1
|
Padhiar NH, Katneni U, Komar AA, Motorin Y, Kimchi-Sarfaty C. Advances in methods for tRNA sequencing and quantification. Trends Genet 2024; 40:276-290. [PMID: 38123442 DOI: 10.1016/j.tig.2023.11.001] [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: 08/18/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 12/23/2023]
Abstract
In the past decade tRNA sequencing (tRNA-seq) has attracted considerable attention as an important tool for the development of novel approaches to quantify highly modified tRNA species and to propel tRNA research aimed at understanding the cellular physiology and disease and development of tRNA-based therapeutics. Many methods are available to quantify tRNA abundance while accounting for modifications and tRNA charging/acylation. Advances in both library preparation methods and bioinformatic workflows have enabled developments in next-generation sequencing (NGS) workflows. Other approaches forgo NGS applications in favor of hybridization-based approaches. In this review we provide a brief comparative overview of various tRNA quantification approaches, focusing on the advantages and disadvantages of these methods, which together facilitate reliable tRNA quantification.
Collapse
Affiliation(s)
- Nigam H Padhiar
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics, Office of Therapeutic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Upendra Katneni
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics, Office of Therapeutic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Anton A Komar
- Department of Biological, Geological, and Environmental Sciences, Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, OH, USA
| | - Yuri Motorin
- CNRS-Université de Lorraine, UAR 2008, IBSLor UMR 7365 IMoPA, Nancy, France.
| | - Chava Kimchi-Sarfaty
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics, Office of Therapeutic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA.
| |
Collapse
|
2
|
Lucas MC, Pryszcz LP, Medina R, Milenkovic I, Camacho N, Marchand V, Motorin Y, Ribas de Pouplana L, Novoa EM. Quantitative analysis of tRNA abundance and modifications by nanopore RNA sequencing. Nat Biotechnol 2024; 42:72-86. [PMID: 37024678 DOI: 10.1038/s41587-023-01743-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 03/08/2023] [Indexed: 04/08/2023]
Abstract
Transfer RNAs (tRNAs) play a central role in protein translation. Studying them has been difficult in part because a simple method to simultaneously quantify their abundance and chemical modifications is lacking. Here we introduce Nano-tRNAseq, a nanopore-based approach to sequence native tRNA populations that provides quantitative estimates of both tRNA abundances and modification dynamics in a single experiment. We show that default nanopore sequencing settings discard the vast majority of tRNA reads, leading to poor sequencing yields and biased representations of tRNA abundances based on their transcript length. Re-processing of raw nanopore current intensity signals leads to a 12-fold increase in the number of recovered tRNA reads and enables recapitulation of accurate tRNA abundances. We then apply Nano-tRNAseq to Saccharomyces cerevisiae tRNA populations, revealing crosstalks and interdependencies between different tRNA modification types within the same molecule and changes in tRNA populations in response to oxidative stress.
Collapse
Affiliation(s)
- Morghan C Lucas
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Leszek P Pryszcz
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Rebeca Medina
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ivan Milenkovic
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Noelia Camacho
- Institute for Research in Biomedicine (IRB), Barcelona, Spain
| | - Virginie Marchand
- CNRS-Université de Lorraine, UAR2008 IBSLor/UMR7365 IMoPA, Nancy, France
| | - Yuri Motorin
- CNRS-Université de Lorraine, UAR2008 IBSLor/UMR7365 IMoPA, Nancy, France
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB), Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Eva Maria Novoa
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| |
Collapse
|
3
|
Lieber CM, Aggarwal M, Yoon JJ, Cox RM, Kang HJ, Sourimant J, Toots M, Johnson SK, Jones CA, Sticher ZM, Kolykhalov AA, Saindane MT, Tompkins SM, Planz O, Painter GR, Natchus MG, Sakamoto K, Plemper RK. 4'-Fluorouridine mitigates lethal infection with pandemic human and highly pathogenic avian influenza viruses. PLoS Pathog 2023; 19:e1011342. [PMID: 37068076 PMCID: PMC10138230 DOI: 10.1371/journal.ppat.1011342] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 04/27/2023] [Accepted: 04/03/2023] [Indexed: 04/18/2023] Open
Abstract
Influenza outbreaks are associated with substantial morbidity, mortality and economic burden. Next generation antivirals are needed to treat seasonal infections and prepare against zoonotic spillover of avian influenza viruses with pandemic potential. Having previously identified oral efficacy of the nucleoside analog 4'-Fluorouridine (4'-FlU, EIDD-2749) against SARS-CoV-2 and respiratory syncytial virus (RSV), we explored activity of the compound against seasonal and highly pathogenic influenza (HPAI) viruses in cell culture, human airway epithelium (HAE) models, and/or two animal models, ferrets and mice, that assess IAV transmission and lethal viral pneumonia, respectively. 4'-FlU inhibited a panel of relevant influenza A and B viruses with nanomolar to sub-micromolar potency in HAE cells. In vitro polymerase assays revealed immediate chain termination of IAV polymerase after 4'-FlU incorporation, in contrast to delayed chain termination of SARS-CoV-2 and RSV polymerase. Once-daily oral treatment of ferrets with 2 mg/kg 4'-FlU initiated 12 hours after infection rapidly stopped virus shedding and prevented transmission to untreated sentinels. Treatment of mice infected with a lethal inoculum of pandemic A/CA/07/2009 (H1N1)pdm09 (pdmCa09) with 4'-FlU alleviated pneumonia. Three doses mediated complete survival when treatment was initiated up to 60 hours after infection, indicating a broad time window for effective intervention. Therapeutic oral 4'-FlU ensured survival of animals infected with HPAI A/VN/12/2003 (H5N1) and of immunocompromised mice infected with pdmCa09. Recoverees were protected against homologous reinfection. This study defines the mechanistic foundation for high sensitivity of influenza viruses to 4'-FlU and supports 4'-FlU as developmental candidate for the treatment of seasonal and pandemic influenza.
Collapse
Affiliation(s)
- Carolin M Lieber
- Center for Translational Antiviral Research, Georgia State University Institute for Biomedical Sciences, Atlanta, Georgia, United States of America
| | - Megha Aggarwal
- Center for Translational Antiviral Research, Georgia State University Institute for Biomedical Sciences, Atlanta, Georgia, United States of America
| | - Jeong-Joong Yoon
- Center for Translational Antiviral Research, Georgia State University Institute for Biomedical Sciences, Atlanta, Georgia, United States of America
| | - Robert M Cox
- Center for Translational Antiviral Research, Georgia State University Institute for Biomedical Sciences, Atlanta, Georgia, United States of America
| | - Hae-Ji Kang
- Center for Translational Antiviral Research, Georgia State University Institute for Biomedical Sciences, Atlanta, Georgia, United States of America
| | - Julien Sourimant
- Center for Translational Antiviral Research, Georgia State University Institute for Biomedical Sciences, Atlanta, Georgia, United States of America
| | - Mart Toots
- Center for Translational Antiviral Research, Georgia State University Institute for Biomedical Sciences, Atlanta, Georgia, United States of America
| | - Scott K Johnson
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia, United States of America
| | - Cheryl A Jones
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia, United States of America
| | - Zachary M Sticher
- Emory Institute for Drug Development, Emory University, Atlanta, Georgia, United States of America
| | - Alexander A Kolykhalov
- Emory Institute for Drug Development, Emory University, Atlanta, Georgia, United States of America
| | - Manohar T Saindane
- Emory Institute for Drug Development, Emory University, Atlanta, Georgia, United States of America
| | - Stephen M Tompkins
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia, United States of America
| | - Oliver Planz
- Department of Immunology, Interfaculty Institute for Cell Biology, Eberhard Karls University Tübingen, Tübingen, Germany
| | - George R Painter
- Emory Institute for Drug Development, Emory University, Atlanta, Georgia, United States of America
| | - Michael G Natchus
- Emory Institute for Drug Development, Emory University, Atlanta, Georgia, United States of America
| | - Kaori Sakamoto
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Richard K Plemper
- Center for Translational Antiviral Research, Georgia State University Institute for Biomedical Sciences, Atlanta, Georgia, United States of America
| |
Collapse
|
4
|
Dudek CA, Jahn D. PRODORIC: state-of-the-art database of prokaryotic gene regulation. Nucleic Acids Res 2021; 50:D295-D302. [PMID: 34850133 PMCID: PMC8728284 DOI: 10.1093/nar/gkab1110] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/12/2021] [Accepted: 11/01/2021] [Indexed: 11/14/2022] Open
Abstract
PRODORIC is worldwide one of the largest collections of prokaryotic transcription factor binding sites from multiple bacterial sources with corresponding interpretation and visualization tools. With the introduction of PRODORIC2 in 2017, the transition to a modern web interface and maintainable backend was started. With this latest PRODORIC release the database backend is now fully API-based and provides programmatical access to the complete PRODORIC data. The visualization tools Genome Browser and ProdoNet from the original PRODORIC have been reintroduced and were integrated into the PRODORIC website. Missing input and output options from the original Virtual Footprint were added again for position weight matrix pattern-based searches. The whole PRODORIC dataset was reannotated. Every transcription factor binding site was re-evaluated to increase the overall database quality. During this process, additional parameters, like bound effectors, regulation type and different types of experimental evidence have been added for every transcription factor. Additionally, 109 new transcription factors and 6 new organisms have been added. PRODORIC is publicly available at https://www.prodoric.de.
Collapse
Affiliation(s)
- Christian-Alexander Dudek
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, Braunschweig D-38106, Germany
| | - Dieter Jahn
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, Braunschweig D-38106, Germany
| |
Collapse
|
5
|
Li J, Zhu WY, Yang WQ, Li CT, Liu RJ. The occurrence order and cross-talk of different tRNA modifications. SCIENCE CHINA. LIFE SCIENCES 2021; 64:1423-1436. [PMID: 33881742 DOI: 10.1007/s11427-020-1906-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 03/02/2021] [Indexed: 06/12/2023]
Abstract
Chemical modifications expand the composition of RNA molecules from four standard nucleosides to over 160 modified nucleosides, which greatly increase the complexity and utility of RNAs. Transfer RNAs (tRNAs) are the most heavily modified cellular RNA molecules and contain the largest variety of modifications. Modification of tRNAs is pivotal for protein synthesis and also precisely regulates the noncanonical functions of tRNAs. Defects in tRNA modifications lead to numerous human diseases. Up to now, more than 100 types of modifications have been found in tRNAs. Intriguingly, some modifications occur widely on all tRNAs, while others only occur on a subgroup of tRNAs or even only a specific tRNA. The modification frequency of each tRNA is approximately 7% to 25%, with 5-20 modification sites present on each tRNA. The occurrence and modulation of tRNA modifications are specifically noticeable as plenty of interplays among different sites and modifications have been discovered. In particular, tRNA modifications are responsive to environmental changes, indicating their dynamic and highly organized nature. In this review, we summarized the known occurrence order, cross-talk, and cooperativity of tRNA modifications.
Collapse
Affiliation(s)
- Jing Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Wen-Yu Zhu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Wen-Qing Yang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Cai-Tao Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Ru-Juan Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| |
Collapse
|
6
|
Oh KW, Kim K, Islam MM, Jung HW, Lim D, Lee JC, Shin M. Transcriptional Regulation of the Outer Membrane Protein A in Acinetobacter baumannii. Microorganisms 2020; 8:microorganisms8050706. [PMID: 32403355 PMCID: PMC7284552 DOI: 10.3390/microorganisms8050706] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/05/2020] [Accepted: 05/08/2020] [Indexed: 01/19/2023] Open
Abstract
Acinetobacter baumannii is known for its virulence in severely ill, hospitalized patients and for exhibiting multidrug resistance. A. baumannii infection treatment poses a serious problem in clinical environments. The outer membrane protein A (OmpA) of the Acinetobacter genus is involved in bacterial virulence. Regulatory factors of OmpA in the post-transcriptional stage have been previously identified. However, the regulatory factors that act before the transcriptional stage remain unclear. We investigated the A1S_0316 gene that encodes a putative transcription factor for OmpA expression in A. baumannii. A1S_0316 was purified and examined using size-exclusion chromatography, which revealed that it forms an oligomer. The binding affinity of A1S_0316 to the OmpA promoter region was also examined. We compared the binding affinity to the OmpA promotor region between A1S_0316 and the AbH-NS protein. A1S_0316 showed higher binding affinity to the OmpA promotor region than did H-NS. We examined the regulatory effect of these proteins on OmpA expression in A. baumannii using real-time qPCR and various in vitro tools. Our results indicated that A1S_0316 acts as an anti-repressor on the promotor region of the OmpA gene by inhibiting the binding of the AbH-NS protein. This study was the first demonstration of the transcriptional regulation of OmpA expression.
Collapse
Affiliation(s)
- Kyu-Wan Oh
- Department of Microbiology, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu 41944, Korea; (K.-W.O.); (K.K.); (M.M.I.); (H.-W.J.); (J.C.L.)
| | - Kyeongmin Kim
- Department of Microbiology, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu 41944, Korea; (K.-W.O.); (K.K.); (M.M.I.); (H.-W.J.); (J.C.L.)
| | - Md. Maidul Islam
- Department of Microbiology, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu 41944, Korea; (K.-W.O.); (K.K.); (M.M.I.); (H.-W.J.); (J.C.L.)
| | - Hye-Won Jung
- Department of Microbiology, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu 41944, Korea; (K.-W.O.); (K.K.); (M.M.I.); (H.-W.J.); (J.C.L.)
| | - Daejin Lim
- Department of Microbiology, School of Medicine, Chonnam National University, Gwangju 61468, Korea;
| | - Je Chul Lee
- Department of Microbiology, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu 41944, Korea; (K.-W.O.); (K.K.); (M.M.I.); (H.-W.J.); (J.C.L.)
| | - Minsang Shin
- Department of Microbiology, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu 41944, Korea; (K.-W.O.); (K.K.); (M.M.I.); (H.-W.J.); (J.C.L.)
- Correspondence: ; Tel.: +82-53-420-4841
| |
Collapse
|
7
|
Gupta SK, Angara RK, Yousuf S, Reddy CG, Ranjan A. Ectopic Expression of Rv0023 Mediates Isoniazid/Ethionamide Tolerance via Altering NADH/NAD + Levels in Mycobacterium smegmatis. Front Microbiol 2020; 11:3. [PMID: 32117088 PMCID: PMC7020754 DOI: 10.3389/fmicb.2020.00003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 01/03/2020] [Indexed: 02/01/2023] Open
Abstract
Tuberculosis (TB) caused by Mycobacterium tuberculosis (Mtb) accounts for nearly 1.2 million deaths per annum worldwide. Due to the emergence of multidrug-resistant (MDR) Mtb strains, TB, a curable and avertable disease, remains one of the leading causes of morbidity and mortality. Isoniazid (INH) is a first-line anti-TB drug while ethionamide (ETH) is used as a second-line anti-TB drug. INH and ETH resistance develop through a network of genes involved in various biosynthetic pathways. In this study, we identified Rv0023, an Mtb protein belonging to the xenobiotic response element (XRE) family of transcription regulators, which has a role in generating higher tolerance toward INH and ETH in Mycobacterium smegmatis (Msmeg). Overexpression of Rv0023 in Msmeg leads to the development of INH- and ETH-tolerant strains. The strains expressing Rv0023 have a higher ratio of NADH/NAD+, and this physiological event is known to play a crucial role in the development of INH/ETH co-resistance in Msmeg. Gene expression analysis of some target genes revealed reduction in the expression of the ndh gene, but no direct interaction was observed between Rv0023 and the ndh promoter region. Rv0023 is divergently expressed to Rv0022c (whiB5) and we observed a direct interaction between the recombinant Rv0023 protein with the upstream region of Rv0022c, confirmed using reporter constructs of Msmeg. However, we found no indication that this interaction might play a role in the development of INH/ETH drug tolerance.
Collapse
Affiliation(s)
- Shailesh Kumar Gupta
- Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India.,Graduate Studies, Manipal Academy of Higher Education, Manipal, India
| | - Rajendra Kumar Angara
- Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Suhail Yousuf
- Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Chilakala Gangi Reddy
- Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India.,Regional Centre for Biotechnology, Faridabad, India
| | - Akash Ranjan
- Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| |
Collapse
|
8
|
Desgranges E, Caldelari I, Marzi S, Lalaouna D. Navigation through the twists and turns of RNA sequencing technologies: Application to bacterial regulatory RNAs. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194506. [PMID: 32068131 DOI: 10.1016/j.bbagrm.2020.194506] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 02/11/2020] [Accepted: 02/13/2020] [Indexed: 12/20/2022]
Abstract
Discovered in the 1980s, small regulatory RNAs (sRNAs) are now considered key actors in virtually all aspects of bacterial physiology and virulence. Together with transcriptional and translational regulatory proteins, they integrate and often are hubs of complex regulatory networks, responsible for bacterial response/adaptation to various perceived stimuli. The recent development of powerful RNA sequencing technologies has facilitated the identification and characterization of sRNAs (length, structure and expression conditions) and their RNA targets in several bacteria. Nevertheless, it could be very difficult for non-experts to understand the advantages and drawbacks related to each offered option and, consequently, to make an informed choice. Therefore, the main goal of this review is to provide a guide to navigate through the twists and turns of high-throughput RNA sequencing technologies, with a specific focus on those applied to the study of sRNAs. This article is part of a Special Issue entitled: RNA and gene control in bacteria edited by Dr. M. Guillier and F. Repoila.
Collapse
Affiliation(s)
- Emma Desgranges
- Université de Strasbourg, CNRS, ARN UPR 9002, F-67000 Strasbourg, France
| | - Isabelle Caldelari
- Université de Strasbourg, CNRS, ARN UPR 9002, F-67000 Strasbourg, France
| | - Stefano Marzi
- Université de Strasbourg, CNRS, ARN UPR 9002, F-67000 Strasbourg, France
| | - David Lalaouna
- Université de Strasbourg, CNRS, ARN UPR 9002, F-67000 Strasbourg, France.
| |
Collapse
|
9
|
Deshpande S, Yang Y, Chilkoti A, Zauscher S. Enzymatic synthesis and modification of high molecular weight DNA using terminal deoxynucleotidyl transferase. Methods Enzymol 2019; 627:163-188. [PMID: 31630739 PMCID: PMC7241426 DOI: 10.1016/bs.mie.2019.07.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The recognition that nucleic acids can be used as polymeric materials led to the blossoming of the field of DNA nanotechnology, with a broad range of applications in biotechnology, biosensors, diagnostics, and drug delivery. These applications require efficient methods to synthesize and chemically modify high molecular weight DNA. Here, we discuss terminal deoxynucleotidyl transferase (TdT)-catalyzed enzymatic polymerization (TcEP) as an alternative to conventional enzymatic and solid-phase DNA synthesis. We describe biochemical requirements for TcEP and provide step-by-step protocols to carry out TcEP in solution and from surfaces.
Collapse
Affiliation(s)
- Sonal Deshpande
- Department of Biomedical Engineering, Duke University, Durham, NC, United States
| | - Yunqi Yang
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, United States
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, NC, United States; Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, United States.
| | - Stefan Zauscher
- Department of Biomedical Engineering, Duke University, Durham, NC, United States; Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, United States.
| |
Collapse
|
10
|
Shrestha A, Khan A, Dey N. Identification of Novel Pararetroviral Promoters for Designing Efficient Plant Gene Expression Systems. Methods Mol Biol 2019; 1991:207-222. [PMID: 31041775 DOI: 10.1007/978-1-4939-9458-8_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Plant-infecting viruses, particularly the Pararetroviruses, have been used for many years as versatile genetic resources to design efficient plant expression vectors. The Pararetroviruses (members of the Caulimoviridae) typically contain two transcriptional promoters (the sub-genomic transcript promoter and the full-length transcript promoter) and 6-7 overlapping open reading frames (ORFs) with a genome size of 7-9 kB. Their promoter elements have been extensively exploited during the last two decades to construct effective gene expression systems. At the same time, the caulimoviral promoters have also been genetically manipulated with different molecular approaches to develop synthetic "chimeras" exhibiting precise functionality. Native and "tailor-made" synthetic promoters of Pararetroviruses are particularly attractive for formulating unique gene expression cassettes that perform extremely well in gene-stacking and gene-pyramiding in plant cells. In this chapter, we will mainly discuss important protocols associated with identifying novel/unique pararetroviral promoters that have optimal lengths with appropriate activities for developing efficient plant gene expression systems.
Collapse
Affiliation(s)
- Ankita Shrestha
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, Government of India, Bhubaneswar, Odisha, India
| | - Ahamed Khan
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, Government of India, Bhubaneswar, Odisha, India
| | - Nrisingha Dey
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, Government of India, Bhubaneswar, Odisha, India.
| |
Collapse
|
11
|
Xu H, Fair BJ, Dwyer ZW, Gildea M, Pleiss JA. Detection of splice isoforms and rare intermediates using multiplexed primer extension sequencing. Nat Methods 2018; 16:55-58. [PMID: 30573814 PMCID: PMC6414223 DOI: 10.1038/s41592-018-0258-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 11/08/2018] [Indexed: 01/05/2023]
Abstract
Targeted RNA-sequencing aims to focus coverage on areas of interest that are inadequately sampled in standard RNA-sequencing experiments. Here we present a novel approach for targeted RNA-sequencing that uses complex pools of reverse transcription primers to enable sequencing enrichment at user-selected locations across the genome. We demonstrate this approach by targeting hundreds to thousands of pre-mRNA splice junctions, revealing high-precision detection of splice isoforms, including rare pre-mRNA splicing intermediates.
Collapse
Affiliation(s)
- Hansen Xu
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Benjamin J Fair
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Zachary W Dwyer
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Michael Gildea
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Jeffrey A Pleiss
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
| |
Collapse
|
12
|
Thermal and Nutritional Regulation of Ribosome Hibernation in Staphylococcus aureus. J Bacteriol 2018; 200:JB.00426-18. [PMID: 30297357 PMCID: PMC6256015 DOI: 10.1128/jb.00426-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 09/25/2018] [Indexed: 12/13/2022] Open
Abstract
The dimerization of 70S ribosomes (100S complex) plays an important role in translational regulation and infectivity of the major human pathogen Staphylococcus aureus. Although the dimerizing factor HPF has been characterized biochemically, the pathways that regulate 100S ribosome abundance remain elusive. We identified a metabolite- and nutrient-sensing transcription factor, CodY, that serves both as an activator and a repressor of hpf expression in nutrient- and temperature-dependent manners. Furthermore, CodY-mediated activation of hpf masks a secondary hpf transcript derived from a general stress response SigB promoter. CodY and SigB regulate a repertoire of virulence genes. The unexpected link between ribosome homeostasis and the two master virulence regulators provides new opportunities for alternative druggable sites. The translationally silent 100S ribosome is a poorly understood form of the dimeric 70S complex that is ubiquitously found in all bacterial phyla. The elimination of the hibernating 100S ribosome leads to translational derepression, ribosome instability, antibiotic sensitivity, and biofilm defects in some bacteria. In Firmicutes, such as the opportunistic pathogen Staphylococcus aureus, a 190-amino acid protein called hibernating-promoting factor (HPF) dimerizes and conjoins two 70S ribosomes through a direct interaction between the HPF homodimer, with each HPF monomer tethered on an individual 70S complex. While the formation of the 100S ribosome in gammaproteobacteria and cyanobacteria is exclusively induced during postexponential growth phase and darkness, respectively, the 100S ribosomes in Firmicutes are constitutively produced from the lag-logarithmic phase through the post-stationary phase. Very little is known about the regulatory pathways that control hpf expression and 100S ribosome abundance. Here, we show that a general stress response (GSR) sigma factor (SigB) and a GTP-sensing transcription factor (CodY) integrate nutrient and thermal signals to regulate hpf synthesis in S. aureus, resulting in an enhanced virulence of the pathogen in a mouse model of septicemic infection. CodY-dependent regulation of hpf is strain specific. An epistasis analysis further demonstrated that CodY functions upstream of the GSR pathway in a condition-dependent manner. The results reveal an important link between S. aureus stress physiology, ribosome metabolism, and infection biology. IMPORTANCE The dimerization of 70S ribosomes (100S complex) plays an important role in translational regulation and infectivity of the major human pathogen Staphylococcus aureus. Although the dimerizing factor HPF has been characterized biochemically, the pathways that regulate 100S ribosome abundance remain elusive. We identified a metabolite- and nutrient-sensing transcription factor, CodY, that serves both as an activator and a repressor of hpf expression in nutrient- and temperature-dependent manners. Furthermore, CodY-mediated activation of hpf masks a secondary hpf transcript derived from a general stress response SigB promoter. CodY and SigB regulate a repertoire of virulence genes. The unexpected link between ribosome homeostasis and the two master virulence regulators provides new opportunities for alternative druggable sites.
Collapse
|
13
|
Shrestha A, Khan A, Mishra DR, Bhuyan K, Sahoo B, Maiti IB, Dey N. RETRACTED: WRKY71 and TGA1a physically interact and synergistically regulate the activity of a novel promoter isolated from Petunia vein-clearing virus. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2018; 1861:133-146. [PMID: 29413896 DOI: 10.1016/j.bbagrm.2018.01.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/28/2017] [Accepted: 01/12/2018] [Indexed: 11/23/2022]
Abstract
Caulimoviral promoters have become excellent tools for efficient transgene expression in plants. However, the transcriptional framework controlling their systematic regulation is poorly understood. To understand this regulatory mechanism, we extensively studied a novel caulimoviral promoter, PV8 (-163 to +138, 301 bp), isolated from Petunia vein-clearing virus (PVCV). PVCV was found to be Salicylic acid (SA)-inducible and 2.5-3.0 times stronger than the widely used CaMV35S promoter. In silico analysis of the PV8 sequence revealed a unique clustering of two stress-responsive cis-elements, namely, as-11 and W-box1-2, located within a span of 31 bp (-74 to -47) that bound to the TGA1a and WRKY71 plant transcription factors (TFs), respectively. We found that as-1 (TTACG) and W-box (TGAC) elements occupied both TGA1a and WRKY71 on the PV8 backbone. Mutational studies demonstrated that the combinatorial influence of as-1 (-57) and W-box1-2 (-74 and -47) on the PV8 promoter sequence largely modulated its activity. TGA1a and WRKY71 physically interacted and cooperatively enhanced the transcriptional activity of the PV8 promoter. Biotic stress stimuli induced PV8 promoter activity by ~1.5 times. We also established the possible pathogen-elicitor function of AtWRKY71 and NtabWRKY71 TFs. Altogether, this study elucidates the interplay between TFs, biotic stress and caulimoviral promoter function.
Collapse
Affiliation(s)
- Ankita Shrestha
- Division of Gene Function and Regulation, Institute of Life Sciences, Government of India, Chandrasekharpur, Bhubaneswar, Odisha, India
| | - Ahamed Khan
- Division of Gene Function and Regulation, Institute of Life Sciences, Government of India, Chandrasekharpur, Bhubaneswar, Odisha, India
| | - Dipti Ranjan Mishra
- Division of Gene Function and Regulation, Institute of Life Sciences, Government of India, Chandrasekharpur, Bhubaneswar, Odisha, India
| | - Kashyap Bhuyan
- Division of Gene Function and Regulation, Institute of Life Sciences, Government of India, Chandrasekharpur, Bhubaneswar, Odisha, India
| | - Bhabani Sahoo
- Division of Gene Function and Regulation, Institute of Life Sciences, Government of India, Chandrasekharpur, Bhubaneswar, Odisha, India
| | - Indu B Maiti
- Department of Molecular Plant Virology and Plant Genetic Engineering, KTRDC, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY 40546-0236, United States
| | - Nrisingha Dey
- Division of Gene Function and Regulation, Institute of Life Sciences, Government of India, Chandrasekharpur, Bhubaneswar, Odisha, India
| |
Collapse
|
14
|
Khan A, Shrestha A, Bhuyan K, Maiti IB, Dey N. Structural characterization of a novel full-length transcript promoter from Horseradish Latent Virus (HRLV) and its transcriptional regulation by multiple stress responsive transcription factors. PLANT MOLECULAR BIOLOGY 2018; 96:179-196. [PMID: 29327227 DOI: 10.1007/s11103-017-0693-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/04/2017] [Indexed: 06/07/2023]
Abstract
KEY MESSAGE The promoter fragment described in this study can be employed for strong transgene expression under both biotic and abiotic stress conditions. Plant-infecting Caulimoviruses have evolved multiple regulatory mechanisms to address various environmental stimuli during the course of evolution. One such mechanism involves the retention of discrete stress responsive cis-elements which are required for their survival and host-specificity. Here we describe the characterization of a novel Caulimoviral promoter isolated from Horseradish Latent Virus (HRLV) and its regulation by multiple stress responsive Transcription factors (TFs) namely DREB1, AREB1 and TGA1a. The activity of full length transcript (Flt-) promoter from HRLV (- 677 to + 283) was investigated in both transient and transgenic assays where we identified H12 (- 427 to + 73) as the highest expressing fragment having ~ 2.5-fold stronger activity than the CaMV35S promoter. The H12 promoter was highly active and near-constitutive in the vegetative and reproductive parts of both Tobacco and Arabidopsis transgenic plants. Interestingly, H12 contains a distinct cluster of cis-elements like dehydration-responsive element (DRE-core; GCCGAC), an ABA-responsive element (ABRE; ACGTGTC) and as-1 element (TGACG) which are known to be induced by cold, drought and pathogen/SA respectively. The specific binding of DREB1, AREB1 and TGA1a to DRE, ABRE and as-1 elements respectively were confirmed by the gel-binding assays using H12 promoter-specific probes. Detailed mutational analysis of the H12 promoter suggested that the presence of DRE-core and as-1 element was indispensable for its activity which was further confirmed by the transactivation assays. Our studies imply that H12 could be a valuable genetic tool for regulated transgene expression under diverse environmental conditions.
Collapse
Affiliation(s)
- Ahamed Khan
- Department of Gene Function and Regulation, Department of Biotechnology, Government of India, Institute of Life Sciences, Chandrasekharpur, Bhubaneswar, Odisha, India
| | - Ankita Shrestha
- Department of Gene Function and Regulation, Department of Biotechnology, Government of India, Institute of Life Sciences, Chandrasekharpur, Bhubaneswar, Odisha, India
| | - Kashyap Bhuyan
- Department of Gene Function and Regulation, Department of Biotechnology, Government of India, Institute of Life Sciences, Chandrasekharpur, Bhubaneswar, Odisha, India
| | - Indu B Maiti
- Department of Molecular Plant Virology and Plant Genetic Engineering, KTRDC, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, 40546-0236, USA
| | - Nrisingha Dey
- Department of Gene Function and Regulation, Department of Biotechnology, Government of India, Institute of Life Sciences, Chandrasekharpur, Bhubaneswar, Odisha, India.
| |
Collapse
|
15
|
Baumann DG, Gilmour DS. A sequence-specific core promoter-binding transcription factor recruits TRF2 to coordinately transcribe ribosomal protein genes. Nucleic Acids Res 2017; 45:10481-10491. [PMID: 28977400 PMCID: PMC5737516 DOI: 10.1093/nar/gkx676] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 07/24/2017] [Indexed: 12/13/2022] Open
Abstract
Ribosomal protein (RP) genes must be coordinately expressed for proper assembly of the ribosome yet the mechanisms that control expression of RP genes in metazoans are poorly understood. Recently, TATA-binding protein-related factor 2 (TRF2) rather than the TATA-binding protein (TBP) was found to function in transcription of RP genes in Drosophila. Unlike TBP, TRF2 lacks sequence-specific DNA binding activity, so the mechanism by which TRF2 is recruited to promoters is unclear. We show that the transcription factor M1BP, which associates with the core promoter region, activates transcription of RP genes. Moreover, M1BP directly interacts with TRF2 to recruit it to the RP gene promoter. High resolution ChIP-exo was used to analyze in vivo the association of M1BP, TRF2 and TFIID subunit, TAF1. Despite recent work suggesting that TFIID does not associate with RP genes in Drosophila, we find that TAF1 is present at RP gene promoters and that its interaction might also be directed by M1BP. Although M1BP associates with thousands of genes, its colocalization with TRF2 is largely restricted to RP genes, suggesting that this combination is key to coordinately regulating transcription of the majority of RP genes in Drosophila.
Collapse
Affiliation(s)
- Douglas G Baumann
- The Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - David S Gilmour
- The Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| |
Collapse
|
16
|
[Letter to the Editor] Incorrect assignment of affected nucleotides in footprinting/probing experiments. Biotechniques 2017; 63:105-106. [PMID: 28911313 DOI: 10.2144/000114585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 07/19/2017] [Indexed: 11/23/2022] Open
Abstract
Address correspondence to Sergey Belikov or Lars Wieslander, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden. E-mail: sergey.belikov@su.se or lars.wieslander@su.se.
Collapse
|
17
|
Wongpalee SP, Vashisht A, Sharma S, Chui D, Wohlschlegel JA, Black DL. Large-scale remodeling of a repressed exon ribonucleoprotein to an exon definition complex active for splicing. eLife 2016; 5. [PMID: 27882870 PMCID: PMC5122456 DOI: 10.7554/elife.19743] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 11/02/2016] [Indexed: 12/31/2022] Open
Abstract
Polypyrimidine-tract binding protein PTBP1 can repress splicing during the exon definition phase of spliceosome assembly, but the assembly steps leading to an exon definition complex (EDC) and how PTBP1 might modulate them are not clear. We found that PTBP1 binding in the flanking introns allowed normal U2AF and U1 snRNP binding to the target exon splice sites but blocked U2 snRNP assembly in HeLa nuclear extract. Characterizing a purified PTBP1-repressed complex, as well as an active early complex and the final EDC by SILAC-MS, we identified extensive PTBP1-modulated changes in exon RNP composition. The active early complex formed in the absence of PTBP1 proceeded to assemble an EDC with the eviction of hnRNP proteins, the late recruitment of SR proteins, and binding of the U2 snRNP. These results demonstrate that during early stages of splicing, exon RNP complexes are highly dynamic with many proteins failing to bind during PTBP1 arrest. DOI:http://dx.doi.org/10.7554/eLife.19743.001
Collapse
Affiliation(s)
- Somsakul Pop Wongpalee
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, United States
| | - Ajay Vashisht
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, United States
| | - Shalini Sharma
- Department of Basic Medical Sciences, University of Arizona, Phoenix, United States
| | - Darryl Chui
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, United States
| | - James A Wohlschlegel
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, United States
| | - Douglas L Black
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, United States
| |
Collapse
|
18
|
The Expression of Antibiotic Resistance Methyltransferase Correlates with mRNA Stability Independently of Ribosome Stalling. Antimicrob Agents Chemother 2016; 60:7178-7188. [PMID: 27645242 PMCID: PMC5118997 DOI: 10.1128/aac.01806-16] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 09/12/2016] [Indexed: 12/28/2022] Open
Abstract
Members of the Erm methyltransferase family modify 23S rRNA of the bacterial ribosome and render cross-resistance to macrolides and multiple distantly related antibiotics. Previous studies have shown that the expression of erm is activated when a macrolide-bound ribosome stalls the translation of the leader peptide preceding the cotranscribed erm. Ribosome stalling is thought to destabilize the inhibitory stem-loop mRNA structure and exposes the erm Shine-Dalgarno (SD) sequence for translational initiation. Paradoxically, mutations that abolish ribosome stalling are routinely found in hyper-resistant clinical isolates; however, the significance of the stalling-dead leader sequence is largely unknown. Here, we show that nonsense mutations in the Staphylococcus aureus ErmB leader peptide (ErmBL) lead to high basal and induced expression of downstream ErmB in the absence or presence of macrolide concomitantly with elevated ribosome methylation and resistance. The overexpression of ErmB is associated with the reduced turnover of the ermBL-ermB transcript, and the macrolide appears to mitigate mRNA cleavage at a site immediately downstream of the ermBL SD sequence. The stabilizing effect of antibiotics on mRNA is not limited to ermBL-ermB; cationic antibiotics representing a ribosome-stalling inducer and a noninducer increase the half-life of specific transcripts. These data unveil a new layer of ermB regulation and imply that ErmBL translation or ribosome stalling serves as a “tuner” to suppress aberrant production of ErmB because methylated ribosome may impose a fitness cost on the bacterium as a result of misregulated translation.
Collapse
|
19
|
Rojas-Sánchez S, Figueroa-Angulo E, Moreno-Campos R, Florencio-Martínez LE, Manning-Cela RG, Martínez-Calvillo S. Transcription of Leishmania major U2 small nuclear RNA gene is directed by extragenic sequences located within a tRNA-like and a tRNA-Ala gene. Parasit Vectors 2016; 9:401. [PMID: 27430335 PMCID: PMC4950102 DOI: 10.1186/s13071-016-1682-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 07/05/2016] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Leishmania and other trypanosomatid parasites possess atypical mechanisms of gene expression, including the maturation of mRNAs by trans-splicing and the involvement of RNA Polymerase III in transcription of all snRNA molecules. Since snRNAs are essential for trans-splicing, we are interested in the study of the sequences that direct their expression. Here we report the characterization of L. major U2 snRNA promoter region. RESULTS All species of Leishmania possess a single U2 snRNA gene that contains a divergently-oriented tRNA-Ala gene in the upstream region. Between these two genes we found a tRNA-like sequence that possesses conserved boxes A and B. Primer extension and RT-qPCR analyses with RNA from transiently-transfected cells showed that transcription of L. major U2 snRNA is almost abolished when boxes A and B from the tRNA-like are deleted or mutated. The levels of the U2 snRNA were also highly affected when base substitutions were introduced into box B from the tRNA-Ala gene and the first nucleotides of the U2 snRNA gene itself. We also demonstrate that the tRNA-like is transcribed, generating a main transcript of around 109 bases. As pseudouridines in snRNAs are required for splicing in other organisms, we searched for this modified nucleotide in the L. major U2 snRNA. Our results show the presence of six pseudouridines in the U2 snRNA, including one in the Sm site that has not been reported in other organisms. CONCLUSIONS Four different regions control the transcription of the U2 snRNA gene in L. major: boxes A and B from the neighbor tRNA-like, box B from the upstream tRNA-Ala gene and the first nucleotides of the U2 snRNA. Thus, the promoter region of L. major U2 snRNA is different from any other promoter reported for snRNAs. Pseudouridines could play important roles in L. major U2 snRNA, since they were found in functionally important regions, including the branch point recognition region and the Sm binding site.
Collapse
Affiliation(s)
- Saúl Rojas-Sánchez
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. de los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla, Edo. de México, CP 54090, Mexico
| | - Elisa Figueroa-Angulo
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. de los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla, Edo. de México, CP 54090, Mexico
| | - Rodrigo Moreno-Campos
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. de los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla, Edo. de México, CP 54090, Mexico
| | - Luis E Florencio-Martínez
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. de los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla, Edo. de México, CP 54090, Mexico
| | - Rebeca G Manning-Cela
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Av. IPN 2508, México, DF, CP 07360, Mexico
| | - Santiago Martínez-Calvillo
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. de los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla, Edo. de México, CP 54090, Mexico.
| |
Collapse
|
20
|
Jorjani H, Kehr S, Jedlinski DJ, Gumienny R, Hertel J, Stadler PF, Zavolan M, Gruber AR. An updated human snoRNAome. Nucleic Acids Res 2016; 44:5068-82. [PMID: 27174936 PMCID: PMC4914119 DOI: 10.1093/nar/gkw386] [Citation(s) in RCA: 178] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 04/23/2016] [Indexed: 12/18/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) are a class of non-coding RNAs that guide the post-transcriptional processing of other non-coding RNAs (mostly ribosomal RNAs), but have also been implicated in processes ranging from microRNA-dependent gene silencing to alternative splicing. In order to construct an up-to-date catalog of human snoRNAs we have combined data from various databases, de novo prediction and extensive literature review. In total, we list more than 750 curated genomic loci that give rise to snoRNA and snoRNA-like genes. Utilizing small RNA-seq data from the ENCODE project, our study characterizes the plasticity of snoRNA expression identifying both constitutively as well as cell type specific expressed snoRNAs. Especially, the comparison of malignant to non-malignant tissues and cell types shows a dramatic perturbation of the snoRNA expression profile. Finally, we developed a high-throughput variant of the reverse-transcriptase-based method for identifying 2'-O-methyl modifications in RNAs termed RimSeq. Using the data from this and other high-throughput protocols together with previously reported modification sites and state-of-the-art target prediction methods we re-estimate the snoRNA target RNA interaction network. Our current results assign a reliable modification site to 83% of the canonical snoRNAs, leaving only 76 snoRNA sequences as orphan.
Collapse
Affiliation(s)
- Hadi Jorjani
- Computational and Systems Biology, Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel CH-4056, Switzerland
| | - Stephanie Kehr
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, D-04107 Leipzig, Germany
| | - Dominik J Jedlinski
- Computational and Systems Biology, Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel CH-4056, Switzerland
| | - Rafal Gumienny
- Computational and Systems Biology, Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel CH-4056, Switzerland
| | - Jana Hertel
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, D-04107 Leipzig, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, D-04107 Leipzig, Germany Max Planck Institute for Mathematics in the Sciences, D-04103 Leipzig, Germany RNomics Group, Fraunhofer Institute for Cell Therapy and Immunology, D-04103 Leipzig, Germany Department of Theoretical Chemistry, University of Vienna, A-1090 Vienna, Austria Santa Fe Institute, NM-87501Santa Fe, USA
| | - Mihaela Zavolan
- Computational and Systems Biology, Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel CH-4056, Switzerland
| | - Andreas R Gruber
- Computational and Systems Biology, Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel CH-4056, Switzerland
| |
Collapse
|
21
|
Abstract
The RNase protection assay is a sensitive method for transcription start-site localization. It begins with an RNA probe that is uniformly labeled by incorporation of one [α-(32)P]NTP, usually [α-(32)P]UTP. The RNA probe is synthesized by bacteriophage RNA polymerase (SP6, T7, or T3), which initiates transcription from specific phage promoters that have been engineered into a number of common plasmid vectors. The plasmid template contains a genomic DNA fragment spanning the region thought to contain the transcription start site for the gene of interest. This genomic fragment is subcloned into the plasmid downstream of the phage promoter in the antisense orientation, so that a portion of the 5' end of the resulting RNA probe will be complementary to the mRNA of interest. The radiolabeled probe is annealed to cytoplasmic or total cellular mRNA purified from the cells of interest, with the hybridization reaction proceeding for several hours or overnight. RNase A and/or RNase T1 is then added to the hybridization reactions. These nucleases digest the single-stranded overhang regions of RNA molecules, but RNA-RNA hybrids are resistant to cleavage. This resistance forms the conceptual basis for the procedure; the region of the probe that anneals to the specific mRNA will be resistant to digestion. The length of the resistant region of the probe will correspond to the distance from the 5' end of the probe to the transcription start site. The size of the resistant fragment can be determined by electrophoresis on a high-resolution, denaturing polyacrylamide gel.
Collapse
|