1
|
Wang X, Zhao L, Wu X, Luo H, Wu D, Zhang M, Zhang J, Pakvasa M, Wagstaff W, He F, Mao Y, Zhang Y, Niu C, Wu M, Zhao X, Wang H, Huang L, Shi D, Liu Q, Ni N, Fu K, Hynes K, Strelzow J, El Dafrawy M, He TC, Qi H, Zeng Z. Development of a simplified and inexpensive RNA depletion method for plasmid DNA purification using size selection magnetic beads (SSMBs). Genes Dis 2021; 8:298-306. [PMID: 33997177 PMCID: PMC8093646 DOI: 10.1016/j.gendis.2020.04.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/03/2020] [Accepted: 04/22/2020] [Indexed: 02/07/2023] Open
Abstract
Plasmid DNA (pDNA) isolation from bacterial cells is one of the most common and critical steps in molecular cloning and biomedical research. Almost all pDNA purification involves disruption of bacteria, removal of membrane lipids, proteins and genomic DNA, purification of pDNA from bulk lysate, and concentration of pDNA for downstream applications. While many liquid-phase and solid-phase pDNA purification methods are used, the final pDNA preparations are usually contaminated with varied degrees of host RNA, which cannot be completely digested by RNase A. To develop a simple, cost-effective, and yet effective method for RNA depletion, we investigated whether commercially available size selection magnetic beads (SSMBs), such as Mag-Bind® TotalPure NGS Kit (or Mag-Bind), can completely deplete bacterial RNA in pDNA preparations. In this proof-of-principle study, we demonstrated that, compared with RNase A digestion and two commercial plasmid affinity purification kits, the SSMB method was highly efficient in depleting contaminating RNA from pDNA minipreps. Gene transfection and bacterial colony formation assays revealed that pDNA purified from SSMB method had superior quality and integrity to pDNA samples cleaned up by RNase A digestion and/or commercial plasmid purification kits. We further demonstrated that the SSMB method completely depleted contaminating RNA in large-scale pDNA samples. Furthermore, the Mag-bind-based SSMB method costs only 5-10% of most commercial plasmid purification kits on a per sample basis. Thus, the reported SSMB method can be a valuable and inexpensive tool for the removal of bacterial RNA for routine pDNA preparations.
Collapse
Affiliation(s)
- Xi Wang
- Ministry of Education Key Laboratory of Diagnostic Medicine, School of Laboratory and Diagnostic Medicine, Chongqing Medical University, Chongqing, 400016, PR China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Ling Zhao
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Departments of Gastrointestinal Surgery, Obstetrics and Gynecology, and Nephrology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Xiaoxing Wu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Departments of Gastrointestinal Surgery, Obstetrics and Gynecology, and Nephrology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Huaxiu Luo
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Department of Burn and Plastic Surgery, West China Hospital of Sichuan University, Chengdu, Sichuan Province, 610041, PR China
| | - Di Wu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Meng Zhang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510405, PR China
| | - Jing Zhang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Departments of Gastrointestinal Surgery, Obstetrics and Gynecology, and Nephrology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Mikhail Pakvasa
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - William Wagstaff
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Fang He
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Departments of Gastrointestinal Surgery, Obstetrics and Gynecology, and Nephrology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Yukun Mao
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Departments of Orthopaedic Surgery and Neurosurgery, The Affiliated Zhongnan Hospital of Wuhan University, Wuhan, Hubei Province, 430072, PR China
| | - Yongtao Zhang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Department of Orthopaedic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong Province, 266061, PR China
| | - Changchun Niu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Department of Laboratory Diagnostic Medicine, Chongqing General Hospital, Chongqing, 400021, PR China
| | - Meng Wu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Institute of Bone and Joint Research, The departments of Orthopaedic Surgery and Obstetrics and Gynecology, The First and Second Hospitals of Lanzhou University, Lanzhou, Gansu Province, 730030, PR China
| | - Xia Zhao
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Department of Orthopaedic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong Province, 266061, PR China
| | - Hao Wang
- Ministry of Education Key Laboratory of Diagnostic Medicine, School of Laboratory and Diagnostic Medicine, Chongqing Medical University, Chongqing, 400016, PR China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Linjuan Huang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Departments of Gastrointestinal Surgery, Obstetrics and Gynecology, and Nephrology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Deyao Shi
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, 430022, PR China
| | - Qing Liu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Department of Spine Surgery, Second Xiangya Hospital, Central South University, Changsha, Hunan Province, 410011, PR China
| | - Na Ni
- Ministry of Education Key Laboratory of Diagnostic Medicine, School of Laboratory and Diagnostic Medicine, Chongqing Medical University, Chongqing, 400016, PR China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Kai Fu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Departments of Orthopaedic Surgery and Neurosurgery, The Affiliated Zhongnan Hospital of Wuhan University, Wuhan, Hubei Province, 430072, PR China
| | - Kelly Hynes
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Jason Strelzow
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Mostafa El Dafrawy
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Tong-Chuan He
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Hongbo Qi
- Departments of Gastrointestinal Surgery, Obstetrics and Gynecology, and Nephrology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Zongyue Zeng
- Ministry of Education Key Laboratory of Diagnostic Medicine, School of Laboratory and Diagnostic Medicine, Chongqing Medical University, Chongqing, 400016, PR China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| |
Collapse
|
3
|
Brodhagen J, Weikard R, Thom U, Heimes A, Günther J, Hadlich F, Zerbe H, Petzl W, Meyerholz MM, Hoedemaker M, Schuberth HJ, Engelmann S, Kühn C. Development and evaluation of a milk protein transcript depletion method for differential transcriptome analysis in mammary gland tissue. BMC Genomics 2019; 20:400. [PMID: 31117949 PMCID: PMC6530097 DOI: 10.1186/s12864-019-5781-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 05/07/2019] [Indexed: 11/30/2022] Open
Abstract
Background In the mammary gland transcriptome of lactating dairy cows genes encoding milk proteins are highly abundant, which can impair the detection of lowly expressed transcripts and can bias the outcome in global transcriptome analyses. Therefore, the aim of this study was to develop and evaluate a method to deplete extremely highly expressed transcripts in mRNA from lactating mammary gland tissue. Results Selective RNA depletion was performed by hybridization of antisense oligonucleotides targeting genes encoding the caseins (CSN1S1, CSN1S2, CSN2 and CSN3) and whey proteins (LALBA and PAEP) within total RNA followed by RNase H-mediated elimination of the respective transcripts. The effect of the RNA depletion procedure was monitored by RNA sequencing analysis comparing depleted and non-depleted RNA samples from Escherichia coli (E. coli) challenged and non-challenged udder tissue of lactating cows in a proof of principle experiment. Using RNase H-mediated RNA depletion, the ratio of highly abundant milk protein gene transcripts was reduced in all depleted samples by an average of more than 50% compared to the non-depleted samples. Furthermore, the sensitivity for discovering transcripts with marginal expression levels and transcripts not yet annotated was improved. Finally, the sensitivity to detect significantly differentially expressed transcripts between non-challenged and challenged udder tissue was increased without leading to an inadvertent bias in the pathogen challenge-associated biological signaling pathway patterns. Conclusions The implementation of selective RNase H-mediated RNA depletion of milk protein gene transcripts from the mammary gland transcriptome of lactating cows will be highly beneficial to establish comprehensive transcript catalogues of the tissue that better reflects its transcriptome complexity. Electronic supplementary material The online version of this article (10.1186/s12864-019-5781-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Johanna Brodhagen
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, 18196, Dummerstorf, Germany
| | - Rosemarie Weikard
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, 18196, Dummerstorf, Germany
| | - Ulrike Thom
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, 18196, Dummerstorf, Germany
| | - Annika Heimes
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, 18196, Dummerstorf, Germany
| | - Juliane Günther
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, 18196, Dummerstorf, Germany
| | - Frieder Hadlich
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, 18196, Dummerstorf, Germany
| | - Holm Zerbe
- Clinic for Ruminants with Ambulatory and Herd Health Services, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, 85764, Oberschleissheim, Germany
| | - Wolfgang Petzl
- Clinic for Ruminants with Ambulatory and Herd Health Services, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, 85764, Oberschleissheim, Germany
| | - Marie M Meyerholz
- Clinic for Ruminants with Ambulatory and Herd Health Services, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, 85764, Oberschleissheim, Germany
| | - Martina Hoedemaker
- Clinic for Cattle, University of Veterinary Medicine, Foundation, 30173, Hannover, Germany
| | - Hans-Joachim Schuberth
- Immunology Unit, University of Veterinary Medicine, Foundation, 30559, Hannover, Germany
| | - Susanne Engelmann
- Institute for Microbiology, Technical University Braunschweig, 38106, Braunschweig, Germany.,Microbial Proteomics, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Christa Kühn
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, 18196, Dummerstorf, Germany. .,Agricultural and Environmental Faculty, University Rostock, 18059, Rostock, Germany.
| |
Collapse
|
4
|
Munafó DB, Langhorst BW, Chater CL, Sumner CJ, Rodríguez DN, Russello S, Gardner AF, Slatko BE, Stewart FJ, Sinicropi D, Morlan J, Qu K, Dimalanta ET, Davis TB. Selective Depletion of Abundant RNAs to Enable Transcriptome Analysis of Low-Input and Highly Degraded Human RNA. ACTA ACUST UNITED AC 2016; 113:7.22.1-7.22.9. [PMID: 31773915 DOI: 10.1002/0471142727.mb0722s113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Ribosomal RNAs (rRNAs) are extremely abundant, often constituting 80% to 90% of total RNA. Since rRNA sequences are often not of interest in genomic RNA sequencing experiments, rRNAs can be removed from the sample before the library preparation step, in order to prevent the majority of the library and the majority of sequencing reads from being rRNA. Removal of rRNA can be especially challenging for low quality and formalin-fixed paraffin-embedded (FFPE) RNA samples due to the fragmented nature of these RNA molecules. The NEBNext rRNA Depletion Kit (Human/Mouse/Rat) depletes both cytoplasmic (5 S rRNA, 5.8 S rRNA, 18 S rRNA, and 28 S rRNA) and mitochondrial rRNA (12 S rRNA and 16 S rRNA) from total RNA preparations from human, mouse, and rat samples. Due to the high similarity among mammalian rRNA sequences, it is likely that rRNA depletion can also be achieved for other mammals but has not been empirically tested. This product is compatible with both intact and degraded RNA (e.g., FFPE RNA). The resulting rRNA-depleted RNA is suitable for RNA-seq, random-primed cDNA synthesis, or other downstream RNA analysis applications. Regardless of the quality or amount of input RNA, this method efficiently removes rRNA, while retaining non-coding and other non-poly(A) RNAs. The NEBNext rRNA Depletion Kit thus provides a more complete picture of the transcript repertoire than oligo d(T) poly(A) mRNA enrichment methods. © 2016 by John Wiley & Sons, Inc.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - John Morlan
- Genomic Health, Inc, Redwood City, California
| | - Kunbin Qu
- Genomic Health, Inc, Redwood City, California
| | | | | |
Collapse
|