humans. Here, we perform the first study of immune-repertoire aging in an emerging model of vertebrate aging, the African turquoise killifish (Nothobranchius furzeri). Despite their extremely short lifespans, these killifish exhibit complex and individualized heavy-chain repertoires, with a generative process capable of producing millions of distinct productive sequences. Whole-body killifish repertoires decline rapidly in within-individual diversity with age, while between-individual variability increases. Large, expanded B-cell clones exhibit far greater diversity loss with age than small clones, suggesting important differences in how age affects different B-cell populations. The immune repertoires of isolated intestinal samples exhibit especially dramatic age-related diversity loss, related to an elevated prevalence of expanded clones. Lower intestinal repertoire diversity was also associated with transcriptomic signatures of reduced B-cell activity, supporting a functional role for diversity changes in killifish immunosenescence. Our results highlight important differences in systemic vs. organ-specific aging dynamics in the adaptive immune system.
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Affiliation(s)
- William John Bradshaw
- Evolutionary and Experimental Biology of Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Michael Poeschla
- Evolutionary and Experimental Biology of Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Aleksandra Placzek
- Evolutionary and Experimental Biology of Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Samuel Kean
- Evolutionary and Experimental Biology of Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Dario Riccardo Valenzano
- Evolutionary and Experimental Biology of Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany
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8
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Pimentel SC, Upton HE, Collins K. Separable structural requirements for cDNA synthesis, nontemplated extension, and template jumping by a non-LTR retroelement reverse transcriptase. J Biol Chem 2022; 298:101624. [PMID: 35065960 PMCID: PMC8857657 DOI: 10.1016/j.jbc.2022.101624] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 11/16/2022] Open
Abstract
Broad evolutionary expansion of polymerase families has enabled specialization of their activities for distinct cellular roles. In addition to template-complementary synthesis, many polymerases extend their duplex products by nontemplated nucleotide addition (NTA). This activity is exploited for laboratory strategies of cloning and sequencing nucleic acids and could have important biological function, although the latter has been challenging to test without separation-of-function mutations. Several retroelement and retroviral reverse transcriptases (RTs) support NTA and also template jumping, by which the RT performs continuous complementary DNA (cDNA) synthesis using physically separate templates. Previous studies that aimed to dissect the relationship between NTA and template jumping leave open questions about structural requirements for each activity and their interdependence. Here, we characterize the structural requirements for cDNA synthesis, NTA, template jumping, and the unique terminal transferase activity of Bombyx mori R2 non-long terminal repeat retroelement RT. With sequence alignments and structure modeling to guide mutagenesis, we generated enzyme variants across motifs generally conserved or specific to RT subgroups. Enzyme variants had diverse NTA profiles not correlated with other changes in cDNA synthesis activity or template jumping. Using these enzyme variants and panels of activity assay conditions, we show that template jumping requires NTA. However, template jumping by NTA-deficient enzymes can be rescued using primer duplex with a specific length of 3′ overhang. Our findings clarify the relationship between NTA and template jumping as well as additional activities of non-long terminal repeat RTs, with implications for the specialization of RT biological functions and laboratory applications.
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Affiliation(s)
- Sydney C Pimentel
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California, USA
| | - Heather E Upton
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California, USA
| | - Kathleen Collins
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California, USA.
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Abstract
Transcription start site (TSS) usage is a critical factor in the regulation of gene expression. A number of methods for global TSS mapping have been developed, but barriers of expense, technical difficulty, time, and/or cost have limited their broader adoption. To address these issues, we developed Survey of TRanscription Initiation at Promoter Elements with high-throughput sequencing (STRIPE-seq). Requiring only three enzymatic steps with intervening bead cleanups, a STRIPE-seq library can be prepared from as little as 50 ng total RNA in ~5 h at a cost of ~$12 (US). In addition to profiling TSS usage, STRIPE-seq provides information on transcript levels that can be used for differential expression analysis. Thanks to its simplicity and low cost, we envision that STRIPE-seq could be employed by any molecular biology laboratory interested in profiling transcription initiation.
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Affiliation(s)
| | - Gabriel E Zentner
- Department of Biology, Indiana University, Bloomington, IN, USA.
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN, USA.
- eGenesis, Inc., Cambridge, MA, USA.
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Jia E, Shi H, Wang Y, Zhou Y, Liu Z, Pan M, Bai Y, Zhao X, Ge Q. Optimization of library preparation based on SMART for ultralow RNA-seq in mice brain tissues. BMC Genomics 2021; 22:809. [PMID: 34758728 PMCID: PMC8579666 DOI: 10.1186/s12864-021-08132-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/28/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Single-cell RNA sequencing (scRNA-seq) provides new insights to address biological and medical questions, and it will benefit more from the ultralow input RNA or subcellular sequencing. RESULTS Here, we present a highly sensitive library construction protocol for ultralow input RNA sequencing (ulRNA-seq). We systematically evaluate experimental conditions of this protocol, such as reverse transcriptase, template-switching oligos (TSO), and template RNA structure. It was found that Maxima H Minus reverse transcriptase and rN modified TSO, as well as all RNA templates capped with m7G improved the sequencing sensitivity and low abundance gene detection ability. RNA-seq libraries were successfully prepared from total RNA samples as low as 0.5 pg, and more than 2000 genes have been identified. CONCLUSIONS The ability of low abundance gene detection and sensitivity were largely enhanced with this optimized protocol. It was also confirmed in single-cell sequencing, that more genes and cell markers were identified compared to conventional sequencing method. We expect that ulRNA-seq will sequence and transcriptome characterization for the subcellular of disease tissue, to find the corresponding treatment plan.
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Affiliation(s)
- Erteng Jia
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Huajuan Shi
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Ying Wang
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Ying Zhou
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Zhiyu Liu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Min Pan
- School of Medicine, Southeast University, Nanjing, 210097, China
| | - Yunfei Bai
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Xiangwei Zhao
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Qinyu Ge
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China.
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11
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Methyltransferase-directed orthogonal tagging and sequencing of miRNAs and bacterial small RNAs. BMC Biol 2021; 19:129. [PMID: 34158037 PMCID: PMC8220740 DOI: 10.1186/s12915-021-01053-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/24/2021] [Indexed: 12/13/2022] Open
Abstract
Background Targeted installation of designer chemical moieties on biopolymers provides an orthogonal means for their visualisation, manipulation and sequence analysis. Although high-throughput RNA sequencing is a widely used method for transcriptome analysis, certain steps, such as 3′ adapter ligation in strand-specific RNA sequencing, remain challenging due to structure- and sequence-related biases introduced by RNA ligases, leading to misrepresentation of particular RNA species. Here, we remedy this limitation by adapting two RNA 2′-O-methyltransferases from the Hen1 family for orthogonal chemo-enzymatic click tethering of a 3′ sequencing adapter that supports cDNA production by reverse transcription of the tagged RNA. Results We showed that the ssRNA-specific DmHen1 and dsRNA-specific AtHEN1 can be used to efficiently append an oligonucleotide adapter to the 3′ end of target RNA for sequencing library preparation. Using this new chemo-enzymatic approach, we identified miRNAs and prokaryotic small non-coding sRNAs in probiotic Lactobacillus casei BL23. We found that compared to a reference conventional RNA library preparation, methyltransferase-Directed Orthogonal Tagging and RNA sequencing, mDOT-seq, avoids misdetection of unspecific highly-structured RNA species, thus providing better accuracy in identifying the groups of transcripts analysed. Our results suggest that mDOT-seq has the potential to advance analysis of eukaryotic and prokaryotic ssRNAs. Conclusions Our findings provide a valuable resource for studies of the RNA-centred regulatory networks in Lactobacilli and pave the way to developing novel transcriptome and epitranscriptome profiling approaches in vitro and inside living cells. As RNA methyltransferases share the structure of the AdoMet-binding domain and several specific cofactor binding features, the basic principles of our approach could be easily translated to other AdoMet-dependent enzymes for the development of modification-specific RNA-seq techniques. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01053-w.
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Abstract
Narnaviruses are RNA viruses detected in diverse fungi, plants, protists, arthropods, and nematodes. Though initially described as simple single-gene nonsegmented viruses encoding RNA-dependent RNA polymerase (RdRp), a subset of narnaviruses referred to as "ambigrammatic" harbor a unique genomic configuration consisting of overlapping open reading frames (ORFs) encoded on opposite strands. Phylogenetic analysis supports selection to maintain this unusual genome organization, but functional investigations are lacking. Here, we establish the mosquito-infecting Culex narnavirus 1 (CxNV1) as a model to investigate the functional role of overlapping ORFs in narnavirus replication. In CxNV1, a reverse ORF without homology to known proteins covers nearly the entire 3.2-kb segment encoding the RdRp. Additionally, two opposing and nearly completely overlapping novel ORFs are found on the second putative CxNV1 segment, the 0.8-kb "Robin" RNA. We developed a system to launch CxNV1 in a naive mosquito cell line and then showed that functional RdRp is required for persistence of both segments, and an intact reverse ORF is required on the RdRp segment for persistence. Mass spectrometry of persistently CxNV1-infected cells provided evidence for translation of this reverse ORF. Finally, ribosome profiling yielded a striking pattern of footprints for all four CxNV1 RNA strands that was distinct from actively translating ribosomes on host mRNA or coinfecting RNA viruses. Taken together, these data raise the possibility that the process of translation itself is important for persistence of ambigrammatic narnaviruses, potentially by protecting viral RNA with ribosomes, thus suggesting a heretofore undescribed viral tactic for replication and transmission. IMPORTANCE Fundamental to our understanding of RNA viruses is a description of which strand(s) of RNA are transmitted as the viral genome relative to which encode the viral proteins. Ambigrammatic narnaviruses break the mold. These viruses, found broadly in fungi, plants, and insects, have the unique feature of two overlapping genes encoded on opposite strands, comprising nearly the full length of the viral genome. Such extensive overlap is not seen in other RNA viruses and comes at the cost of reduced evolutionary flexibility in the sequence. The present study is motivated by investigating the benefits which balance that cost. We show for the first time a functional requirement for the ambigrammatic genome configuration in Culex narnavirus 1, which suggests a model for how translation of both strands might benefit this virus. Our work highlights a new blueprint for viral persistence, distinct from strategies defined by canonical definitions of the coding strand.
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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: 132] [Impact Index Per Article: 33.0] [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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14
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Oscorbin IP, Wong PF, Boyarskikh UA, Khrapov EA, Filipenko ML. The attachment of a DNA-binding Sso7d-like protein improves processivity and resistance to inhibitors of M-MuLV reverse transcriptase. FEBS Lett 2020; 594:4338-4356. [PMID: 32970841 DOI: 10.1002/1873-3468.13934] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/23/2020] [Accepted: 09/08/2020] [Indexed: 11/09/2022]
Abstract
Reverse transcriptases (RTs) are a standard tool in both fundamental studies and diagnostics. RTs should possess elevated temperature optimum, high thermal stability, processivity and tolerance to contaminants. Here, we constructed a set of chimeric RTs, based on the combination of the Moloney murine leukaemia virus (M-MuLV) RT and either of two DNA-binding domains: the DNA-binding domain of the DNA ligase from Pyrococcus abyssi or the DNA-binding Sto7d protein from Sulfolobus tokodaii. The processivity and efficiency of cDNA synthesis of the chimeric RT with Sto7d at the C-end are increased several fold. The attachment of Sto7d enhances the tolerance of M-MuLV RT to the most common amplification inhibitors: NaCl, urea, guanidinium chloride, formamide, components of human whole blood and human blood plasma. Thus, fusing M-MuLV RT with an additional domain results in more robust and efficient RTs.
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Affiliation(s)
- Igor P Oscorbin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Pei Fong Wong
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Ulyana A Boyarskikh
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Evgeny A Khrapov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Maksim L Filipenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
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15
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Oikonomopoulos S, Bayega A, Fahiminiya S, Djambazian H, Berube P, Ragoussis J. Methodologies for Transcript Profiling Using Long-Read Technologies. Front Genet 2020; 11:606. [PMID: 32733532 PMCID: PMC7358353 DOI: 10.3389/fgene.2020.00606] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 05/19/2020] [Indexed: 12/28/2022] Open
Abstract
RNA sequencing using next-generation sequencing technologies (NGS) is currently the standard approach for gene expression profiling, particularly for large-scale high-throughput studies. NGS technologies comprise high throughput, cost efficient short-read RNA-Seq, while emerging single molecule, long-read RNA-Seq technologies have enabled new approaches to study the transcriptome and its function. The emerging single molecule, long-read technologies are currently commercially available by Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT), while new methodologies based on short-read sequencing approaches are also being developed in order to provide long range single molecule level information-for example, the ones represented by the 10x Genomics linked read methodology. The shift toward long-read sequencing technologies for transcriptome characterization is based on current increases in throughput and decreases in cost, making these attractive for de novo transcriptome assembly, isoform expression quantification, and in-depth RNA species analysis. These types of analyses were challenging with standard short sequencing approaches, due to the complex nature of the transcriptome, which consists of variable lengths of transcripts and multiple alternatively spliced isoforms for most genes, as well as the high sequence similarity of highly abundant species of RNA, such as rRNAs. Here we aim to focus on single molecule level sequencing technologies and single-cell technologies that, combined with perturbation tools, allow the analysis of complete RNA species, whether short or long, at high resolution. In parallel, these tools have opened new ways in understanding gene functions at the tissue, network, and pathway levels, as well as their detailed functional characterization. Analysis of the epi-transcriptome, including RNA methylation and modification and the effects of such modifications on biological systems is now enabled through direct RNA sequencing instead of classical indirect approaches. However, many difficulties and challenges remain, such as methodologies to generate full-length RNA or cDNA libraries from all different species of RNAs, not only poly-A containing transcripts, and the identification of allele-specific transcripts due to current error rates of single molecule technologies, while the bioinformatics analysis on long-read data for accurate identification of 5' and 3' UTRs is still in development.
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Affiliation(s)
- Spyros Oikonomopoulos
- McGill Genome Centre, Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - Anthony Bayega
- McGill Genome Centre, Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - Somayyeh Fahiminiya
- McGill Genome Centre, Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - Haig Djambazian
- McGill Genome Centre, Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - Pierre Berube
- McGill Genome Centre, Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - Jiannis Ragoussis
- McGill Genome Centre, Department of Human Genetics, McGill University, Montréal, QC, Canada
- Department of Bioengineering, McGill University, Montréal, QC, Canada
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16
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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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17
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AP-TSS: A New Method for the Analysis of RNA Expression from Particular and Challenging Transcription Start Sites. Biomolecules 2020; 10:biom10060827. [PMID: 32481529 PMCID: PMC7355800 DOI: 10.3390/biom10060827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/12/2020] [Accepted: 05/21/2020] [Indexed: 11/25/2022] Open
Abstract
Alternative promoter usage involved in the regulation of transcription, splicing, and translation contributes to proteome diversity and is involved in a large number of diseases, in particular, cancer. Epigenetic mechanisms and cis regulatory elements are involved in alternative promoter activity. Multiple transcript isoforms can be produced from a gene, due to the initiation of transcription at different transcription start sites (TSS). These transcripts may not have regions that allow discrimination during RT-qPCR, making quantification technically challenging. This study presents a general method for the relative quantification of a transcript synthesized from a particular TSS that we called AP-TSS (analysis of particular TSS). AP-TSS is based on the specific elongation of the cDNA of interest, followed by its quantification by qPCR. As proof of principle, AP-TSS was applied to two non-coding RNA: telomeric repeat-containing RNAs (TERRA) from a particular subtelomeric TSS, and Alu transcripts. The treatment of cells with a DNA methylation inhibitor was associated with a global increase of the total TERRA level, but the TERRA expression from the TSS of interest did not change in HT1080 cells, and only modestly increased in HeLa cells. This result suggests that TERRA upregulation induced by global demethylation of the genome is mainly due to activation from sites other than this particular TSS. For Alu RNA, the signal obtained by AP-TSS is specific for the RNA Polymerase III-dependent Alu transcript. In summary, our method provides a tool to study regulation of gene expression from a given transcription start site, in different conditions that could be applied to many genes. In particular, AP-TSS can be used to investigate the epigenetic regulation of alternative TSS usage that is of importance for the development of epigenetic-targeted therapies.
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18
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Poulain S, Arnaud O, Kato S, Chen I, Ishida H, Carninci P, Plessy C. Machine-driven parameter screen of biochemical reactions. Nucleic Acids Res 2020; 48:e37. [PMID: 32025730 PMCID: PMC7144897 DOI: 10.1093/nar/gkaa079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 01/14/2020] [Accepted: 01/29/2020] [Indexed: 11/15/2022] Open
Abstract
The development of complex methods in molecular biology is a laborious, costly, iterative and often intuition-bound process where optima are sought in a multidimensional parameter space through step-by-step optimizations. The difficulty of miniaturizing reactions under the microliter volumes usually handled in multiwell plates by robots, plus the cost of the experiments, limit the number of parameters and the dynamic ranges that can be explored. Nevertheless, because of non-linearities of the response of biochemical systems to their reagent concentrations, broad dynamic ranges are necessary. Here we use a high-performance nanoliter handling platform and computer generation of liquid transfer programs to explore in quadruplicates 648 combinations of 4 parameters of a biochemical reaction, the reverse-transcription, which lead us to uncover non-linear responses, parameter interactions and novel mechanistic insights. With the increased availability of computer-driven laboratory platforms for biotechnology, our results demonstrate the feasibility and advantage of methods development based on reproducible, computer-aided exhaustive characterization of biochemical systems.
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Affiliation(s)
- Stéphane Poulain
- RIKEN Center for Life Science Technologies, Division of Genomics Technologies, Yokohama, Japan
- RIKEN Center for Integrative Medical Sciences, Division of Genomic Medicine, Yokohama, Japan
- Biomedical Microsystems Lab., Institute of Industrial Science, The University of Tokyo, Tokyo, Japan
| | - Ophélie Arnaud
- RIKEN Center for Life Science Technologies, Division of Genomics Technologies, Yokohama, Japan
| | - Sachi Kato
- RIKEN Center for Life Science Technologies, Division of Genomics Technologies, Yokohama, Japan
- RIKEN Center for Integrative Medical Sciences, Division of Genomic Medicine, Yokohama, Japan
| | | | | | - Piero Carninci
- RIKEN Center for Life Science Technologies, Division of Genomics Technologies, Yokohama, Japan
- RIKEN Center for Integrative Medical Sciences, Division of Genomic Medicine, Yokohama, Japan
| | - Charles Plessy
- RIKEN Center for Life Science Technologies, Division of Genomics Technologies, Yokohama, Japan
- RIKEN Center for Integrative Medical Sciences, Division of Genomic Medicine, Yokohama, Japan
- Okinawa Institute of Science and Technology Graduate University, Genomics and Regulatory Systems Unit, Onna-son, Japan
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19
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Attaf N, Cervera-Marzal I, Dong C, Gil L, Renand A, Spinelli L, Milpied P. FB5P-seq: FACS-Based 5-Prime End Single-Cell RNA-seq for Integrative Analysis of Transcriptome and Antigen Receptor Repertoire in B and T Cells. Front Immunol 2020; 11:216. [PMID: 32194545 PMCID: PMC7062913 DOI: 10.3389/fimmu.2020.00216] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 01/27/2020] [Indexed: 01/22/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) allows the identification, characterization, and quantification of cell types in a tissue. When focused on B and T cells of the adaptive immune system, scRNA-seq carries the potential to track the clonal lineage of each analyzed cell through the unique rearranged sequence of its antigen receptor (BCR or TCR, respectively) and link it to the functional state inferred from transcriptome analysis. Here we introduce FB5P-seq, a FACS-based 5'-end scRNA-seq method for cost-effective, integrative analysis of transcriptome and paired BCR or TCR repertoire in phenotypically defined B and T cell subsets. We describe in detail the experimental workflow and provide a robust bioinformatics pipeline for computing gene count matrices and reconstructing repertoire sequences from FB5P-seq data. We further present two applications of FB5P-seq for the analysis of human tonsil B cell subsets and peripheral blood antigen-specific CD4 T cells. We believe that our novel integrative scRNA-seq method will be a valuable option to study rare adaptive immune cell subsets in immunology research.
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Affiliation(s)
- Noudjoud Attaf
- Aix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Iñaki Cervera-Marzal
- Aix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Chuang Dong
- Aix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Laurine Gil
- Aix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Amédée Renand
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM Université de Nantes, Nantes, France
| | - Lionel Spinelli
- Aix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Pierre Milpied
- Aix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, Marseille, France
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20
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Brown EM, Ke X, Hitchcock D, Jeanfavre S, Avila-Pacheco J, Nakata T, Arthur TD, Fornelos N, Heim C, Franzosa EA, Watson N, Huttenhower C, Haiser HJ, Dillow G, Graham DB, Finlay BB, Kostic AD, Porter JA, Vlamakis H, Clish CB, Xavier RJ. Bacteroides-Derived Sphingolipids Are Critical for Maintaining Intestinal Homeostasis and Symbiosis. Cell Host Microbe 2019; 25:668-680.e7. [PMID: 31071294 DOI: 10.1016/j.chom.2019.04.002] [Citation(s) in RCA: 246] [Impact Index Per Article: 49.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 02/19/2019] [Accepted: 04/02/2019] [Indexed: 12/28/2022]
Abstract
Sphingolipids are structural membrane components and important eukaryotic signaling molecules. Sphingolipids regulate inflammation and immunity and were recently identified as the most differentially abundant metabolite in stool from inflammatory bowel disease (IBD) patients. Commensal bacteria from the Bacteroidetes phylum also produce sphingolipids, but the impact of these metabolites on host pathways is largely uncharacterized. To determine whether bacterial sphingolipids modulate intestinal health, we colonized germ-free mice with a sphingolipid-deficient Bacteroides thetaiotaomicron strain. A lack of Bacteroides-derived sphingolipids resulted in intestinal inflammation and altered host ceramide pools in mice. Using lipidomic analysis, we described a sphingolipid biosynthesis pathway and revealed a variety of Bacteroides-derived sphingolipids including ceramide phosphoinositol and deoxy-sphingolipids. Annotating Bacteroides sphingolipids in an IBD metabolomic dataset revealed lower abundances in IBD and negative correlations with inflammation and host sphingolipid production. These data highlight the role of bacterial sphingolipids in maintaining homeostasis and symbiosis in the gut.
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Affiliation(s)
- Eric M Brown
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Xiaobo Ke
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Novartis Institute for Biomedical Research Inc., Cambridge, MA 02139, USA
| | | | - Sarah Jeanfavre
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Toru Nakata
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Nadine Fornelos
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Cortney Heim
- Novartis Institute for Biomedical Research Inc., Cambridge, MA 02139, USA
| | - Eric A Franzosa
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Nicki Watson
- W. M. Keck Microscopy Facility, The Whitehead Institute, Cambridge, MA 02142, USA
| | - Curtis Huttenhower
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Henry J Haiser
- Novartis Institute for Biomedical Research Inc., Cambridge, MA 02139, USA
| | - Glen Dillow
- Novartis Institute for Biomedical Research Inc., Cambridge, MA 02139, USA
| | - Daniel B Graham
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - B Brett Finlay
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Aleksandar D Kostic
- Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA; Department of Microbiology and Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Jeffrey A Porter
- Novartis Institute for Biomedical Research Inc., Cambridge, MA 02139, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Clary B Clish
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
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21
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Lentzsch AM, Yao J, Russell R, Lambowitz AM. Template-switching mechanism of a group II intron-encoded reverse transcriptase and its implications for biological function and RNA-Seq. J Biol Chem 2019; 294:19764-19784. [PMID: 31712313 DOI: 10.1074/jbc.ra119.011337] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 11/01/2019] [Indexed: 12/18/2022] Open
Abstract
The reverse transcriptases (RTs) encoded by mobile group II introns and other non-LTR retroelements differ from retroviral RTs in being able to template-switch efficiently from the 5' end of one template to the 3' end of another with little or no complementarity between the donor and acceptor templates. Here, to establish a complete kinetic framework for the reaction and to identify conditions that more efficiently capture acceptor RNAs or DNAs, we used a thermostable group II intron RT (TGIRT; GsI-IIC RT) that can template switch directly from synthetic RNA template/DNA primer duplexes having either a blunt end or a 3'-DNA overhang end. We found that the rate and amplitude of template switching are optimal from starter duplexes with a single nucleotide 3'-DNA overhang complementary to the 3' nucleotide of the acceptor RNA, suggesting a role for nontemplated nucleotide addition of a complementary nucleotide to the 3' end of cDNAs synthesized from natural templates. Longer 3'-DNA overhangs progressively decreased the template-switching rate, even when complementary to the 3' end of the acceptor template. The reliance on only a single bp with the 3' nucleotide of the acceptor together with discrimination against mismatches and the high processivity of group II intron RTs enable synthesis of full-length DNA copies of nucleic acids beginning directly at their 3' end. We discuss the possible biological functions of the template-switching activity of group II intron- and other non-LTR retroelement-encoded RTs, as well as the optimization of this activity for adapter addition in RNA- and DNA-Seq protocols.
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Affiliation(s)
- Alfred M Lentzsch
- Institute for Cellular and Molecular Biology, Departments of Molecular Biosciences and Oncology, University of Texas at Austin, Austin, Texas 78712
| | - Jun Yao
- Institute for Cellular and Molecular Biology, Departments of Molecular Biosciences and Oncology, University of Texas at Austin, Austin, Texas 78712
| | - Rick Russell
- Institute for Cellular and Molecular Biology, Departments of Molecular Biosciences and Oncology, University of Texas at Austin, Austin, Texas 78712
| | - Alan M Lambowitz
- Institute for Cellular and Molecular Biology, Departments of Molecular Biosciences and Oncology, University of Texas at Austin, Austin, Texas 78712
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22
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Foley JW, Zhu C, Jolivet P, Zhu SX, Lu P, Meaney MJ, West RB. Gene expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ. Genome Res 2019; 29:1816-1825. [PMID: 31519740 PMCID: PMC6836736 DOI: 10.1101/gr.234807.118] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 06/20/2019] [Indexed: 11/25/2022]
Abstract
RNA sequencing (RNA-seq) is a sensitive and accurate method for quantifying gene expression. Small samples or those whose RNA is degraded, such as formalin-fixed paraffin-embedded (FFPE) tissue, remain challenging to study with nonspecialized RNA-seq protocols. Here, we present a new method, Smart-3SEQ, that accurately quantifies transcript abundance even with small amounts of total RNA and effectively characterizes small samples extracted by laser-capture microdissection (LCM) from FFPE tissue. We also obtain distinct biological profiles from FFPE single cells, which have been impossible to study with previous RNA-seq protocols, and we use these data to identify possible new macrophage phenotypes associated with the tumor microenvironment. We propose Smart-3SEQ as a highly cost-effective method to enable large gene expression profiling experiments unconstrained by sample size and tissue availability. In particular, Smart-3SEQ's compatibility with FFPE tissue unlocks an enormous number of archived clinical samples; combined with LCM it allows unprecedented studies of small cell populations and single cells isolated by their in situ context.
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Affiliation(s)
- Joseph W Foley
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
- Ludmer Centre for Neuroinformatics and Mental Health, Douglas Hospital Research Centre, McGill University, Montreal, Quebec H4H 1R3, Canada
| | - Chunfang Zhu
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Philippe Jolivet
- Ludmer Centre for Neuroinformatics and Mental Health, Douglas Hospital Research Centre, McGill University, Montreal, Quebec H4H 1R3, Canada
- Department of Biochemistry, Université de Montréal, Montreal, Quebec H3C 3J7, Canada
| | - Shirley X Zhu
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Peipei Lu
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Michael J Meaney
- Ludmer Centre for Neuroinformatics and Mental Health, Douglas Hospital Research Centre, McGill University, Montreal, Quebec H4H 1R3, Canada
| | - Robert B West
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
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23
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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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24
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Nadal-Ribelles M, Islam S, Wei W, Latorre P, Nguyen M, de Nadal E, Posas F, Steinmetz LM. Sensitive high-throughput single-cell RNA-seq reveals within-clonal transcript correlations in yeast populations. Nat Microbiol 2019; 4:683-692. [PMID: 30718850 PMCID: PMC6433287 DOI: 10.1038/s41564-018-0346-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 12/07/2018] [Indexed: 12/19/2022]
Abstract
Single-cell RNA-seq has revealed extensive cellular heterogeneity within
many organisms, but few methods have been developed for microbial clonal
populations. The yeast genome displays unusually dense transcript spacing, with
interleaved and overlapping transcription from both strands, resulting in a
minuscule but complex pool of RNA protected by a resilient cell wall. Here, we
have developed a sensitive, scalable, and inexpensive yeast single-cell RNA-seq
(yscRNA-seq) method that digitally counts transcript start sites in a strand-
and isoform-specific manner. YscRNA-seq detects the expression of low-abundant,
non-coding RNAs, and at least half of the protein-coding genome in each cell.
Within clonal cells, we observed a negative correlation for the expression of
sense/antisense pairs, while paralogs and divergent transcripts co-express.
Combining yscRNA-seq with index sorting, we uncovered a linear relationship
between cell size and RNA content. Although we detected an average of
~3.5 molecules/gene, the number of expressed isoforms are restricted at
the single-cell level. Remarkably, the expression of metabolic genes is highly
variable, while their stochastic expression primes cells for increased fitness
towards the corresponding environmental challenge. These findings suggest that
functional transcript diversity acts as a mechanism for providing a selective
advantage to individual cells within otherwise transcriptionally heterogeneous
populations.
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Affiliation(s)
- Mariona Nadal-Ribelles
- Department of Genetics, Stanford University, School of Medicine, Stanford, CA, USA.,Stanford Genome Technology Center, Stanford University, Stanford, CA, USA.,Cell Signaling Research Group. Departament de Ciències Experimentals i de la Salut., Universitat Pompeu Fabra , Barcelona, Spain.,Cell Signaling. Institute for Research in Biomedicine. Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Saiful Islam
- Department of Genetics, Stanford University, School of Medicine, Stanford, CA, USA.,Stanford Genome Technology Center, Stanford University, Stanford, CA, USA
| | - Wu Wei
- Department of Genetics, Stanford University, School of Medicine, Stanford, CA, USA.,Stanford Genome Technology Center, Stanford University, Stanford, CA, USA.,CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Pablo Latorre
- Cell Signaling Research Group. Departament de Ciències Experimentals i de la Salut., Universitat Pompeu Fabra , Barcelona, Spain.,Cell Signaling. Institute for Research in Biomedicine. Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Michelle Nguyen
- Department of Genetics, Stanford University, School of Medicine, Stanford, CA, USA.,Stanford Genome Technology Center, Stanford University, Stanford, CA, USA
| | - Eulàlia de Nadal
- Cell Signaling Research Group. Departament de Ciències Experimentals i de la Salut., Universitat Pompeu Fabra , Barcelona, Spain.,Cell Signaling. Institute for Research in Biomedicine. Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Francesc Posas
- Cell Signaling Research Group. Departament de Ciències Experimentals i de la Salut., Universitat Pompeu Fabra , Barcelona, Spain.,Cell Signaling. Institute for Research in Biomedicine. Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Lars M Steinmetz
- Department of Genetics, Stanford University, School of Medicine, Stanford, CA, USA. .,Stanford Genome Technology Center, Stanford University, Stanford, CA, USA. .,Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
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25
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Kolb L, Allazetta S, Karlsson M, Girgin M, Weber W, Lutolf MP. High-throughput stem cell-based phenotypic screening through microniches. Biomater Sci 2019; 7:3471-3479. [DOI: 10.1039/c8bm01180j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Methods for screening combinations of signals for their effects on stem cell behavior are needed in the field of tissue engineering. We introduce a microgel-based screening platform for testing combinations of proteins on stem cell fate.
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Affiliation(s)
- Laura Kolb
- Institute of Bioengineering (IBI)
- Ecole Polytechnique Fédérale de Lausanne (EPFL)
- 1015 Lausanne
- Switzerland
| | - Simone Allazetta
- Institute of Bioengineering (IBI)
- Ecole Polytechnique Fédérale de Lausanne (EPFL)
- 1015 Lausanne
- Switzerland
| | - Maria Karlsson
- BIOSS Centre for Biological Signalling Studies
- University of Freiburg
- 79108 Freiburg
- Germany
| | - Mehmet Girgin
- Institute of Bioengineering (IBI)
- Ecole Polytechnique Fédérale de Lausanne (EPFL)
- 1015 Lausanne
- Switzerland
| | - Wilfried Weber
- BIOSS Centre for Biological Signalling Studies
- University of Freiburg
- 79108 Freiburg
- Germany
| | - Matthias P. Lutolf
- Institute of Bioengineering (IBI)
- Ecole Polytechnique Fédérale de Lausanne (EPFL)
- 1015 Lausanne
- Switzerland
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26
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Sasagawa Y, Hayashi T, Nikaido I. Strategies for Converting RNA to Amplifiable cDNA for Single-Cell RNA Sequencing Methods. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1129:1-17. [PMID: 30968357 DOI: 10.1007/978-981-13-6037-4_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
This review describes the features of molecular biology techniques for single-cell RNA sequencing (scRNA-seq), including methods developed in our laboratory. Existing scRNA-seq methods require the conversion of first-strand cDNA to amplifiable cDNA followed by whole-transcript amplification. There are three primary strategies for this conversion: poly-A tagging, template switching, and RNase H-DNA polymerase I-mediated second-strand cDNA synthesis for in vitro transcription. We discuss the merits and limitations of these strategies and describe our Reverse Transcription with Random Displacement Amplification technology that allows for direct first-strand cDNA amplification from RNA without the need for conversion to an amplifiable cDNA. We believe that this review provides all users of single-cell transcriptome technologies with an understanding of the relationship between the quantitative performance of various methods and their molecular features.
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Affiliation(s)
- Yohei Sasagawa
- Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Research, Wako, Saitama, Japan
| | - Tetsutaro Hayashi
- Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Research, Wako, Saitama, Japan
| | - Itoshi Nikaido
- Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Research, Wako, Saitama, Japan.
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27
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Lafzi A, Moutinho C, Picelli S, Heyn H. Tutorial: guidelines for the experimental design of single-cell RNA sequencing studies. Nat Protoc 2018; 13:2742-2757. [DOI: 10.1038/s41596-018-0073-y] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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28
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Cvetesic N, Leitch HG, Borkowska M, Müller F, Carninci P, Hajkova P, Lenhard B. SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA. Genome Res 2018; 28:1943-1956. [PMID: 30404778 PMCID: PMC6280763 DOI: 10.1101/gr.235937.118] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 10/25/2018] [Indexed: 01/22/2023]
Abstract
Cap analysis of gene expression (CAGE) is a methodology for genome-wide quantitative mapping of mRNA 5′ ends to precisely capture transcription start sites at a single nucleotide resolution. In combination with high-throughput sequencing, CAGE has revolutionized our understanding of the rules of transcription initiation, led to discovery of new core promoter sequence features, and discovered transcription initiation at enhancers genome-wide. The biggest limitation of CAGE is that even the most recently improved version (nAnT-iCAGE) still requires large amounts of total cellular RNA (5 µg), preventing its application to scarce biological samples such as those from early embryonic development or rare cell types. Here, we present SLIC-CAGE, a Super-Low Input Carrier-CAGE approach to capture 5′ ends of RNA polymerase II transcripts from as little as 5–10 ng of total RNA. This dramatic increase in sensitivity is achieved by specially designed, selectively degradable carrier RNA. We demonstrate the ability of SLIC-CAGE to generate data for genome-wide promoterome with 1000-fold less material than required by existing CAGE methods, by generating a complex, high-quality library from mouse embryonic day 11.5 primordial germ cells.
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Affiliation(s)
- Nevena Cvetesic
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom.,MRC London Institute of Medical Sciences, London W12 0NN, United Kingdom
| | - Harry G Leitch
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom.,MRC London Institute of Medical Sciences, London W12 0NN, United Kingdom
| | - Malgorzata Borkowska
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom.,MRC London Institute of Medical Sciences, London W12 0NN, United Kingdom
| | - Ferenc Müller
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston B15 2TT, United Kingdom
| | - Piero Carninci
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama City, Kanagawa 230-0045, Japan.,RIKEN Omics Science Center, Yokohama City, Kanagawa 230-0045, Japan
| | - Petra Hajkova
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom.,MRC London Institute of Medical Sciences, London W12 0NN, United Kingdom
| | - Boris Lenhard
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom.,MRC London Institute of Medical Sciences, London W12 0NN, United Kingdom.,Sars International Centre for Marine Molecular Biology, University of Bergen, N-5008 Bergen, Norway
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29
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Abstract
Single-cell RNA sequencing (scRNA-seq) is currently transforming our understanding of biology, as it is a powerful tool to resolve cellular heterogeneity and molecular networks. Over 50 protocols have been developed in recent years and also data processing and analyzes tools are evolving fast. Here, we review the basic principles underlying the different experimental protocols and how to benchmark them. We also review and compare the essential methods to process scRNA-seq data from mapping, filtering, normalization and batch corrections to basic differential expression analysis. We hope that this helps to choose appropriate experimental and computational methods for the research question at hand.
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Affiliation(s)
- Christoph Ziegenhain
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Str. 2, Martinsried, Germany
| | - Beate Vieth
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Str. 2, Martinsried, Germany
| | - Swati Parekh
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Str. 2, Martinsried, Germany
| | - Ines Hellmann
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Str. 2, Martinsried, Germany
| | - Wolfgang Enard
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Str. 2, Martinsried, Germany
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30
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Boone M, De Koker A, Callewaert N. Capturing the 'ome': the expanding molecular toolbox for RNA and DNA library construction. Nucleic Acids Res 2018; 46:2701-2721. [PMID: 29514322 PMCID: PMC5888575 DOI: 10.1093/nar/gky167] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 02/05/2018] [Accepted: 02/23/2018] [Indexed: 12/14/2022] Open
Abstract
All sequencing experiments and most functional genomics screens rely on the generation of libraries to comprehensively capture pools of targeted sequences. In the past decade especially, driven by the progress in the field of massively parallel sequencing, numerous studies have comprehensively assessed the impact of particular manipulations on library complexity and quality, and characterized the activities and specificities of several key enzymes used in library construction. Fortunately, careful protocol design and reagent choice can substantially mitigate many of these biases, and enable reliable representation of sequences in libraries. This review aims to guide the reader through the vast expanse of literature on the subject to promote informed library generation, independent of the application.
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Affiliation(s)
- Morgane Boone
- Center for Medical Biotechnology, VIB, Zwijnaarde 9052, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent 9000, Belgium
| | - Andries De Koker
- Center for Medical Biotechnology, VIB, Zwijnaarde 9052, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent 9000, Belgium
| | - Nico Callewaert
- Center for Medical Biotechnology, VIB, Zwijnaarde 9052, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent 9000, Belgium
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31
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Ma KY, He C, Wendel BS, Williams CM, Xiao J, Yang H, Jiang N. Immune Repertoire Sequencing Using Molecular Identifiers Enables Accurate Clonality Discovery and Clone Size Quantification. Front Immunol 2018; 9:33. [PMID: 29467754 PMCID: PMC5808239 DOI: 10.3389/fimmu.2018.00033] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 01/04/2018] [Indexed: 11/13/2022] Open
Abstract
Unique molecular identifiers (MIDs) have been demonstrated to effectively improve immune repertoire sequencing (IR-seq) accuracy, especially to identify somatic hypermutations in antibody repertoire sequencing. However, evaluating the sensitivity to detect rare T cells and the degree of clonal expansion in IR-seq has been difficult due to the lack of knowledge of T cell receptor (TCR) RNA molecule copy number and a generalized approach to estimate T cell clone size from TCR RNA molecule quantification. This limited the application of TCR repertoire sequencing (TCR-seq) in clinical settings, such as detecting minimal residual disease in lymphoid malignancies after treatment, evaluating effectiveness of vaccination and assessing degree of infection. Here, we describe using an MID Clustering-based IR-Seq (MIDCIRS) method to quantitatively study TCR RNA molecule copy number and clonality in T cells. First, we demonstrated the necessity of performing MID sub-clustering to eliminate erroneous sequences. Further, we showed that MIDCIRS enables a sensitive detection of a single cell in as many as one million naïve T cells and an accurate estimation of the degree of T cell clonal expression. The demonstrated accuracy, sensitivity, and wide dynamic range of MIDCIRS TCR-seq provide foundations for future applications in both basic research and clinical settings.
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Affiliation(s)
- Ke-Yue Ma
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States
| | - Chenfeng He
- Department of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Ben S Wendel
- McKetta Department of Chemical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Chad M Williams
- Department of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Jun Xiao
- ImmuDX, LLC, Austin, TX, United States
| | - Hui Yang
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Research Center of Special Environmental Biomechanics & Medical Engineering, Xi'an, Shaanxi, China
| | - Ning Jiang
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States.,Department of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX, United States
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32
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Wendel BS, He C, Qu M, Wu D, Hernandez SM, Ma KY, Liu EW, Xiao J, Crompton PD, Pierce SK, Ren P, Chen K, Jiang N. Accurate immune repertoire sequencing reveals malaria infection driven antibody lineage diversification in young children. Nat Commun 2017; 8:531. [PMID: 28912592 PMCID: PMC5599618 DOI: 10.1038/s41467-017-00645-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 07/15/2017] [Indexed: 12/03/2022] Open
Abstract
Accurately measuring antibody repertoire sequence composition in a small amount of blood is challenging yet important for understanding repertoire responses to infection and vaccination. We develop molecular identifier clustering-based immune repertoire sequencing (MIDCIRS) and use it to study age-related antibody repertoire development and diversification before and during acute malaria in infants (< 12 months old) and toddlers (12-47 months old) with 4-8 ml of blood. Here, we show this accurate and high-coverage repertoire-sequencing method can use as few as 1000 naive B cells. Unexpectedly, we discover high levels of somatic hypermutation in infants as young as 3 months old. Antibody clonal lineage analysis reveals that somatic hypermutation levels are increased in both infants and toddlers upon infection, and memory B cells isolated from individuals who previously experienced malaria continue to induce somatic hypermutations upon malaria rechallenge. These results highlight the potential of antibody repertoire diversification in infants and toddlers.Somatic hypermutation of antibodies can occur in infants but are difficult to track. Here the authors present a new method called MIDCIRS for deep quantitative repertoire sequencing with few cells, and show infants as young as 3 months can expand antibody lineage complexity in response to malaria infection.
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Affiliation(s)
- Ben S Wendel
- McKetta Department of Chemical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Chenfeng He
- Department of Biomedical engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Mingjuan Qu
- Department of Biomedical engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX, 78712, USA
- School of Life Sciences, Ludong University, Yantai, Shandong, 264025, China
| | - Di Wu
- Department of Biomedical engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Stefany M Hernandez
- McKetta Department of Chemical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Ke-Yue Ma
- Institute for Cellular and Molecular Biology, College of Natural Sciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Eugene W Liu
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Atlanta, 30329, GA, USA
| | - Jun Xiao
- ImmuDX, LLC, Austin, TX, 78750, USA
| | - Peter D Crompton
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Susan K Pierce
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Pengyu Ren
- Department of Biomedical engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Keke Chen
- Department of Computer Science and Engineering, Wright State University, Dayton, OH, 45435, USA
| | - Ning Jiang
- Department of Biomedical engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX, 78712, USA.
- Institute for Cellular and Molecular Biology, College of Natural Sciences, University of Texas at Austin, Austin, TX, 78712, USA.
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33
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Arguel MJ, LeBrigand K, Paquet A, Ruiz García S, Zaragosi LE, Barbry P, Waldmann R. A cost effective 5΄ selective single cell transcriptome profiling approach with improved UMI design. Nucleic Acids Res 2017; 45:e48. [PMID: 27940562 PMCID: PMC5397152 DOI: 10.1093/nar/gkw1242] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 11/28/2016] [Indexed: 12/16/2022] Open
Abstract
Single cell RNA sequencing approaches are instrumental in studies of cell-to-cell variability. 5΄ selective transcriptome profiling approaches allow simultaneous definition of the transcription start size and have advantages over 3΄ selective approaches which just provide internal sequences close to the 3΄ end. The only currently existing 5΄ selective approach requires costly and labor intensive fragmentation and cell barcoding after cDNA amplification. We developed an optimized 5΄ selective workflow where all the cell indexing is done prior to fragmentation. With our protocol, cell indexing can be performed in the Fluidigm C1 microfluidic device, resulting in a significant reduction of cost and labor. We also designed optimized unique molecular identifiers that show less sequence bias and vulnerability towards sequencing errors resulting in an improved accuracy of molecule counting. We provide comprehensive experimental workflows for Illumina and Ion Proton sequencers that allow single cell sequencing in a cost range comparable to qPCR assays.
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Affiliation(s)
- Marie-Jeanne Arguel
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, F06560 Sophia Antipolis, France
| | - Kevin LeBrigand
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, F06560 Sophia Antipolis, France
| | - Agnès Paquet
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, F06560 Sophia Antipolis, France
| | - Sandra Ruiz García
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, F06560 Sophia Antipolis, France
| | - Laure-Emmanuelle Zaragosi
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, F06560 Sophia Antipolis, France
| | - Pascal Barbry
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, F06560 Sophia Antipolis, France
| | - Rainer Waldmann
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, F06560 Sophia Antipolis, France
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34
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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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35
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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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36
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Winz ML, Cahová H, Nübel G, Frindert J, Höfer K, Jäschke A. Capture and sequencing of NAD-capped RNA sequences with NAD captureSeq. Nat Protoc 2016; 12:122-149. [PMID: 27977022 DOI: 10.1038/nprot.2016.163] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Here we describe a protocol for NAD captureSeq that allows for the identification of nicotinamide-adenine dinucleotide (NAD)-capped RNA sequences in total RNA samples from different organisms. NAD-capped RNA is first chemo-enzymatically biotinylated with high efficiency, permitting selective capture on streptavidin beads. Then, a highly efficient library preparation protocol tailored to immobilized, 5'-modified RNA is applied, with adaptor ligation to the RNA's 3' terminus and reverse transcription (RT) performed on-bead. Then, cDNA is released into solution, tailed, ligated to a second adaptor and PCR-amplified. After next-generation sequencing (NGS) of the DNA library, enriched sequences are identified by comparison with a control sample in which the first step of chemo-enzymatic biotinylation is omitted. Because the downstream protocol does not necessarily rely on NAD-modified but on 'clickable' or biotin-modified RNA, it can be applied to other RNA modifications or RNA-biomolecule interactions. The central part of this protocol can be completed in ∼7 d, excluding preparatory steps, sequencing and bioinformatic analysis.
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Affiliation(s)
- Marie-Luise Winz
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
| | - Hana Cahová
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
| | - Gabriele Nübel
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
| | - Jens Frindert
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
| | - Katharina Höfer
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
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37
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Nottingham RM, Wu DC, Qin Y, Yao J, Hunicke-Smith S, Lambowitz AM. RNA-seq of human reference RNA samples using a thermostable group II intron reverse transcriptase. RNA (NEW YORK, N.Y.) 2016; 22:597-613. [PMID: 26826130 PMCID: PMC4793214 DOI: 10.1261/rna.055558.115] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 12/30/2015] [Indexed: 05/20/2023]
Abstract
Next-generation RNA sequencing (RNA-seq) has revolutionized our ability to analyze transcriptomes. Current RNA-seq methods are highly reproducible, but each has biases resulting from different modes of RNA sample preparation, reverse transcription, and adapter addition, leading to variability between methods. Moreover, the transcriptome cannot be profiled comprehensively because highly structured RNAs, such as tRNAs and snoRNAs, are refractory to conventional RNA-seq methods. Recently, we developed a new method for strand-specific RNA-seq using thermostable group II intron reverse transcriptases (TGIRTs). TGIRT enzymes have higher processivity and fidelity than conventional retroviral reverse transcriptases plus a novel template-switching activity that enables RNA-seq adapter addition during cDNA synthesis without using RNA ligase. Here, we obtained TGIRT-seq data sets for well-characterized human RNA reference samples and compared them to previous data sets obtained for these RNAs by the Illumina TruSeq v2 and v3 methods. We find that TGIRT-seq recapitulates the relative abundance of human transcripts and RNA spike-ins in ribo-depleted, fragmented RNA samples comparably to non-strand-specific TruSeq v2 and better than strand-specific TruSeq v3. Moreover, TGIRT-seq is more strand specific than TruSeq v3 and eliminates sampling biases from random hexamer priming, which are inherent to TruSeq. The TGIRT-seq data sets also show more uniform 5' to 3' gene coverage and identify more splice junctions, particularly near the 5' ends of mRNAs, than do the TruSeq data sets. Finally, TGIRT-seq enables the simultaneous profiling of mRNAs and lncRNAs in the same RNA-seq experiment as structured small ncRNAs, including tRNAs, which are essentially absent with TruSeq.
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Affiliation(s)
- Ryan M Nottingham
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, 78712, USA Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, 78712, USA
| | - Douglas C Wu
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, 78712, USA Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, 78712, USA
| | - Yidan Qin
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, 78712, USA Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, 78712, USA
| | - Jun Yao
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, 78712, USA Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, 78712, USA
| | - Scott Hunicke-Smith
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, 78712, USA
| | - Alan M Lambowitz
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, 78712, USA Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, 78712, USA
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Rubelt F, Bolen CR, McGuire HM, Vander Heiden JA, Gadala-Maria D, Levin M, Euskirchen GM, Mamedov MR, Swan GE, Dekker CL, Cowell LG, Kleinstein SH, Davis MM. Individual heritable differences result in unique cell lymphocyte receptor repertoires of naïve and antigen-experienced cells. Nat Commun 2016; 7:11112. [PMID: 27005435 PMCID: PMC5191574 DOI: 10.1038/ncomms11112] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 02/20/2016] [Indexed: 01/10/2023] Open
Abstract
The adaptive immune system's capability to protect the body requires a highly diverse lymphocyte antigen receptor repertoire. However, the influence of individual genetic and epigenetic differences on these repertoires is not typically measured. By leveraging the unique characteristics of B, CD4+ T and CD8+ T-lymphocyte subsets from monozygotic twins, we quantify the impact of heritable factors on both the V(D)J recombination process and on thymic selection. We show that the resulting biases in both V(D)J usage and N/P addition lengths, which are found in naïve and antigen experienced cells, contribute to significant variation in the CDR3 region. Moreover, we show that the relative usage of V and J gene segments is chromosomally biased, with ∼1.5 times as many rearrangements originating from a single chromosome. These data refine our understanding of the heritable mechanisms affecting the repertoire, and show that biases are evident on a chromosome-wide level. The diversity of antigen receptor specificities is largely generated by random recombination of its segments. Here the authors show, by genetic comparison of monozygotic twin lymphocyte subsets, that individual genetic and epigenetic biases also contribute to the shape of the B and T cell repertoires.
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Affiliation(s)
- Florian Rubelt
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Christopher R Bolen
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Helen M McGuire
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Jason A Vander Heiden
- Interdepartmental Program in Computational Biology and Bioinformatics, Deaptment of Computational Biology &Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
| | - Daniel Gadala-Maria
- Interdepartmental Program in Computational Biology and Bioinformatics, Deaptment of Computational Biology &Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
| | - Mikhail Levin
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Ghia M Euskirchen
- Department of Genetics, Stanford University School of Medicine, Palo Alto, California 94304, USA
| | - Murad R Mamedov
- Program in Immunology, Department of Microbiology and Immunology, Stanford University, Stanford, California 94305, USA
| | - Gary E Swan
- Stanford Prevention Research Center, Stanford University School of Medicine, Stanford, California 94304, USA
| | - Cornelia L Dekker
- Department of Pediatrics (Infectious Diseases), Stanford University School of Medicine, Stanford, California 94305, USA
| | - Lindsay G Cowell
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Steven H Kleinstein
- Interdepartmental Program in Computational Biology and Bioinformatics, Deaptment of Computational Biology &Bioinformatics, Yale University, New Haven, Connecticut 06520, USA.,Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, 06520, USA.,Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Mark M Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305, USA.,Institute of Immunity, Department of Microbiology and Immunology, Transplantation and Infection, Stanford University School of Medicine, Stanford, California 94305, USA
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39
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Monat C, Cousineau B. Circularization pathway of a bacterial group II intron. Nucleic Acids Res 2015; 44:1845-53. [PMID: 26673697 PMCID: PMC4770220 DOI: 10.1093/nar/gkv1381] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 11/26/2015] [Indexed: 12/03/2022] Open
Abstract
Group II introns are large RNA enzymes that can excise as lariats, circles or in a linear form through branching, circularization or hydrolysis, respectively. Branching is by far the main and most studied splicing pathway while circularization was mostly overlooked. We previously showed that removal of the branch point A residue from Ll.LtrB, the group II intron from Lactococcus lactis, exclusively leads to circularization. However, the majority of the released intron circles harbored an additional C residue of unknown origin at the splice junction. Here, we exploited the Ll.LtrB-ΔA mutant to study the circularization pathway of bacterial group II introns in vivo. We demonstrated that the non-encoded C residue, present at the intron circle splice junction, corresponds to the first nt of exon 2. Intron circularization intermediates, harboring the first 2 or 3 nts of exon 2, were found to accumulate showing that branch point removal leads to 3′ splice site misrecognition. Traces of properly ligated exons were also detected functionally confirming that a small proportion of Ll.LtrB-ΔA circularizes accurately. Overall, our data provide the first detailed molecular analysis of the group II intron circularization pathway and suggests that circularization is a conserved splicing pathway in bacteria.
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Affiliation(s)
- Caroline Monat
- Department of Microbiology and Immunology, Microbiome and Disease Tolerance Centre (MDTC), McGill University, Montréal, Québec, Canada H3A 2B4
| | - Benoit Cousineau
- Department of Microbiology and Immunology, Microbiome and Disease Tolerance Centre (MDTC), McGill University, Montréal, Québec, Canada H3A 2B4
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40
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Cumbie JS, Ivanchenko MG, Megraw M. NanoCAGE-XL and CapFilter: an approach to genome wide identification of high confidence transcription start sites. BMC Genomics 2015; 16:597. [PMID: 26268438 PMCID: PMC4534009 DOI: 10.1186/s12864-015-1670-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 05/29/2015] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Identifying the transcription start sites (TSS) of genes is essential for characterizing promoter regions. Several protocols have been developed to capture the 5' end of transcripts via Cap Analysis of Gene Expression (CAGE) or linker-ligation strategies such as Paired-End Analysis of Transcription Start Sites (PEAT), but often require large amounts of tissue. More recently, nanoCAGE was developed for sequencing on the Illumina GAIIx to overcome these difficulties. RESULTS Here we present the first publicly available adaptation of nanoCAGE for sequencing on recent ultra-high throughput platforms such as Illumina HiSeq-2000, and CapFilter, a computational pipeline that greatly increases confidence in TSS identification. We report excellent gene coverage, reproducibility, and precision in transcription start site discovery for samples from Arabidopsis thaliana roots. CONCLUSION nanoCAGE-XL together with CapFilter allows for genome wide identification of high confidence transcription start sites in large eukaryotic genomes.
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Affiliation(s)
- Jason S Cumbie
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA.
| | - Maria G Ivanchenko
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA.
| | - Molly Megraw
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA.
- Department of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, 97331, USA.
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, 97331, USA.
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Stäubert C, Bhuiyan H, Lindahl A, Broom OJ, Zhu Y, Islam S, Linnarsson S, Lehtiö J, Nordström A. Rewired metabolism in drug-resistant leukemia cells: a metabolic switch hallmarked by reduced dependence on exogenous glutamine. J Biol Chem 2015; 290:8348-59. [PMID: 25697355 DOI: 10.1074/jbc.m114.618769] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Cancer cells that escape induction therapy are a major cause of relapse. Understanding metabolic alterations associated with drug resistance opens up unexplored opportunities for the development of new therapeutic strategies. Here, we applied a broad spectrum of technologies including RNA sequencing, global untargeted metabolomics, and stable isotope labeling mass spectrometry to identify metabolic changes in P-glycoprotein overexpressing T-cell acute lymphoblastic leukemia (ALL) cells, which escaped a therapeutically relevant daunorubicin treatment. We show that compared with sensitive ALL cells, resistant leukemia cells possess a fundamentally rewired central metabolism characterized by reduced dependence on glutamine despite a lack of expression of glutamate-ammonia ligase (GLUL), a higher demand for glucose and an altered rate of fatty acid β-oxidation, accompanied by a decreased pantothenic acid uptake capacity. We experimentally validate our findings by selectively targeting components of this metabolic switch, using approved drugs and starvation approaches followed by cell viability analyses in both the ALL cells and in an acute myeloid leukemia (AML) sensitive/resistant cell line pair. We demonstrate how comparative metabolomics and RNA expression profiling of drug-sensitive and -resistant cells expose targetable metabolic changes and potential resistance markers. Our results show that drug resistance is associated with significant metabolic costs in cancer cells, which could be exploited using new therapeutic strategies.
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Affiliation(s)
- Claudia Stäubert
- From the Department of Molecular Biology, Umeå University, 90187 Umeå, Sweden, the Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden, the Institute of Biochemistry, Faculty of Medicine, University of Leipzig, 04103 Leipzig, Germany
| | - Hasanuzzaman Bhuiyan
- Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, 17177 Stockholm, Sweden, and
| | - Anna Lindahl
- Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, 17177 Stockholm, Sweden, and
| | - Oliver Jay Broom
- From the Department of Molecular Biology, Umeå University, 90187 Umeå, Sweden
| | - Yafeng Zhu
- Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, 17177 Stockholm, Sweden, and
| | - Saiful Islam
- the Departments of Medical Biochemistry and Biophysics and
| | | | - Janne Lehtiö
- Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, 17177 Stockholm, Sweden, and
| | - Anders Nordström
- From the Department of Molecular Biology, Umeå University, 90187 Umeå, Sweden, the Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden, Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, 17177 Stockholm, Sweden, and
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42
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Artieri CG, Fraser HB. Accounting for biases in riboprofiling data indicates a major role for proline in stalling translation. Genome Res 2014; 24:2011-21. [PMID: 25294246 PMCID: PMC4248317 DOI: 10.1101/gr.175893.114] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The recent advent of ribosome profiling-sequencing of short ribosome-bound fragments of mRNA-has offered an unprecedented opportunity to interrogate the sequence features responsible for modulating translational rates. Nevertheless, numerous analyses of the first riboprofiling data set have produced equivocal and often incompatible results. Here we analyze three independent yeast riboprofiling data sets, including two with much higher coverage than previously available, and find that all three show substantial technical sequence biases that confound interpretations of ribosomal occupancy. After accounting for these biases, we find no effect of previously implicated factors on ribosomal pausing. Rather, we find that incorporation of proline, whose unique side-chain stalls peptide synthesis in vitro, also slows the ribosome in vivo. We also reanalyze a method that implicated positively charged amino acids as the major determinant of ribosomal stalling and demonstrate that it produces false signals of stalling in low-coverage data. Our results suggest that any analysis of riboprofiling data should account for sequencing biases and sparse coverage. To this end, we establish a robust methodology that enables analysis of ribosome profiling data without prior assumptions regarding which positions spanned by the ribosome cause stalling.
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Affiliation(s)
- Carlo G Artieri
- Department of Biology, Stanford University, Stanford, California 94305, USA
| | - Hunter B Fraser
- Department of Biology, Stanford University, Stanford, California 94305, USA
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