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Guo X, Zhu Y, Pan Z, Pan H, Li H. Single primer site-specific nested PCR for accurate and rapid genome-walking. J Microbiol Methods 2024; 220:106926. [PMID: 38555034 DOI: 10.1016/j.mimet.2024.106926] [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] [Received: 01/29/2024] [Revised: 03/27/2024] [Accepted: 03/27/2024] [Indexed: 04/02/2024]
Abstract
Genome-walking is a molecular tool used to unveil uncharacterized DNA regions flanking a known DNA, which has been widely used in bioscience and related areas. This study developed a reliable and efficient PCR-based genome-walking approach, named as single primer site-specific nested PCR (SPN-PCR). A SPN-PCR set sequentially consists of three single-primer nested PCR amplifications. The primary relaxed thermal cycle promotes outmost nested site-specific primer (NSSP) to partially combine with numerous places on DNA template, synthesizing many single-stranded DNAs (ssDNA). Among them, the target ssDNA is exponentially amplified in the subsequent stringent cycles, as its 3' part possesses the outmost NSSP complement; but a non-target ssDNA cannot be amplified, because it does not possess such a complement. Stringent secondary and tertiary PCRs also exclusively enrich this target DNA. Finally, the target DNA product becomes predominant. The feasibility of SPN-PCR was validated by genome-walking several selected genes from two divergent species.
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Affiliation(s)
- Xinyue Guo
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, PR China; International Institute of Food Innovation, Nanchang University, Nanchang 330047, PR China; Sino-German Joint Research Institute, Nanchang University, Nanchang 330047, PR China
| | - Yisong Zhu
- Hangzhou Xiaoshan Agricultural Development Co., Ltd., Hangzhou 311200, PR China
| | - Zhenkang Pan
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, PR China; International Institute of Food Innovation, Nanchang University, Nanchang 330047, PR China; Sino-German Joint Research Institute, Nanchang University, Nanchang 330047, PR China
| | - Hao Pan
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, PR China; International Institute of Food Innovation, Nanchang University, Nanchang 330047, PR China; Sino-German Joint Research Institute, Nanchang University, Nanchang 330047, PR China
| | - Haixing Li
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, PR China; International Institute of Food Innovation, Nanchang University, Nanchang 330047, PR China; Sino-German Joint Research Institute, Nanchang University, Nanchang 330047, PR China.
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Li H, Lin Z, Guo X, Pan Z, Pan H, Wang D. Primer extension refractory PCR: an efficient and reliable genome walking method. Mol Genet Genomics 2024; 299:27. [PMID: 38466442 DOI: 10.1007/s00438-024-02126-5] [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: 05/18/2023] [Accepted: 02/10/2024] [Indexed: 03/13/2024]
Abstract
Genome walking, a molecular technique for obtaining unknown flanking genomic sequences from a known genomic sequence, has been broadly applied to determine transgenic sites, mine new genetic resources, and fill in chromosomal gaps. This technique has advanced genomics, genetics, and related disciplines. Here, an efficient and reliable genome walking technique, called primer extension refractory PCR (PER-PCR), is presented. PER-PCR uses a set of primary, secondary, and tertiary walking primers. The middle 15 nt of the primary walking primer overlaps with the 3' parts of the secondary and tertiary primers. The 5' parts of the three primers are heterologous to each other. The short overlap allows the walking primer to anneal to its predecessor only in a relaxed-stringency PCR cycle, resulting in a series of single-stranded DNAs; however, the heterologous 5' part prevents the creation of a perfect binding site for the walking primer. In the next stringent cycle, the target single strand can be extended into a double-stranded DNA molecule by the sequence-specific primer and thus can be exponentially amplified by the remaining stringent cycles. The nontarget single strand fails to be enriched due to the lack of a perfect binding site for any primer. PER-PCR was validated by extension into unknown flanking regions of the hyg gene in rice and the gadR gene in Levilactobacillus brevis CD0817. In summary, in this study, a new practical PER-PCR method was constructed as a potential alternative to existing genome walking methods.
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Affiliation(s)
- Haixing Li
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, People's Republic of China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, 330047, People's Republic of China
| | - Zhiyu Lin
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, People's Republic of China
- Boya Bio-Pharmaceutical Group Co., Ltd, High-Tech Industrial Development Zone, Fuzhou, 344100, People's Republic of China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, 330047, People's Republic of China
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang, 330047, People's Republic of China
| | - Xinyue Guo
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, People's Republic of China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, 330047, People's Republic of China
| | - Zhenkang Pan
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, People's Republic of China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, 330047, People's Republic of China
| | - Hao Pan
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, People's Republic of China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, 330047, People's Republic of China
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang, 330047, People's Republic of China
| | - Dongying Wang
- Physical Education Department, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, People's Republic of China.
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Pei J, Sun T, Wang L, Pan Z, Guo X, Li H. Fusion primer driven racket PCR: A novel tool for genome walking. Front Genet 2022; 13:969840. [PMID: 36330444 PMCID: PMC9623105 DOI: 10.3389/fgene.2022.969840] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/26/2022] [Indexed: 11/13/2022] Open
Abstract
The limitations of the current genome-walking strategies include strong background and cumbersome experimental processes. Herein, we report a genome-walking method, fusion primer-driven racket PCR (FPR-PCR), for the reliable retrieval of unknown flanking DNA sequences. Four sequence-specific primers (SSP1, SSP2, SSP3, and SSP4) were sequentially selected from known DNA (5'→3′) to perform FPR-PCR. SSP3 is the fragment that mediates intra-strand annealing (FISA). The FISA fragment is attached to the 5′ end of SSP1, generating a fusion primer. FPR-PCR comprises two rounds of amplification reactions. The single-fusion primary FPR-PCR begins with the selective synthesis of the target first strand, then allows the primer to partially anneal to some place(s) on the unknown region of this strand, producing the target second strand. Afterward, a new first strand is synthesized using the second strand as the template. The 3′ end of this new first strand undergoes intra-strand annealing to the FISA site, followed by the formation of a racket-like DNA by a loop-back extension. This racket-like DNA is exponentially amplified in the secondary FPR-PCR performed using SSP2 and SSP4. We validated this FPR-PCR method by identifying the unknown flanks of Lactobacillus brevis CD0817 glutamic acid decarboxylase genes and the rice hygromycin gene.
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Affiliation(s)
- Jinfeng Pei
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, China
| | - Tianyi Sun
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, China
- Key Laboratory of Poyang Lake Environment and Resource Utilization of Ministry of Education, School of Chemistry and Chemical Engineering, Nanchang University, Nanchang, China
| | - Lingqin Wang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, China
| | - Zhenkang Pan
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, China
| | - Xinyue Guo
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, China
| | - Haixing Li
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, China
- *Correspondence: Haixing Li,
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Wang L, Jia M, Li Z, Liu X, Sun T, Pei J, Wei C, Lin Z, Li H. Wristwatch PCR: A Versatile and Efficient Genome Walking Strategy. Front Bioeng Biotechnol 2022; 10:792848. [PMID: 35497369 PMCID: PMC9039356 DOI: 10.3389/fbioe.2022.792848] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 03/08/2022] [Indexed: 11/16/2022] Open
Abstract
Genome walking is a method used to retrieve unknown flanking DNA. Here, we reported wristwatch (WW) PCR, an efficient genome walking technique mediated by WW primers (WWPs). WWPs feature 5′- and 3′-overlap and a heterologous interval. Therefore, a wristwatch-like structure can be formed between WWPs under relatively low temperatures. Each WW-PCR set is composed of three nested (primary, secondary, and tertiary) PCRs individually performed by three WWPs. The WWP is arbitrarily annealed somewhere on the genome in the one low-stringency cycle of the primary PCR, or directionally to the previous WWP site in one reduced-stringency cycle of the secondary/tertiary PCR, producing a pool of single-stranded DNAs (ssDNAs). A target ssDNA incorporates a gene-specific primer (GSP) complementary at the 3′-end and the WWP at the 5′-end and thus can be exponentially amplified in the next high-stringency cycles. Nevertheless, a non-target ssDNA cannot be amplified as it lacks a perfect binding site for any primers. The practicability of the WW-PCR was validated by successfully accessing unknown regions flanking Lactobacillus brevis CD0817 glutamate decarboxylase gene and the hygromycin gene of rice. The WW-PCR is an attractive alternative to the existing genome walking techniques.
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Affiliation(s)
- Lingqin Wang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, China
| | - Mengya Jia
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, China
| | - Zhaoqin Li
- Charles W. Davidson College of Engineering, San Jose State University, San Jose, CA, United States
| | - Xiaohua Liu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, China
| | - Tianyi Sun
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, China
- Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, School of Environmental and Chemical Engineering, Nanchang University, Nanchang, China
| | - Jinfeng Pei
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, China
| | - Cheng Wei
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, China
| | - Zhiyu Lin
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, China
- Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, School of Environmental and Chemical Engineering, Nanchang University, Nanchang, China
| | - Haixing Li
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, China
- *Correspondence: Haixing Li,
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McEwen GK, Alquezar-Planas DE, Dayaram A, Gillett A, Tarlinton R, Mongan N, Chappell KJ, Henning J, Tan M, Timms P, Young PR, Roca AL, Greenwood AD. Retroviral integrations contribute to elevated host cancer rates during germline invasion. Nat Commun 2021; 12:1316. [PMID: 33637755 PMCID: PMC7910482 DOI: 10.1038/s41467-021-21612-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 02/01/2021] [Indexed: 12/16/2022] Open
Abstract
Repeated retroviral infections of vertebrate germlines have made endogenous retroviruses ubiquitous features of mammalian genomes. However, millions of years of evolution obscure many of the immediate repercussions of retroviral endogenisation on host health. Here we examine retroviral endogenisation during its earliest stages in the koala (Phascolarctos cinereus), a species undergoing germline invasion by koala retrovirus (KoRV) and affected by high cancer prevalence. We characterise KoRV integration sites (IS) in tumour and healthy tissues from 10 koalas, detecting 1002 unique IS, with hotspots of integration occurring in the vicinity of known cancer genes. We find that tumours accumulate novel IS, with proximate genes over-represented for cancer associations. We detect dysregulation of genes containing IS and identify a highly-expressed transduced oncogene. Our data provide insights into the tremendous mutational load suffered by the host during active retroviral germline invasion, a process repeatedly experienced and overcome during the evolution of vertebrate lineages.
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Affiliation(s)
- Gayle K McEwen
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - David E Alquezar-Planas
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
- Australian Museum Research Institute, Australian Museum, Sydney, NSW, Australia
| | - Anisha Dayaram
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
- Institute for Neurophysiology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Amber Gillett
- Australia Zoo Wildlife Hospital, Beerwah, QLD, Australia
| | - Rachael Tarlinton
- Faculty of Medicine and Health Sciences, University of Nottingham, Leicestershire, UK
| | - Nigel Mongan
- Faculty of Medicine and Health Sciences, University of Nottingham, Leicestershire, UK
| | - Keith J Chappell
- School of Chemistry & Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia
| | - Joerg Henning
- School of Veterinary Science, University of Queensland, Brisbane, QLD, Australia
| | - Milton Tan
- Illinois Natural History Survey, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - Peter Timms
- Genecology Research Center, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Paul R Young
- School of Chemistry & Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia
| | - Alfred L Roca
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Alex D Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.
- Department of Veterinary Medicine, Freie Universität, Berlin, Germany.
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