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Wang C, Xu J, Luo S, Huang J, Ji D, Qiu X, Song X, Cao X, Niu C, Zeng X, Zhang Z, Ma Y, Chen J, Chen D, Zhong X, Wei Y. Parental Exposure to Environmentally Relevant Concentrations of Bisphenol-A Bis(diphenyl phosphate) Impairs Vascular Development in Offspring through DNA/RNA Methylation-Dependent Transmission. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:16176-16189. [PMID: 37847870 DOI: 10.1021/acs.est.3c03579] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
Abstract
Bisphenol-A bis(diphenyl phosphate) (BDP) has been increasingly detected in indoor environmental and human samples. Little is known about its developmental toxicity, particularly the intergenerational effects of parental exposure. In this study, adult zebrafish were exposed to BDP at 30-30,000 ng/L for 28 days, with results showing that exposure did not cause a transfer of BDP or its metabolites to offspring. Vascular morphometric profiling revealed that parental exposure to BDP at 30 and 300 ng/L exerted significant effects on the vascular development of offspring, encompassing diverse alterations in multiple types of blood vessels. N6-Methyladenosine (m6A) methylated RNA immunoprecipitation sequencing of larvae in the 300 ng/L group revealed 378 hypomethylated and 350 hypermethylated m6A peaks that were identified in mRNA transcripts of genes crucial for vascular development, including the Notch/Vegf signaling pathway. Concomitant changes in 5 methylcytosine (m5C) DNA methylation and gene expression of m6A modulators (alkbh5, kiaa1429, and ythdf1) were observed in both parental gonads and offspring exposed to BDP. These results reveal that parental exposure to low concentrations of BDP caused offspring vascular disorders by interfering with DNA and RNA methylation, uncovering a unique DNA-RNA modification pattern in the intergenerational transmission of BDP's developmental toxicity.
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Affiliation(s)
- Can Wang
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, California 92521, United States
| | - Jinkun Xu
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Shili Luo
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Jiajing Huang
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Di Ji
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Xuelin Qiu
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Xin Song
- School of Environment and Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, China
| | - Xiaolian Cao
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Congying Niu
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Xiangyu Zeng
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Zhuyi Zhang
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Ya Ma
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Junzhou Chen
- School of Intelligent Systems Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Da Chen
- School of Environment and Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, China
| | - Xiali Zhong
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Yanhong Wei
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
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Tselika M, Belmezos N, Kallemi P, Andronis C, Chiumenti M, Navarro B, Lavigne M, Di Serio F, Kalantidis K, Katsarou K. PSTVd infection in Nicotiana benthamiana plants has a minor yet detectable effect on CG methylation. FRONTIERS IN PLANT SCIENCE 2023; 14:1258023. [PMID: 38023875 PMCID: PMC10645062 DOI: 10.3389/fpls.2023.1258023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/13/2023] [Indexed: 12/01/2023]
Abstract
Viroids are small circular RNAs infecting a wide range of plants. They do not code for any protein or peptide and therefore rely on their structure for their biological cycle. Observed phenotypes of viroid infected plants are thought to occur through changes at the transcriptional/translational level of the host. A mechanism involved in such changes is RNA-directed DNA methylation (RdDM). Till today, there are contradictory works about viroids interference of RdDM. In this study, we investigated the epigenetic effect of viroid infection in Nicotiana benthamiana plants. Using potato spindle tuber viroid (PSTVd) as the triggering pathogen and via bioinformatic analyses, we identified endogenous gene promoters and transposable elements targeted by 24 nt host siRNAs that differentially accumulated in PSTVd-infected and healthy plants. The methylation status of these targets was evaluated following digestion with methylation-sensitive restriction enzymes coupled with PCR amplification, and bisulfite sequencing. In addition, we used Methylation Sensitive Amplification Polymorphism (MSAP) followed by sequencing (MSAP-seq) to study genomic DNA methylation of 5-methylcytosine (5mC) in CG sites upon viroid infection. In this study we identified a limited number of target loci differentially methylated upon PSTVd infection. These results enhance our understanding of the epigenetic host changes as a result of pospiviroid infection.
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Affiliation(s)
- Martha Tselika
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | | | - Paraskevi Kallemi
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Christos Andronis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Michela Chiumenti
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Beatriz Navarro
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Matthieu Lavigne
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Kriton Kalantidis
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Konstantina Katsarou
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
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3
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Kong Y, Mead EA, Fang G. Navigating the pitfalls of mapping DNA and RNA modifications. Nat Rev Genet 2023; 24:363-381. [PMID: 36653550 PMCID: PMC10722219 DOI: 10.1038/s41576-022-00559-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2022] [Indexed: 01/19/2023]
Abstract
Chemical modifications to nucleic acids occur across the kingdoms of life and carry important regulatory information. Reliable high-resolution mapping of these modifications is the foundation of functional and mechanistic studies, and recent methodological advances based on next-generation sequencing and long-read sequencing platforms are critical to achieving this aim. However, mapping technologies may have limitations that sometimes lead to inconsistent results. Some of these limitations are technical in nature and specific to certain types of technology. Here, however, we focus on common (yet not always widely recognized) pitfalls that are shared among frequently used mapping technologies and discuss strategies to help technology developers and users mitigate their effects. Although the emphasis is primarily on DNA modifications, RNA modifications are also discussed.
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Affiliation(s)
- Yimeng Kong
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edward A Mead
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gang Fang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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4
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Epigenetic Targets and Pathways Linked to SARS-CoV-2 Infection and Pathology. Microorganisms 2023; 11:microorganisms11020341. [PMID: 36838306 PMCID: PMC9967649 DOI: 10.3390/microorganisms11020341] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/19/2023] [Accepted: 01/19/2023] [Indexed: 02/03/2023] Open
Abstract
The scale at which the SARS-CoV-2/COVID-19 pandemic has spread remains enormous. Provided the genetic makeup of the virus and humans is readily available, the quest for knowing the mechanism and epidemiology continues to prevail across the entire scientific community. Several aspects, including immunology, molecular biology, and host-pathogen interaction, are continuously being dug into for preparing the human race for future pandemics. The exact reasons for vast differences in symptoms, pathophysiological implications of COVID-infections, and mortality differences remain elusive. Hence, researchers are also looking beyond traditional genomics, proteomics, and transcriptomics approach, especially entrusting the environmental regulation of the genetic landscape of COVID-human interactions. In line with these questions lies a critical process called epigenetics. The epigenetic perturbations in both host and parasites are a matter of great interest to unravel the disparities in COVID-19 mortalities and pathology. This review provides a deeper insight into current research on the epigenetic landscape of SARS-CoV-2 infection in humans and potential targets for augmenting the ongoing investigation. It also explores the potential targets, pathways, and networks associated with the epigenetic regulation of processes involved in SARS-CoV-2 pathology.
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D'Addario C, Pucci M. DNA Methylation Analysis of Cnr1 Gene Promoter. Methods Mol Biol 2023; 2576:373-384. [PMID: 36152203 DOI: 10.1007/978-1-0716-2728-0_31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
DNA methylation pattern could be considered a biomarker to be exploited for the study and management of several human diseases. In this chapter, detailed protocols are provided for two experimental approaches used for quantitative methylation analysis of bisulfite converted DNA: methylation-specific PCR (MSP) and pyrosequencing.
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Affiliation(s)
- Claudio D'Addario
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Mariangela Pucci
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy.
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6
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Athanasopoulou K, Daneva GN, Boti MA, Dimitroulis G, Adamopoulos PG, Scorilas A. The Transition from Cancer "omics" to "epi-omics" through Next- and Third-Generation Sequencing. LIFE (BASEL, SWITZERLAND) 2022; 12:life12122010. [PMID: 36556377 PMCID: PMC9785810 DOI: 10.3390/life12122010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/25/2022] [Accepted: 11/30/2022] [Indexed: 12/05/2022]
Abstract
Deciphering cancer etiopathogenesis has proven to be an especially challenging task since the mechanisms that drive tumor development and progression are far from simple. An astonishing amount of research has revealed a wide spectrum of defects, including genomic abnormalities, epigenomic alterations, disturbance of gene transcription, as well as post-translational protein modifications, which cooperatively promote carcinogenesis. These findings suggest that the adoption of a multidimensional approach can provide a much more precise and comprehensive picture of the tumor landscape, hence serving as a powerful tool in cancer research and precision oncology. The introduction of next- and third-generation sequencing technologies paved the way for the decoding of genetic information and the elucidation of cancer-related cellular compounds and mechanisms. In the present review, we discuss the current and emerging applications of both generations of sequencing technologies, also referred to as massive parallel sequencing (MPS), in the fields of cancer genomics, transcriptomics and proteomics, as well as in the progressing realms of epi-omics. Finally, we provide a brief insight into the expanding scope of sequencing applications in personalized cancer medicine and pharmacogenomics.
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7
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Ahmed YW, Alemu BA, Bekele SA, Gizaw ST, Zerihun MF, Wabalo EK, Teklemariam MD, Mihrete TK, Hanurry EY, Amogne TG, Gebrehiwot AD, Berga TN, Haile EA, Edo DO, Alemu BD. Epigenetic tumor heterogeneity in the era of single-cell profiling with nanopore sequencing. Clin Epigenetics 2022; 14:107. [PMID: 36030244 PMCID: PMC9419648 DOI: 10.1186/s13148-022-01323-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 08/12/2022] [Indexed: 11/29/2022] Open
Abstract
Nanopore sequencing has brought the technology to the next generation in the science of sequencing. This is achieved through research advancing on: pore efficiency, creating mechanisms to control DNA translocation, enhancing signal-to-noise ratio, and expanding to long-read ranges. Heterogeneity regarding epigenetics would be broad as mutations in the epigenome are sensitive to cause new challenges in cancer research. Epigenetic enzymes which catalyze DNA methylation and histone modification are dysregulated in cancer cells and cause numerous heterogeneous clones to evolve. Detection of this heterogeneity in these clones plays an indispensable role in the treatment of various cancer types. With single-cell profiling, the nanopore sequencing technology could provide a simple sequence at long reads and is expected to be used soon at the bedside or doctor's office. Here, we review the advancements of nanopore sequencing and its use in the detection of epigenetic heterogeneity in cancer.
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Affiliation(s)
- Yohannis Wondwosen Ahmed
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia.
| | - Berhan Ababaw Alemu
- Department of Medical Biochemistry, School of Medicine, St. Paul's Hospital, Millennium Medical College, Addis Ababa, Ethiopia
| | - Sisay Addisu Bekele
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Solomon Tebeje Gizaw
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Muluken Fekadie Zerihun
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Endriyas Kelta Wabalo
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Maria Degef Teklemariam
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Tsehayneh Kelemu Mihrete
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Endris Yibru Hanurry
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Tensae Gebru Amogne
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Assaye Desalegne Gebrehiwot
- Department of Medical Anatomy, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Tamirat Nida Berga
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Ebsitu Abate Haile
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Dessiet Oma Edo
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Bizuwork Derebew Alemu
- Department of Statistics, College of Natural and Computational Sciences, Mizan Tepi University, Tepi, Ethiopia
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8
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Schaffner SL, Kobor MS. DNA methylation as a mediator of genetic and environmental influences on Parkinson's disease susceptibility: Impacts of alpha-Synuclein, physical activity, and pesticide exposure on the epigenome. Front Genet 2022; 13:971298. [PMID: 36061205 PMCID: PMC9437223 DOI: 10.3389/fgene.2022.971298] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/25/2022] [Indexed: 12/15/2022] Open
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder with a complex etiology and increasing prevalence worldwide. As PD is influenced by a combination of genetic and environment/lifestyle factors in approximately 90% of cases, there is increasing interest in identification of the interindividual mechanisms underlying the development of PD as well as actionable lifestyle factors that can influence risk. This narrative review presents an outline of the genetic and environmental factors contributing to PD risk and explores the possible roles of cytosine methylation and hydroxymethylation in the etiology and/or as early-stage biomarkers of PD, with an emphasis on epigenome-wide association studies (EWAS) of PD conducted over the past decade. Specifically, we focused on variants in the SNCA gene, exposure to pesticides, and physical activity as key contributors to PD risk. Current research indicates that these factors individually impact the epigenome, particularly at the level of CpG methylation. There is also emerging evidence for interaction effects between genetic and environmental contributions to PD risk, possibly acting across multiple omics layers. We speculated that this may be one reason for the poor replicability of the results of EWAS for PD reported to date. Our goal is to provide direction for future epigenetics studies of PD to build upon existing foundations and leverage large datasets, new technologies, and relevant statistical approaches to further elucidate the etiology of this disease.
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Affiliation(s)
- Samantha L. Schaffner
- Edwin S. H. Leong Healthy Aging Program, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Department of Medical Genetics, British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Michael S. Kobor
- Edwin S. H. Leong Healthy Aging Program, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Department of Medical Genetics, British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
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9
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Plant DNA Methylation Responds to Nutrient Stress. Genes (Basel) 2022; 13:genes13060992. [PMID: 35741754 PMCID: PMC9222553 DOI: 10.3390/genes13060992] [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: 04/26/2022] [Revised: 05/23/2022] [Accepted: 05/30/2022] [Indexed: 12/16/2022] Open
Abstract
Nutrient stress as abiotic stress has become one of the important factors restricting crop yield and quality. DNA methylation is an essential epigenetic modification that can effectively regulate genome stability. Exploring DNA methylation responses to nutrient stress could lay the foundation for improving plant tolerance to nutrient stress. This article summarizes the plant DNA methylation patterns, the effects of nutrient stress, such as nitrogen, phosphorus, iron, zinc and sulfur stress, on plant DNA methylation and research techniques for plant DNA methylation, etc. Our discussion provides insight for further research on epigenetics response to nutrient stress in the future.
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10
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FFPE-Based NGS Approaches into Clinical Practice: The Limits of Glory from a Pathologist Viewpoint. J Pers Med 2022; 12:jpm12050750. [PMID: 35629172 PMCID: PMC9146170 DOI: 10.3390/jpm12050750] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 01/02/2023] Open
Abstract
The introduction of next-generation sequencing (NGS) in the molecular diagnostic armamentarium is deeply changing pathology practice and laboratory frameworks. NGS allows for the comprehensive molecular characterization of neoplasms, in order to provide the best treatment to oncologic patients. On the other hand, NGS raises technical issues and poses several challenges in terms of education, infrastructures and costs. The aim of this review is to give an overview of the main NGS sequencing platforms that can be used in current molecular diagnostics and gain insights into the clinical applications of NGS in precision oncology. Hence, we also focus on the preanalytical, analytical and interpretative issues raised by the incorporation of NGS in routine pathology diagnostics.
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11
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Rodems TS, Juang DS, Stahlfeld CN, Gilsdorf CS, Krueger TEG, Heninger E, Zhao SG, Sperger JM, Beebe DJ, Haffner MC, Lang JM. SEEMLIS: a flexible semi-automated method for enrichment of methylated DNA from low-input samples. Clin Epigenetics 2022; 14:37. [PMID: 35272673 PMCID: PMC8908705 DOI: 10.1186/s13148-022-01252-4] [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: 11/05/2021] [Accepted: 02/18/2022] [Indexed: 01/02/2023] Open
Abstract
Background DNA methylation alterations have emerged as hallmarks of cancer and have been proposed as screening, prognostic, and predictive biomarkers. Traditional approaches for methylation analysis have relied on bisulfite conversion of DNA, which can damage DNA and is not suitable for targeted gene analysis in low-input samples. Here, we have adapted methyl-CpG-binding domain protein 2 (MBD2)-based DNA enrichment for use on a semi-automated exclusion-based sample preparation (ESP) platform for robust and scalable enrichment of methylated DNA from low-input samples, called SEEMLIS. Results We show that combining methylation-sensitive enzyme digestion with ESP-based MBD2 enrichment allows for single gene analysis with high sensitivity for GSTP1 in highly impure, heterogenous samples. We also show that ESP-based MBD2 enrichment coupled with targeted pre-amplification allows for analysis of multiple genes with sensitivities approaching the single cell level in pure samples for GSTP1 and RASSF1 and sensitivity down to 14 cells for these genes in highly impure samples. Finally, we demonstrate the potential clinical utility of SEEMLIS by successful detection of methylated gene signatures in circulating tumor cells (CTCs) from patients with prostate cancer with varying CTC number and sample purity. Conclusions SEEMLIS is a robust assay for targeted DNA methylation analysis in low-input samples, with flexibility at multiple steps. We demonstrate the feasibility of this assay to analyze DNA methylation in prostate cancer cells using CTCs from patients with prostate cancer as a real-world example of a low-input analyte of clinical importance. In summary, this novel assay provides a platform for determining methylation signatures in rare cell populations with broad implications for research as well as clinical applications. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-022-01252-4.
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Affiliation(s)
- Tamara S Rodems
- University of Wisconsin Carbone Cancer Center, Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Duane S Juang
- Department of Pathology, University of Washington, 1959 NE Pacific St., Seattle, WA, 98195, USA
| | - Charlotte N Stahlfeld
- University of Wisconsin Carbone Cancer Center, Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Cole S Gilsdorf
- University of Wisconsin Carbone Cancer Center, Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Tim E G Krueger
- University of Wisconsin Carbone Cancer Center, Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Erika Heninger
- University of Wisconsin Carbone Cancer Center, Madison, 1111 Highland Ave., Madison, WI, 53705, USA.,Department of Medicine, University of Wisconsin, Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Shuang G Zhao
- Department of Human Oncology, University of Wisconsin, Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Jamie M Sperger
- University of Wisconsin Carbone Cancer Center, Madison, 1111 Highland Ave., Madison, WI, 53705, USA.,Department of Medicine, University of Wisconsin, Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - David J Beebe
- University of Wisconsin Carbone Cancer Center, Madison, 1111 Highland Ave., Madison, WI, 53705, USA.,Department of Pathology, University of Wisconsin, Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Michael C Haffner
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave, N., Seattle, WA, 98109, USA.,Department of Pathology, University of Washington, 1959 NE Pacific St., Seattle, WA, 98195, USA.,Department of Pathology, Johns Hopkins School of Medicine, 600 N Wolfe St., Baltimore, MD, 21287, USA
| | - Joshua M Lang
- University of Wisconsin Carbone Cancer Center, Madison, 1111 Highland Ave., Madison, WI, 53705, USA. .,Department of Medicine, University of Wisconsin, Madison, 1111 Highland Ave., Madison, WI, 53705, USA. .,7151 WI Institutes for Medical Research, 1111 Highland Ave., Madison, WI, 53705, USA.
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12
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Okada T, Sun X, McIlfatrick S, St. John JC. Low guanine content and biased nucleotide distribution in vertebrate mtDNA can cause overestimation of non-CpG methylation. NAR Genom Bioinform 2022; 4:lqab119. [PMID: 35047811 PMCID: PMC8759572 DOI: 10.1093/nargab/lqab119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/24/2021] [Accepted: 01/09/2022] [Indexed: 11/12/2022] Open
Abstract
Mitochondrial DNA (mtDNA) methylation in vertebrates has been hotly debated for over 40 years. Most contrasting results have been reported following bisulfite sequencing (BS-seq) analyses. We addressed whether BS-seq experimental and analysis conditions influenced the estimation of the levels of methylation in specific mtDNA sequences. We found false positive non-CpG methylation in the CHH context (fpCHH) using unmethylated Sus scrofa mtDNA BS-seq data. fpCHH methylation was detected on the top/plus strand of mtDNA within low guanine content regions. These top/plus strand sequences of fpCHH regions would become extremely AT-rich sequences after BS-conversion, whilst bottom/minus strand sequences remained almost unchanged. These unique sequences caused BS-seq aligners to falsely assign the origin of each strand in fpCHH regions, resulting in false methylation calls. fpCHH methylation detection was enhanced by short sequence reads, short library inserts, skewed top/bottom read ratios and non-directional read mapping modes. We confirmed no detectable CHH methylation in fpCHH regions by BS-amplicon sequencing. The fpCHH peaks were located in the D-loop, ATP6, ND2, ND4L, ND5 and ND6 regions and identified in our S. scrofa ovary and oocyte data and human BS-seq data sets. We conclude that non-CpG methylation could potentially be overestimated in specific sequence regions by BS-seq analysis.
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13
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Yoshizawa-Sugata N, Yamazaki S, Mita-Yoshida K, Ono T, Nishito Y, Masai H. Loss of full-length DNA replication regulator Rif1 in two-cell embryos is associated with zygotic transcriptional activation. J Biol Chem 2021; 297:101367. [PMID: 34736895 PMCID: PMC8686075 DOI: 10.1016/j.jbc.2021.101367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/17/2021] [Accepted: 10/20/2021] [Indexed: 11/21/2022] Open
Abstract
Rif1 regulates DNA replication timing and double-strand break repair, and its depletion induces transcriptional bursting of two-cell (2C) zygote-specific genes in mouse ES cells. However, how Rif1 regulates zygotic transcription is unclear. We show here that Rif1 depletion promotes the formation of a unique Zscan4 enhancer structure harboring both histone H3 lysine 27 acetylation (H3K27ac) and moderate levels of silencing chromatin mark H3K9me3. Curiously, another enhancer mark H3K4me1 is missing, whereas DNA methylation is still maintained in the structure, which spreads across gene bodies and neighboring regions within the Zscan4 gene cluster. We also found by function analyses of Rif1 domains in ES cells that ectopic expression of Rif1 lacking N-terminal domain results in upregulation of 2C transcripts. This appears to be caused by dominant negative inhibition of endogenous Rif1 protein localization at the nuclear periphery through formation of hetero-oligomers between the N-terminally truncated and endogenous forms. Strikingly, in murine 2C embryos, most of Rif1-derived polypeptides are expressed as truncated forms in soluble nuclear or cytosolic fraction and are likely nonfunctional. Toward the morula stage, the full-length form of Rif1 gradually increased. Our results suggest that the absence of the functional full-length Rif1 due to its instability or alternative splicing and potential inactivation of Rif1 through dominant inhibition by N-terminally truncated Rif1 polypeptides may be involved in 2C-specific transcription program.
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Key Words
- 2c, two-cell (embryo)
- 4-oht, 4-hydroxytamoxifen
- dox, doxycycline
- erv, endogenous retrovirus
- es, embryonic stem
- hpf, hours post fertilization
- idr, intrinsic disordered region
- ivf, in vitro fertilization
- kd, knockdown
- ko, knockout
- rt, room temperature
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Affiliation(s)
| | - Satoshi Yamazaki
- Genome Dynamics Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Kaoru Mita-Yoshida
- Center for Basic Technology Research, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Tomio Ono
- Center for Basic Technology Research, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Yasumasa Nishito
- Center for Basic Technology Research, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Hisao Masai
- Genome Dynamics Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.
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14
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Rykov SV, Filippova EA, Loginov VI, Braga EA. Gene Methylation in Circulating Cell-Free DNA from the Blood Plasma as Prognostic and Predictive Factor in Breast Cancer. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421110120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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15
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Kerachian MA, Azghandi M, Mozaffari-Jovin S, Thierry AR. Guidelines for pre-analytical conditions for assessing the methylation of circulating cell-free DNA. Clin Epigenetics 2021; 13:193. [PMID: 34663458 PMCID: PMC8525023 DOI: 10.1186/s13148-021-01182-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/04/2021] [Indexed: 02/06/2023] Open
Abstract
Methylation analysis of circulating cell-free DNA (cirDNA), as a liquid biopsy, has a significant potential to advance the detection, prognosis, and treatment of cancer, as well as many genetic disorders. The role of epigenetics in disease development has been reported in several hereditary disorders, and epigenetic modifications are regarded as one of the earliest and most significant genomic aberrations that arise during carcinogenesis. Liquid biopsy can be employed for the detection of these epigenetic biomarkers. It consists of isolation (pre-analytical) and detection (analytical) phases. The choice of pre-analytical variables comprising cirDNA extraction and bisulfite conversion methods can affect the identification of cirDNA methylation. Indeed, different techniques give a different return of cirDNA, which confirms the importance of pre-analytical procedures in clinical diagnostics. Although novel techniques have been developed for the simplification of methylation analysis, the process remains complex, as the steps of DNA extraction, bisulfite treatment, and methylation detection are each carried out separately. Recent studies have noted the absence of any standard method for the pre-analytical processing of methylated cirDNA. We have therefore conducted a comprehensive and systematic review of the important pre-analytical and analytical variables and the patient-related factors which form the basis of our guidelines for analyzing methylated cirDNA in liquid biopsy.
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Affiliation(s)
- Mohammad Amin Kerachian
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran.
| | - Marjan Azghandi
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Sina Mozaffari-Jovin
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Alain R Thierry
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier, France.
- INSERM, U1194, Montpellier, France.
- University of Montpellier, Montpellier, France.
- ICM, Regional Institute of Cancer of Montpellier, Montpellier, France.
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16
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Assessment of Circulating Nucleic Acids in Cancer: From Current Status to Future Perspectives and Potential Clinical Applications. Cancers (Basel) 2021; 13:cancers13143460. [PMID: 34298675 PMCID: PMC8307284 DOI: 10.3390/cancers13143460] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/01/2021] [Accepted: 07/06/2021] [Indexed: 02/06/2023] Open
Abstract
Current approaches for cancer detection and characterization are based on radiological procedures coupled with tissue biopsies, despite relevant limitations in terms of overall accuracy and feasibility, including relevant patients' discomfort. Liquid biopsies enable the minimally invasive collection and analysis of circulating biomarkers released from cancer cells and stroma, representing therefore a promising candidate for the substitution or integration in the current standard of care. Despite the potential, the current clinical applications of liquid biopsies are limited to a few specific purposes. The lack of standardized procedures for the pre-analytical management of body fluids samples and the detection of circulating biomarkers is one of the main factors impacting the effective advancement in the applicability of liquid biopsies to clinical practice. The aim of this work, besides depicting current methods for samples collection, storage, quality check and biomarker extraction, is to review the current techniques aimed at analyzing one of the main circulating biomarkers assessed through liquid biopsy, namely cell-free nucleic acids, with particular regard to circulating tumor DNA (ctDNA). ctDNA current and potential applications are reviewed as well.
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17
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Verma N, Alyethodi RR, Kathuria A, Alex R, Hussain S, Singh U, Tyagi S, Sirohi AS, Kumar S, Sengar GS, Raja TV, Prakash B. Comparative CpG methylation kinetic patterns of cis-regulatory regions of heat stress-related genes in Sahiwal and Frieswal cattle upon persistent heat stress. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2021; 65:1025-1032. [PMID: 33683454 DOI: 10.1007/s00484-021-02084-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 11/24/2020] [Accepted: 01/18/2021] [Indexed: 06/12/2023]
Abstract
The kinetic patterns of CpG methylation of the cis-regulatory region of heat stress-related genes on exposed to heat stress (at 42 °C) between the Sahiwal and Frieswal cattle was compared in the present study. Using an in vitro whole blood culture model, cells were continuously exposed to heat stress (at 42 °C) for 6 h. Methylation levels of five genes, viz., GPX1, HSP70, HSP90, c-FOS, and JUN were estimated by SyberGreen-based quantitative methylation-specific PCR (qMSP) assay. CpG methylation kinetics at different time points of heat stress (0.5, 1, 2, 4, 6 h) were analyzed using mixed ANOVA. The initial methylation level, estimated at 37 °C, of HSP70 was significantly high in the Sahiwal breed. A significant (p<0.001) time-dependent hypomethylation of an antioxidant gene (GPX1) CpG islands was detected at the acute phase of the stress. Heat shock protein gene (HSP70) showed a similar CpG methylation kinetics where the hypomethylation was prominent from 1 h and persisted up to 4 h. The heat stress responses of both Sahiwal and Frieswal cattle were identical as there was no distinctiveness in the methylation kinetics of CpG islands of studied genes. The acclimatization of Frieswal cattle-a breed developed in India over the years to the tropical climatic conditions, maybe one of the reasons for this similarity. Thus, the present study results could pave a path to understand the molecular mechanism of heat stress and adaptation of indigenous and crossbred cattle populations to the changing scenario in tropical climate conditions.
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Affiliation(s)
- Nitika Verma
- Department of Biotechnology and Microbiology, MIET, Meerut, India
| | - Rafeeque R Alyethodi
- ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India.
| | - Ashima Kathuria
- Department of Biotechnology and Microbiology, MIET, Meerut, India
| | - Rani Alex
- ICAR-National Dairy Research Institute, Karnal, India
| | - Shaziya Hussain
- Department of Biotechnology and Microbiology, MIET, Meerut, India
| | - Umesh Singh
- ICAR-Central Institute for Research on Cattle, Meerut, UP, India
| | - S Tyagi
- ICAR-Central Institute for Research on Cattle, Meerut, UP, India
| | | | - Sushil Kumar
- ICAR-Central Institute for Research on Cattle, Meerut, UP, India
| | | | - T V Raja
- ICAR-Central Institute for Research on Cattle, Meerut, UP, India
| | - B Prakash
- ICAR-Central Institute for Research on Cattle, Meerut, UP, India
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18
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Knight P, Gauthier MPL, Pardo CE, Darst RP, Kapadia K, Browder H, Morton E, Riva A, Kladde MP, Bacher R. Methylscaper: an R/shiny app for joint visualization of DNA methylation and nucleosome occupancy in single-molecule and single-cell data. Bioinformatics 2021; 37:4857-4859. [PMID: 34125875 PMCID: PMC8665741 DOI: 10.1093/bioinformatics/btab438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 04/19/2021] [Accepted: 06/11/2021] [Indexed: 11/13/2022] Open
Abstract
SUMMARY Differential DNA methylation and chromatin accessibility are associated with disease development, particularly cancer. Methods that allow profiling of these epigenetic mechanisms in the same reaction and at the single-molecule or single-cell level continue to emerge. However, a challenge lies in jointly visualizing and analyzing the heterogeneous nature of the data and extracting regulatory insight. Here, we present methylscaper, a visualization framework for simultaneous analysis of DNA methylation and chromatin accessibility landscapes. Methylscaper implements a weighted principal component analysis that orders DNA molecules, each providing a record of the chromatin state of one epiallele, and reveals patterns of nucleosome positioning, transcription factor occupancy, and DNA methylation. We demonstrate methylscaper's utility on a long-read, single-molecule methyltransferase accessibility protocol for individual templates (MAPit-BGS) dataset and a single-cell nucleosome, methylation, and transcription sequencing (scNMT-seq) dataset. In comparison to other procedures, methylscaper is able to readily identify chromatin features that are biologically relevant to transcriptional status while scaling to larger datasets. AVAILABILITY AND IMPLEMENTATION Methylscaper, is implemented in R (version > 4.1) and available on Bioconductor: https://bioconductor.org/packages/methylscaper/, GitHub: https://github.com/rhondabacher/methylscaper/, and Web: https://methylscaper.com. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Parker Knight
- Department of Biostatistics, University of Florida, Gainesville, FL
| | | | - Carolina E Pardo
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL
| | - Russell P Darst
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL
| | - Kevin Kapadia
- Department of Statistics, University of Florida, Gainesville, FL
| | - Hadley Browder
- Department of Statistics, University of Florida, Gainesville, FL
| | - Eliza Morton
- Department of Statistics, University of Florida, Gainesville, FL
| | - Alberto Riva
- Bioinformatics Core, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida
| | - Michael P Kladde
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL
| | - Rhonda Bacher
- Department of Biostatistics, University of Florida, Gainesville, FL
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19
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Wojewodzic MW, Leithaug M, Lauritzen M, Lyle R, Haglund S, Rubin CJ, Ewels PA, Grotmol T, Rounge TB. Ultralow amounts of DNA from long-term archived serum samples produce high-quality methylomes. Clin Epigenetics 2021; 13:107. [PMID: 33980276 PMCID: PMC8114536 DOI: 10.1186/s13148-021-01097-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/02/2021] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Long-term stored serum is considered challenging for epigenomic analyses: as there are no cells, circulating DNA is scarce, and amplification removes epigenetic signals. Additionally, pre-analytical treatments and storage might introduce biases and fragmentation to the DNA. In particular, starting with low-input DNA can result in low-diversity libraries. However, successful whole-genome bisulphite sequencing (WGBS) of such serum samples has the potential to open biobanks for epigenetic analyses and deliver novel prediagnostic biomarkers. Here, we perform WGBS using the Accel-NGS library preparation kit on ultralow amounts of DNA from long-term archived samples with diverse pretreatments from the Janus Serum Bank. RESULTS Ninety-four of the 96 samples produced satisfactory methylation calls; an average of 578 M reads per sample generated a mean coverage of 17× and mean duplication level of 35%. Failed samples were related to poor bisulphite conversion rather than to sequencing or library preparation. We demonstrate the feasibility of WGBS on ultralow DNA yields from serum samples stored up to 48 years. CONCLUSIONS Our results show the potential of large serum biobank collections for future epigenomic studies and biomarker discovery.
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Affiliation(s)
| | - Magnus Leithaug
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | | | - Robert Lyle
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Sofia Haglund
- Science for Life Laboratory (SciLifeLab), Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Carl-Johan Rubin
- Department of Medical Biochemistry and Microbiology, Uppsala University, 75123, Uppsala, Sweden
| | - Philip A Ewels
- Science for Life Laboratory (SciLifeLab), Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Tom Grotmol
- Department of Research, Cancer Registry of Norway, Oslo, Norway
| | - Trine B Rounge
- Department of Research, Cancer Registry of Norway, Oslo, Norway
- Centre for Bioinformatics, University of Oslo, Oslo, Norway
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20
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Hoedt EC, Bottacini F, Cash N, Bongers RS, van Limpt K, Ben Amor K, Knol J, MacSharry J, van Sinderen D. Broad Purpose Vector for Site-Directed Insertional Mutagenesis in Bifidobacterium breve. Front Microbiol 2021; 12:636822. [PMID: 33833740 PMCID: PMC8021953 DOI: 10.3389/fmicb.2021.636822] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/02/2021] [Indexed: 11/28/2022] Open
Abstract
Members of the genus Bifidobacterium are notoriously recalcitrant to genetic manipulation due to their extensive and variable repertoire of Restriction-Modification (R-M) systems. Non-replicating plasmids are currently employed to achieve insertional mutagenesis in Bifidobacterium. One of the limitations of using such insertion vectors is the presence within their sequence of various restriction sites, making them sensitive to the activity of endogenous restriction endonucleases encoded by the target strain. For this reason, vectors have been developed with the aim of methylating and protecting the vector using a methylase-positive Escherichia coli strain, in some cases containing a cloned bifidobacterial methylase. Here, we present a mutagenesis approach based on a modified and synthetically produced version of the suicide vector pORI28 (named pFREM28), where all known restriction sites targeted by Bifidobacterium breve R-M systems were removed by base substitution (thus preserving the codon usage). After validating the integrity of the erythromycin marker, the vector was successfully employed to target an α-galactosidase gene responsible for raffinose metabolism, an alcohol dehydrogenase gene responsible for mannitol utilization and a gene encoding a priming glycosyltransferase responsible for exopolysaccharides (EPS) production in B. breve. The advantage of using this modified approach is the reduction of the amount of time, effort and resources required to generate site-directed mutants in B. breve and a similar approach may be employed to target other (bifido)bacterial species.
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Affiliation(s)
- Emily C Hoedt
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,NHMRC Centre of Research Excellence in Digestive Health, School of Medicine and Public Health, The University of Newcastle, Callaghan, NSW, Australia
| | - Francesca Bottacini
- NHMRC Centre of Research Excellence in Digestive Health, School of Medicine and Public Health, The University of Newcastle, Callaghan, NSW, Australia.,Department of Biological Sciences, Munster Technological University, Cork, Ireland
| | - Nora Cash
- NHMRC Centre of Research Excellence in Digestive Health, School of Medicine and Public Health, The University of Newcastle, Callaghan, NSW, Australia
| | | | | | | | - Jan Knol
- Danone Nutricia Research, Utrecht, Netherlands.,Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | - John MacSharry
- NHMRC Centre of Research Excellence in Digestive Health, School of Medicine and Public Health, The University of Newcastle, Callaghan, NSW, Australia.,School of Microbiology, University College Cork, Cork, Ireland.,School of Medicine, University College Cork, Cork, Ireland
| | - Douwe van Sinderen
- NHMRC Centre of Research Excellence in Digestive Health, School of Medicine and Public Health, The University of Newcastle, Callaghan, NSW, Australia.,School of Microbiology, University College Cork, Cork, Ireland
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21
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Yang F, Li L, Lin S. Methylation Pattern and Expression Dynamics of Methylase and Photosystem Genes Under varying light Intensities in Fugacium kawagutii (Symbiodiniaceae). JOURNAL OF PHYCOLOGY 2020; 56:1738-1747. [PMID: 32920818 DOI: 10.1111/jpy.13070] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 06/11/2023]
Abstract
Previous studies have documented extensive methylation of CpG islands and abundant methyltransferase gene (DNMT) in Fugacium kawagutii (formerly Symbiodinium kawagutii) genome. However, whether DNA methylation plays a role in regulating gene expression in this and other dinoflagellates remains unclear. Here, we characterized gene body methylation levels using methylation-specific PCR (MS-PCR) and bisulfite sequencing PCR (BSP) and measured transcriptional levels for three photosystem genes in F. kawagutii under different light conditions (20, 100, and 600 µE · m-2 · s-1 ). To explore the association of methylation with DNA methylase, the expression of DNA methyltransferase (Symbio-DIRS-Dnmt3) was also measured. Our results showed that peridinin-chlorophyll a-binding protein (PCP), light-harvesting complex (LHC), and chlorophyll a-c-binding protein complex (acpPC) gene expression was all significantly up-regulated under low light in which their methylation level was down-regulated, constant, and elevated, respectively. Symbio-DIRS-Dnmt3 exhibited elevated transcriptional level under increased light intensity. The results led us to hypothesize that DNA methylation level can be modulated by environmental conditions such as irradiance, probably through the regulation of Symbio-DIRS-Dnmt3 transcription level, and in turn may regulate the expression of genes in F. kawagutii. Further study is needed to determine whether the same gene methylation and expression characteristics reported here occur in other dinoflagellates and to explore their ecological implications.
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Affiliation(s)
- Feng Yang
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, 36100, China
| | - Ling Li
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, 36100, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, 36100, China
- Department of Marine Sciences, University of Connecticut, Groton, CT, 06340, United States
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22
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Chapman KB, Higgs BW. Selective amplification of hypermethylated DNA from diverse tumor types via MSRE-PCR. Oncotarget 2020; 11:4387-4400. [PMID: 33315971 PMCID: PMC7720775 DOI: 10.18632/oncotarget.27825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 11/12/2020] [Indexed: 12/02/2022] Open
Abstract
DNA methylation biomarkers are increasingly utilized for the detection, prognosis and monitoring of cancer. Here we use publicly-available whole genome bisulfite sequencing data to identify differentially methylated regions (cDMRs) in diverse tumor types and further define a set of genomic target regions that have optimal characteristics for Methylation Sensitive Restriction Enzyme-PCR (MSRE-PCR)-based detection: conserved hypermethylation in tumors, abundant MSRE sites and low methylation levels in normal tissues. The identified MSRE-PCR target regions (n = 1,294) were primarily encompassed within CpG islands (97%) and promoters (81%) with 39% of the target regions overlapping the transcription start site. Gene set enrichment analysis of the target regions identified significant enrichment of genes involved in neuronal development. A multiplexed MSRE-PCR assay was developed interrogating 47 target regions and was tested on a set of genomic DNAs (n = 100) from diverse tumor and normal tissue types including colon, breast, lung, stomach and blood. A logistic regression model containing seven target region amplicons distinguished between tumor and normal tissue in the training (n = 50) with a ROC AUC of 0.97 (95% CI [0.92, 1]) and independent test set (n = 50) with an AUC of 0.93 (95% CI [0.84, 1]). These findings show that genomic regions with conserved hypermethylation across diverse tumor types, abundant MSRE sites and low methylation levels in normal tissues provide target regions for the detection of tumor DNA via MSRE-PCR. The selective amplification of tumor-derived DNA via MSRE-PCR may have utility in the development of non-invasive cancer detection and surveillance strategies.
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Affiliation(s)
- Karen B. Chapman
- Center for Biotechnology Education, Krieger School of Arts and Sciences, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Brandon W. Higgs
- Center for Biotechnology Education, Krieger School of Arts and Sciences, Johns Hopkins University, Baltimore, MD 21218, USA
- Genmab, Princeton, NJ 08540, USA
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23
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Saak CC, Dinh CB, Dutton RJ. Experimental approaches to tracking mobile genetic elements in microbial communities. FEMS Microbiol Rev 2020; 44:606-630. [PMID: 32672812 PMCID: PMC7476777 DOI: 10.1093/femsre/fuaa025] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/29/2020] [Indexed: 12/19/2022] Open
Abstract
Horizontal gene transfer is an important mechanism of microbial evolution and is often driven by the movement of mobile genetic elements between cells. Due to the fact that microbes live within communities, various mechanisms of horizontal gene transfer and types of mobile elements can co-occur. However, the ways in which horizontal gene transfer impacts and is impacted by communities containing diverse mobile elements has been challenging to address. Thus, the field would benefit from incorporating community-level information and novel approaches alongside existing methods. Emerging technologies for tracking mobile elements and assigning them to host organisms provide promise for understanding the web of potential DNA transfers in diverse microbial communities more comprehensively. Compared to existing experimental approaches, chromosome conformation capture and methylome analyses have the potential to simultaneously study various types of mobile elements and their associated hosts. We also briefly discuss how fermented food microbiomes, given their experimental tractability and moderate species complexity, make ideal models to which to apply the techniques discussed herein and how they can be used to address outstanding questions in the field of horizontal gene transfer in microbial communities.
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Affiliation(s)
- Christina C Saak
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Cong B Dinh
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Rachel J Dutton
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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24
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Mahajan V, Farquhar C, Ponnampalam AP. Could DNA hydroxymethylation be crucial in influencing steroid hormone signaling in endometrial biology and endometriosis? Mol Reprod Dev 2019; 87:7-16. [PMID: 31749216 DOI: 10.1002/mrd.23299] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 10/30/2019] [Indexed: 12/17/2022]
Abstract
Endometriosis affects 10% of reproductive-aged women. It is characterized by the growth of the endometrium, outside the uterus and is associated with infertility and chronic abdominal pain. Lack of noninvasive diagnostic tools and early screening tests results in delayed treatment and subsequently increased disease severity. Endometriosis is a disease associated with a deregulated hormonal response, therefore, understanding the molecular mechanisms that govern this hormonal interplay is of paramount importance. DNA methylation is an epigenetic mark that regulates gene expression and is often associated with genes that code for steroid receptors and enzymes associated with estrogen synthesis and metabolism in endometriosis. DNA hydroxymethylation, which is structurally similar to methylation but functionally different, is a biologically critical mechanism that is also known to regulate gene expression. Ten Eleven Translocation (TET) proteins mediate hydroxymethylation. However, the role of DNA hydroxymethylation or TETs in the endometrium remains relatively unexplored. Currently, the "gold standard" technique used to study methylation patterns is bisulfite genomic sequencing. This technique also detects hydroxymethylation but fails to distinguish between the two, thereby limiting our understanding of these two processes. The presence of TETs in the male and female reproductive tract and its contribution to endometrial cancer makes it an important factor to study in endometriosis. This review summarizes the role of DNA methylation in aberrant steroid hormone signaling and hypothesizes that hydroxymethylation could be a factor influencing hormonal instability seen in endometriosis.
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Affiliation(s)
- Vishakha Mahajan
- The Liggins Institute, The University of Auckland, Auckland, New Zealand
| | - Cynthia Farquhar
- Department of Obstetrics and Gynaecology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Anna P Ponnampalam
- The Liggins Institute, The University of Auckland, Auckland, New Zealand.,Department of Obstetrics and Gynaecology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand.,Department of Physiology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
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25
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Ramesh PS, Madegowda V, Kumar S, Narasimha S, S R P, Manoli NN, Devegowda D. DNA extraction from archived hematoxylin and eosin-stained tissue slides for downstream molecular analysis. World J Methodol 2019; 9:32-43. [PMID: 31799154 PMCID: PMC6885493 DOI: 10.5662/wjm.v9.i3.32] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 09/27/2019] [Accepted: 10/15/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Histopathologically stained archived tissue slides are stored in hospital archives for years to decades. They are the largest available source of biological materials and are a potentially useful resource that can be used for retrospective epidemiological studies. DNA recovered from the slides can be used for several downstream molecular processes including polymerase chain reaction, single nucleotide polymorphism analysis, and whole genome sequencing. The DNA from these slides can be utilized to compare gene signatures of normal and diseased tissues. However, extraction of high-quality DNA from archived stained hematoxylin and eosin (H&E) slides remains challenging.
AIM To standardize a new protocol for extracting DNA from archived H&E-stained tissue slides for further molecular assays.
METHODS A total of 100 archived H&E-stained cancer slides were subjected to a total of five methods of DNA extraction. Methods were varied in the deparaffinization step, tissue rehydration, duration of lysis, and presence or absence of proteinase K. The extracted DNA was quantified using a NanoDrop spectrophometer and the quality was analyzed by agarose gel electrophoresis. Then each sample was subjected to polymerase chain reaction (PCR) to amplify the internal control gene GAPDH, thereby confirming the DNA intactness, which could be further utilized for other downstream applications.
RESULTS Of the five different methods tested, the third method wherein xylene was used for tissue deparaffinization followed by 72 h of digestion and without proteinase K inactivation yielded the highest amount of DNA with good purity. The yield was significantly higher when compared to other methods. In addition, 90% of the extracted DNA showed amplifiable GAPDH gene.
CONCLUSION Here we present a step-by-step, cost-effective, and reproducible protocol for the extraction of PCR-friendly DNA from archived H&E-stained cancer tissue slides that can be used for further downstream molecular applications.
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Affiliation(s)
- Pushkal Sinduvadi Ramesh
- Center of Excellence in Molecular Biology and Regenerative Medicine, Department of Biochemistry, JSS Medical College, JSS Academy of Higher Education and Research, Mysuru 570015, India
| | - Venkatesh Madegowda
- Center of Excellence in Molecular Biology and Regenerative Medicine, Department of Biochemistry, JSS Medical College, JSS Academy of Higher Education and Research, Mysuru 570015, India
| | - Suprith Kumar
- Center of Excellence in Molecular Biology and Regenerative Medicine, Department of Biochemistry, JSS Medical College, JSS Academy of Higher Education and Research, Mysuru 570015, India
| | - Shailashree Narasimha
- Center of Excellence in Molecular Biology and Regenerative Medicine, Department of Biochemistry, JSS Medical College, JSS Academy of Higher Education and Research, Mysuru 570015, India
| | - Parichay S R
- CIPHER Healthcare Pvt Ltd., Hyderabad 500034, India
| | - Nandini Nandish Manoli
- Department of Pathology, JSS Medical College, JSS Academy of Higher Education and Research, Mysuru 570015, India
| | - Devananda Devegowda
- Center of Excellence in Molecular Biology and Regenerative Medicine, Department of Biochemistry, JSS Medical College, JSS Academy of Higher Education and Research, Mysuru 570015, India
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26
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Kader F, Ghai M, Olaniran AO. Characterization of DNA methylation-based markers for human body fluid identification in forensics: a critical review. Int J Legal Med 2019; 134:1-20. [PMID: 31713682 DOI: 10.1007/s00414-019-02181-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 10/15/2019] [Indexed: 02/07/2023]
Abstract
Body fluid identification in crime scene investigations aids in reconstruction of crime scenes. Several studies have identified and reported differentially methylated sites (DMSs) and regions (DMRs) which differ between forensically relevant tissues (tDMRs) and body fluids. Diverse factors affect methylation patterns such as the environment, diets, lifestyle, disease, ethnicity, genetic variation, amongst others. Thus, it is important to analyse the stability of markers employed for forensic identification. Furthermore, even though epigenetic modifications are described as stable and heritable, epigenetic inheritance of potential markers for body fluid identification needs to be assessed in the long term. Here, we discuss the current status of reported DNA methylation-based markers and their verification studies. Such thorough investigation is crucial to develop a stable panel of DNA methylation-based markers for accurate body fluid identification.
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Affiliation(s)
- Farzeen Kader
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Private Bag X54001, Durban, Republic of South Africa
| | - Meenu Ghai
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Private Bag X54001, Durban, Republic of South Africa.
| | - Ademola O Olaniran
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Private Bag X54001, Durban, Republic of South Africa
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27
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Oberbeckmann E, Wolff M, Krietenstein N, Heron M, Ellins JL, Schmid A, Krebs S, Blum H, Gerland U, Korber P. Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome. Genome Res 2019; 29:1996-2009. [PMID: 31694866 PMCID: PMC6886505 DOI: 10.1101/gr.253419.119] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 10/31/2019] [Indexed: 12/23/2022]
Abstract
Mapping of nucleosomes, the basic DNA packaging unit in eukaryotes, is fundamental for understanding genome regulation because nucleosomes modulate DNA access by their positioning along the genome. A cell-population nucleosome map requires two observables: nucleosome positions along the DNA ("Where?") and nucleosome occupancies across the population ("In how many cells?"). All available genome-wide nucleosome mapping techniques are yield methods because they score either nucleosomal (e.g., MNase-seq, chemical cleavage-seq) or nonnucleosomal (e.g., ATAC-seq) DNA but lose track of the total DNA population for each genomic region. Therefore, they only provide nucleosome positions and maybe compare relative occupancies between positions, but cannot measure absolute nucleosome occupancy, which is the fraction of all DNA molecules occupied at a given position and time by a nucleosome. Here, we established two orthogonal and thereby cross-validating approaches to measure absolute nucleosome occupancy across the Saccharomyces cerevisiae genome via restriction enzymes and DNA methyltransferases. The resulting high-resolution (9-bp) map shows uniform absolute occupancies. Most nucleosome positions are occupied in most cells: 97% of all nucleosomes called by chemical cleavage-seq have a mean absolute occupancy of 90 ± 6% (±SD). Depending on nucleosome position calling procedures, there are 57,000 to 60,000 nucleosomes per yeast cell. The few low absolute occupancy nucleosomes do not correlate with highly transcribed gene bodies, but correlate with increased presence of the nucleosome-evicting chromatin structure remodeling (RSC) complex, and are enriched upstream of highly transcribed or regulated genes. Our work provides a quantitative method and reference frame in absolute terms for future chromatin studies.
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Affiliation(s)
- Elisa Oberbeckmann
- Molecular Biology Division, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Michael Wolff
- Physik Department, Technische Universität München, 85748 Garching, Germany
| | - Nils Krietenstein
- Molecular Biology Division, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Mark Heron
- Quantitative and Computational Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.,Gene Center, Faculty of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Jessica L Ellins
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom
| | - Andrea Schmid
- Molecular Biology Division, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Stefan Krebs
- Laboratory of Functional Genome Analysis (LAFUGA), Gene Center, Faculty of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Helmut Blum
- Laboratory of Functional Genome Analysis (LAFUGA), Gene Center, Faculty of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Ulrich Gerland
- Physik Department, Technische Universität München, 85748 Garching, Germany
| | - Philipp Korber
- Molecular Biology Division, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
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28
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Quantitative Methylation-Specific PCR: A Simple Method for Studying Epigenetic Modifications of Cell-Free DNA. Methods Mol Biol 2019; 1909:137-162. [PMID: 30580429 DOI: 10.1007/978-1-4939-8973-7_11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Aberrant DNA methylation of cell-free circulating DNA (cfDNA) has recently gained attention for its use as biomarker in cancer diagnosis, prognosis, and prediction of therapeutic response. Quantification of cfDNA methylation levels requires methods with high sensitivity and specificity due to low amounts of cfDNA available in plasma, high degradation of cfDNA, and/or contamination with genomic DNA. To date, several approaches for measuring cfDNA methylation have been established, including quantitative methylation-specific PCR (qMSP), which represents a simple, fast, and cost-effective technique that can be easily implemented into clinical practice. In this chapter, we provide a detailed protocol for SYBR Green qMSP analysis which is currently used in our laboratory for cfDNA methylation detection. Useful information regarding successful qMSP primers design are also provided.
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29
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Gao S, Hu X, Xu F, Gao C, Xiong K, Zhao X, Chen H, Zhao S, Wang M, Fu D, Zhao X, Bai J, Mao L, Li B, Wu S, Wang J, Li S, Yang H, Bolund L, Pedersen CNS. BS-virus-finder: virus integration calling using bisulfite sequencing data. Gigascience 2018; 7:1-7. [PMID: 29267855 PMCID: PMC5788064 DOI: 10.1093/gigascience/gix123] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 11/30/2017] [Indexed: 01/10/2023] Open
Abstract
Background DNA methylation plays a key role in the regulation of gene expression and carcinogenesis. Bisulfite sequencing studies mainly focus on calling single nucleotide polymorphism, different methylation region, and find allele-specific DNA methylation. Until now, only a few software tools have focused on virus integration using bisulfite sequencing data. Findings We have developed a new and easy-to-use software tool, named BS-virus-finder (BSVF, RRID:SCR_015727), to detect viral integration breakpoints in whole human genomes. The tool is hosted at https://github.com/BGI-SZ/BSVF. Conclusions BS-virus-finder demonstrates high sensitivity and specificity. It is useful in epigenetic studies and to reveal the relationship between viral integration and DNA methylation. BS-virus-finder is the first software tool to detect virus integration loci by using bisulfite sequencing data.
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Affiliation(s)
- Shengjie Gao
- Bioinformatics Research Center, Aarhus University, C. F. Møllers Allé 8, DK-8000, Aarhus C, Denmark.,Forensics Genomics International (FGI), BGI-Shenzhen, BeiShan Industrial Zone, Yantian District, Shenzhen, Guangdong 518083, China.,BGI-Shenzhen, BeiShan Industrial Zone, Yantian District, Shenzhen, Guangdong 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou 310058, China.,The Affiliated Luohu Hospital of Shenzhen University, Shenzhen University, Shenzhen 518000, China.,Department of Biomedicine, Aarhus University, Vennelyst Boulevard 4, DK-8000 Aarhus C, Denmark
| | - Xuesong Hu
- Forensics Genomics International (FGI), BGI-Shenzhen, BeiShan Industrial Zone, Yantian District, Shenzhen, Guangdong 518083, China.,BGI-Shenzhen, BeiShan Industrial Zone, Yantian District, Shenzhen, Guangdong 518083, China
| | - Fengping Xu
- BGI-Shenzhen, BeiShan Industrial Zone, Yantian District, Shenzhen, Guangdong 518083, China.,Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Changduo Gao
- College of Computer Science and Technology, Qingdao University, Qingdao 266071, China
| | - Kai Xiong
- Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, Grønnegårdsvej 15, DK-1870 Frederiksberg C, Denmark
| | - Xiao Zhao
- Forensics Genomics International (FGI), BGI-Shenzhen, BeiShan Industrial Zone, Yantian District, Shenzhen, Guangdong 518083, China.,BGI Education Center, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haixiao Chen
- BGI-Shenzhen, BeiShan Industrial Zone, Yantian District, Shenzhen, Guangdong 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Shancen Zhao
- BGI-Shenzhen, BeiShan Industrial Zone, Yantian District, Shenzhen, Guangdong 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Mengyao Wang
- BGI-Shenzhen, BeiShan Industrial Zone, Yantian District, Shenzhen, Guangdong 518083, China
| | - Dongke Fu
- Forensics Genomics International (FGI), BGI-Shenzhen, BeiShan Industrial Zone, Yantian District, Shenzhen, Guangdong 518083, China
| | - Xiaohui Zhao
- College of Mathematics & Statistics, Changsha University of Science and Technology, Changsha 410114, China
| | - Jie Bai
- BGI-Shenzhen, BeiShan Industrial Zone, Yantian District, Shenzhen, Guangdong 518083, China
| | - Likai Mao
- BGI-Shenzhen, BeiShan Industrial Zone, Yantian District, Shenzhen, Guangdong 518083, China
| | - Bo Li
- Forensics Genomics International (FGI), BGI-Shenzhen, BeiShan Industrial Zone, Yantian District, Shenzhen, Guangdong 518083, China.,BGI-Shenzhen, BeiShan Industrial Zone, Yantian District, Shenzhen, Guangdong 518083, China
| | - Song Wu
- The Affiliated Luohu Hospital of Shenzhen University, Shenzhen University, Shenzhen 518000, China
| | - Jian Wang
- BGI-Shenzhen, BeiShan Industrial Zone, Yantian District, Shenzhen, Guangdong 518083, China
| | - Shengbin Li
- Forensics Genomics International (FGI), BGI-Shenzhen, BeiShan Industrial Zone, Yantian District, Shenzhen, Guangdong 518083, China.,Shenzhen Key Laboratory of Forensics, BGI-Shenzhen, Shenzhen 518083, China.,College of Medicine and Forensics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Huangming Yang
- BGI-Shenzhen, BeiShan Industrial Zone, Yantian District, Shenzhen, Guangdong 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou 310058, China.,BGI Education Center, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lars Bolund
- Department of Biomedicine, Aarhus University, Vennelyst Boulevard 4, DK-8000 Aarhus C, Denmark
| | - Christian N S Pedersen
- Bioinformatics Research Center, Aarhus University, C. F. Møllers Allé 8, DK-8000, Aarhus C, Denmark
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30
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Taman H, Fenton CG, Hensel IV, Anderssen E, Florholmen J, Paulssen RH. Genome-wide DNA Methylation in Treatment-naïve Ulcerative Colitis. J Crohns Colitis 2018; 12:1338-1347. [PMID: 30137272 PMCID: PMC6236200 DOI: 10.1093/ecco-jcc/jjy117] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND AND AIMS The aim of this study was to investigate the genome-wide DNA methylation status in treatment-naïve ulcerative colitis [UC], and to explore the relationship between DNA methylation patterns and gene expression levels in tissue biopsies from a well-stratified treatment-naïve UC patient group. METHODS Mucosal biopsies from treatment-naïve patients [n = 10], and a healthy control group [n = 11] underwent genome-wide DNA bisulfite sequencing. Principal component analysis [PCA] and diverse statistical methods were applied to obtain a dataset of differentially methylated genes. DNA methylation annotation was investigated using the UCSC Genome Browser. Gene set enrichments were obtained using the Kyoto Encyclopaedia of Genes and Genomes [KEGG] and PANTHER. RESULTS Of all significantly differentially expressed genes [DEGs], 25% correlated with DNA methylation patterns; 30% of these genes were methylated at CpG sites near their transcription start site [TSS]. Hyper-methylation was observed for genes involved in homeostasis and defence, whereas hypo-methylation was observed for genes playing a role in immune response [i.e. chemokines and interleukins]. Of the differentially DNA methylated genes, 25 were identified as inflammatory bowel disease [IBD] susceptibility genes. Four genes [DEFFA6, REG1B, BTNL3, OLFM4] showed DNA methylation in the absence of known CpG islands. CONCLUSIONS Genome-wide DNA methylation analysis revealed distinctive functional patterns for hyper-and hypo-methylation in treatment-naïve UC. These distinct patterns could be of importance in the development and pathogenesis of UC. Further investigation of DNA methylation patterns may be useful in the development of the targeting of epigenetic processes, and may allow new treatment and target strategies for UC patients.
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Affiliation(s)
- Hagar Taman
- Genomics Support Centre Tromsø [GSCT], Department of Clinical Medicine, Arctic University of Norway, Tromsø, Norway
| | - Christopher G Fenton
- Genomics Support Centre Tromsø [GSCT], Department of Clinical Medicine, Arctic University of Norway, Tromsø, Norway
| | - Inga V Hensel
- Genomics Support Centre Tromsø [GSCT], Department of Clinical Medicine, Arctic University of Norway, Tromsø, Norway,Gastroenterology and Nutrition Research Group, Department of Clinical Medicine, Arctic University of Norway, Tromsø, Norway
| | - Endre Anderssen
- Genomics Support Centre Tromsø [GSCT], Department of Clinical Medicine, Arctic University of Norway, Tromsø, Norway
| | - Jon Florholmen
- Gastroenterology and Nutrition Research Group, Department of Clinical Medicine, Arctic University of Norway, Tromsø, Norway,Department of Gastroenterology, University Hospital of North Norway, Tromsø, Norway
| | - Ruth H Paulssen
- Genomics Support Centre Tromsø [GSCT], Department of Clinical Medicine, Arctic University of Norway, Tromsø, Norway,Gastroenterology and Nutrition Research Group, Department of Clinical Medicine, Arctic University of Norway, Tromsø, Norway,Corresponding author: Ruth H. Paulssen, PhD, Department of Clinical Medicine, Gastroenterology and Nutrition Research Group, UiT The Arctic University of Norway, Faculty of Health, Sykehusveien 38, N-9038 Tromsø, Norway/ Tel.: +47 77 64 54 80;
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31
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Gardiner LJ, Joynson R, Omony J, Rusholme-Pilcher R, Olohan L, Lang D, Bai C, Hawkesford M, Salt D, Spannagl M, Mayer KFX, Kenny J, Bevan M, Hall N, Hall A. Hidden variation in polyploid wheat drives local adaptation. Genome Res 2018; 28:1319-1332. [PMID: 30093548 PMCID: PMC6120627 DOI: 10.1101/gr.233551.117] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 07/16/2018] [Indexed: 12/20/2022]
Abstract
Wheat has been domesticated into a large number of agricultural environments and has the ability to adapt to diverse environments. To understand this process, we survey genotype, repeat content, and DNA methylation across a bread wheat landrace collection representing global genetic diversity. We identify independent variation in methylation, genotype, and transposon copy number. We show that these, so far unexploited, sources of variation have had a significant impact on the wheat genome and that ancestral methylation states become preferentially "hard coded" as single nucleotide polymorphisms (SNPs) via 5-methylcytosine deamination. These mechanisms also drive local adaption, impacting important traits such as heading date and salt tolerance. Methylation and transposon diversity could therefore be used alongside SNP-based markers for breeding.
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Affiliation(s)
| | - Ryan Joynson
- Earlham Institute, Norwich, NR4 7UZ, United Kingdom
| | - Jimmy Omony
- HelmholtzZentrum München, German Research Center for Environmental Health, Munich, 85764, Germany
| | | | - Lisa Olohan
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Daniel Lang
- HelmholtzZentrum München, German Research Center for Environmental Health, Munich, 85764, Germany
| | - Caihong Bai
- Rothamsted Research, Harpenden, AL5 2JQ, United Kingdom
| | | | - David Salt
- University of Nottingham, Sutton Bonington Campus, Sutton Bonington, LE12 5RD, United Kingdom
| | - Manuel Spannagl
- HelmholtzZentrum München, German Research Center for Environmental Health, Munich, 85764, Germany
| | - Klaus F X Mayer
- HelmholtzZentrum München, German Research Center for Environmental Health, Munich, 85764, Germany.,Wissenschaftszentrum Weihenstephan (WZW), Technical University Munich, Freising, 85354, Germany
| | - John Kenny
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | | | - Neil Hall
- Earlham Institute, Norwich, NR4 7UZ, United Kingdom.,School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | - Anthony Hall
- Earlham Institute, Norwich, NR4 7UZ, United Kingdom.,School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
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32
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Kint S, De Spiegelaere W, De Kesel J, Vandekerckhove L, Van Criekinge W. Evaluation of bisulfite kits for DNA methylation profiling in terms of DNA fragmentation and DNA recovery using digital PCR. PLoS One 2018; 13:e0199091. [PMID: 29902267 PMCID: PMC6002050 DOI: 10.1371/journal.pone.0199091] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 05/31/2018] [Indexed: 02/06/2023] Open
Abstract
DNA methylation is one of the most important epigenetic modifications in the regulation of gene transcription. The current gold standard to study this modification is bisulfite sequencing. Although multiple commercial bisulfite treatment kits provide good conversion efficiencies, DNA loss and especially DNA fragmentation remain troublesome. This hampers DNA methylation profiling of long DNA sequences. Here, we explored the performance of twelve commercial bisulfite kits by an in-depth comparison of DNA fragmentation using gel electrophoresis, qPCR and digital PCR, DNA recovery by spectroscopic measurements and digital PCR and conversion efficiency by next generation sequencing. The results show a clear performance difference between the bisulfite kits, and depending on the specific goal of the study, the most appropriate kit might differ. Moreover, we demonstrated that digital PCR is a valuable method to monitor both DNA fragmentation as well as DNA recovery after bisulfite treatment.
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Affiliation(s)
- Sam Kint
- Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- HIV Cure Research Center, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Ghent, Belgium
- * E-mail:
| | - Ward De Spiegelaere
- Department of Morphology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Jonas De Kesel
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Wim Van Criekinge
- Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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33
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Crime investigation through DNA methylation analysis: methods and applications in forensics. EGYPTIAN JOURNAL OF FORENSIC SCIENCES 2018. [DOI: 10.1186/s41935-018-0042-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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34
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Accomando WP, Michels KB. Multiplexed Reduced Representation Bisulfite Sequencing with Magnetic Bead Fragment Size Selection. Methods Mol Biol 2018; 1708:137-159. [PMID: 29224143 DOI: 10.1007/978-1-4939-7481-8_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Reduced representation bisulfite sequencing (RRBS) is a technique for assessing genome-wide DNA methylation in an organism whose genome has been fully sequenced. It allows researchers to target gene regions with particular CpG densities, thereby selecting the desired genomic contexts. Here, we describe an approach that uses magnetic beads to accomplish this selection. In addition, the use of indexed, methylated adapters enables up to 12 samples to be pooled, and subjected to multiplexed RRBS in a single-sequencing lane. First, genomic DNA is fragmented via restriction endonuclease digestion that ensures at least two CpG loci per fragment. The fragmented DNA is then end-repaired and A-tailed. Indexed, methylated adapters are ligated to the A-tailed DNA fragments to create a DNA library. A combination of negative and positive selections, using magnetic beads that preferentially bind to larger DNA fragments, ensures that only the desired sizes of adapter-ligated DNA fragments are included in a library. This allows researchers to dictate what types of genomic regions will be sequenced, since fragment size depends on the proximity of restriction sites. The DNA libraries are then quantified, and up to 12 libraries are pooled in order to be sequenced on a single lane of an Illumina HiSeq2500. The pools are next treated with sodium bisulfite, and then PCR amplified. A final bead cleanup removes any residual contaminants prior to sequencing, which is followed by base calling and alignment to a sequenced genome.
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Affiliation(s)
- William P Accomando
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, 02115, USA.
- Obstetrics and Gynecology Epidemiology Center, Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, 221 Longwood Avenue, Boston, MA, 02115, USA.
| | - Karin B Michels
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA, 90095, USA
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35
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Abstract
Circulating cell-free DNA (ccfDNA) can be found in various body fluids, i.e., blood (serum and plasma), urine, pleural effusions, and ascites. While ccfDNA predominantly originates from physiological processes, a fraction might be related to pathological events, e.g., cancer. Aberrant DNA methylation, which is considered a hallmark of cancer, can be assessed accurately in ccfDNA. Consequently, DNA methylation testing in body fluids represents a powerful diagnostic tool in the clinical management of malignant diseases. Frequently, however, the total amount of disease-related ccfDNA in a sample is low and masked by an excess of physiological ccfDNA. Thus, DNA methylation analysis of tumor-derived DNA is challenging, and high volumes of body fluids need to be analyzed in order to ensure a sufficient abundance of the analyte in the test sample. DNA methylation assays are usually based on prior conversion of cytosines to uracils by means of bisulfite. This reaction takes place under harsh chemical conditions leading to DNA degradation and therefore necessitates a proper DNA purification before downstream analyses. This article describes a protocol which allows for the preparation of ultra-pure bisulfite-converted DNA from up to 3 ml blood plasma and serum, which is well suited for subsequent molecular biological techniques, e.g., methylation-specific real-time PCR.
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Affiliation(s)
- Dimo Dietrich
- Institute of Pathology, University Hospital of Bonn, Bonn, Germany.
- Department of Otolaryngology, Head and Neck Surgery, University Hospital Bonn, Sigmund-Freud-Str. 25, 53105, Bonn, Germany.
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36
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Jung M, Kristiansen G, Dietrich D. DNA Methylation Analysis of Free-Circulating DNA in Body Fluids. Methods Mol Biol 2018; 1708:621-641. [PMID: 29224167 DOI: 10.1007/978-1-4939-7481-8_32] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Circulating cell-free DNA in body fluids is an analyte of great interest in basic and clinical research. The analyses of DNA methylation and hydroxymethylation patterns in body fluids might allow one to determine the certain state of a disease, in particular of cancer. DNA methylation biomarkers in liquid biopsies, i.e. blood plasma samples, may help optimizing personalized therapy for individual patients. DNA methylation analyses of specific loci usually require a bisulfite conversion of the DNA, which requires a sufficiently high amount of DNA at the appropriate concentration. However, free-circulating DNA is generally low concentrated. Therefore, high volumes of body fluids need to be analyzed. This high volume needs to be reduced in order to facilitate the bisulfite conversion. In addition, disease-related free-circulating DNA is even less abundant than normal DNA in the total amount of free-circulating DNA. Accordingly, analytical and pre-analytical methods are needed, which permit an accurate and sensitive quantification of single methylated DNA copies in the presence of unmethylated DNA in abundance.This protocol describes two methods for DNA enrichment from body fluids: DNA extraction by means of magnetic beads and polymer-mediated enrichment of DNA. Subsequent bisulfite conversion is achieved by means of a high-speed conversion protocol. Adaptions of the workflow required for the analysis of hydroxymethylation via oxidation 5-hydroxymethylcytosines to 5-formylcytosines prior to the bisulfite conversion are introduced. A quantitative real-time PCR based on the methylation-specific and HeavyMethyl PCR methodologies is introduced. This qPCR assay allows for an accurate and sensitive quantification of single copies of the DNA methylation biomarkers SHOX2 and SEPT9 in blood plasma. Specific issues regarding the analysis of body fluids and respective trouble shooting approaches are discussed.
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Affiliation(s)
- Maria Jung
- Institute of Pathology, University Hospital Bonn (UKB), Sigmund-Freud-Str. 25, 53127, Bonn, Germany
| | - Glen Kristiansen
- Institute of Pathology, University Hospital Bonn (UKB), Sigmund-Freud-Str. 25, 53127, Bonn, Germany
| | - Dimo Dietrich
- Institute of Pathology, University Hospital Bonn (UKB), Sigmund-Freud-Str. 25, 53127, Bonn, Germany.
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The Utilization of Formalin Fixed-Paraffin-Embedded Specimens in High Throughput Genomic Studies. Int J Genomics 2017; 2017:1926304. [PMID: 28246590 PMCID: PMC5299160 DOI: 10.1155/2017/1926304] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 01/09/2017] [Indexed: 01/09/2023] Open
Abstract
High throughput genomic assays empower us to study the entire human genome in short time with reasonable cost. Formalin fixed-paraffin-embedded (FFPE) tissue processing remains the most economical approach for longitudinal tissue specimen storage. Therefore, the ability to apply high throughput genomic applications to FFPE specimens can expand clinical assays and discovery. Many studies have measured the accuracy and repeatability of data generated from FFPE specimens using high throughput genomic assays. Together, these studies demonstrate feasibility and provide crucial guidance for future studies using FFPE specimens. Here, we summarize the findings of these studies and discuss the limitations of high throughput data generated from FFPE specimens across several platforms that include microarray, high throughput sequencing, and NanoString.
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Rogans SJ, Allie F, Tirant JE, Rey MEC. Small RNA and methylation responses in susceptible and tolerant landraces of cassava infected with South African cassava mosaic virus. Virus Res 2016; 225:10-22. [PMID: 27586073 DOI: 10.1016/j.virusres.2016.08.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 08/23/2016] [Accepted: 08/26/2016] [Indexed: 11/26/2022]
Abstract
Endogenous small RNAs (sRNAs) associated with gene regulatory mechanisms respond to virus infection, and virus-derived small RNAs (vsRNAs) have been implicated in recovery or symptom remission in some geminivirus-host interactions. Transcriptional gene silencing (TGS) (24 nt vsRNAs) and post transcriptional gene silencing (PTGS) (21-23 nt vsRNAs) have been associated with geminivirus intergenic (IR) and coding regions, respectively. In this Illumina deep sequencing study, we compared for the first time, the small RNA response to South African cassava mosaic virus (SACMV) of cassava landrace TME3 which shows a recovery and tolerant phenotype, and T200, a highly susceptible landrace. Interestingly, different patterns in the percentage of SACMV-induced normalized total endogenous sRNA reads were observed between T200 and TME3. Notably in virus-infected T200 there was an increase in 21 nt sRNAs during the early pre-symptomatic response (12dpi) compared to mock, while in TME3, the 22 nt sRNA size class was predominant at 32days post infection with SACMV. While vsRNAs of 21-24 nt size classes mapped to the entire SACMV DNA-A and DNA-B genome components in T200 and TME3, vsRNA population counts were lower at 32 (symptomatic stage) and 67 dpi (recovery stage) in tolerant TME3 compared with T200 (non-recovery). It is suggested that the high accumulation of primary vsRNAs, which correlated with high virus titers and severe symptoms in susceptible T200, may be due to failure to target SACMV-derived mRNA. Likewise, in contrast, in TME3 low vsRNA counts may represent efficient PTGS of viral mRNA, leading to a depletion/sequestration of vsRNA populations, supporting a role for PTGS in tolerance/recovery in TME3. Notably, in TME3 at recovery (67 dpi) the percentage (expressed as a percentage of total vsRNA counts) of redundant and non-redundant (unique) 24 nt vsRNAs increased dramatically. Since methylation of the SACMV genome was not detected by bisulfite sequencing, and vsRNA counts targeting the intergenic region (where the promoters reside) were very low in both the tolerant or susceptible landraces, we could not provide conclusive evidence that 24 nt vsRNA-mediated RNA directed genome methylation plays a central role in disease phenotype in these landraces, notwithstanding recognition for a possible role in histone modification in TME3. This work represents an important step toward understanding variable roles of sRNAs in different cassava genotype-geminivirus interactions.
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Affiliation(s)
- Sarah Jane Rogans
- School of Molecular and Cell Biology, University of the Witwatersrand, Private Bag 3, 2050, South Africa
| | - Farhahna Allie
- School of Molecular and Cell Biology, University of the Witwatersrand, Private Bag 3, 2050, South Africa
| | - Jason Edward Tirant
- School of Molecular and Cell Biology, University of the Witwatersrand, Private Bag 3, 2050, South Africa
| | - Marie Emma Chrissie Rey
- School of Molecular and Cell Biology, University of the Witwatersrand, Private Bag 3, 2050, South Africa.
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Recent Perspective of Next Generation Sequencing: Applications in Molecular Plant Biology and Crop Improvement. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/s40011-016-0770-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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40
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Ding L, Styblo M, Drobná Z, Hegde AN. Expression of the Longest RGS4 Splice Variant in the Prefrontal Cortex Is Associated with Single Nucleotide Polymorphisms in Schizophrenia Patients. Front Psychiatry 2016; 7:26. [PMID: 26973546 PMCID: PMC4770186 DOI: 10.3389/fpsyt.2016.00026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 02/16/2016] [Indexed: 11/23/2022] Open
Abstract
The Regulator of G protein signaling 4 (RGS4) gene is a candidate susceptibility gene for schizophrenia (SCZ). Previous studies showed that the mRNA level of the longest splice variant RGS4-1 was decreased in the dorsolateral prefrontal cortex (DLPFC) of SCZ patients compared with healthy controls. In this pilot study, we examined the possible mechanisms of RGS4-1 mRNA reduction in SCZ. We genotyped SNP1 (rs10917670), rs2661347, SNP4 (rs951436), SNP7 (rs951439), SNP18 (rs2661319), and rs10799897 (SNP9897) and tested the methylation status of CpG islands of the RGS4 gene in the postmortem DLPFC samples obtained from subjects with SCZ and bipolar disorder as well as healthy controls. RGS4-1 mRNA level was associated with five SNPs (SNP1, rs2661347, SNP4, SNP7, and SNP18) and their haplotypes but not with SNP9897. In addition, this study revealed that RGS4-1 mRNA was low in subjects with specific genotypes of SNP1, rs2661347, SNP4, SNP7, and SNP18. Lower RGS4-1 mRNA expression in the DLPFC of SCZ is associated with SNPs in the 5' regulatory region of the RGS4 gene but not with the methylation status of its CpG islands.
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Affiliation(s)
- Lan Ding
- Department of Nutrition, University of North Carolina at Chapel Hill , Chapel Hill, NC , USA
| | - Miroslav Styblo
- Department of Nutrition, University of North Carolina at Chapel Hill , Chapel Hill, NC , USA
| | - Zuzana Drobná
- Department of Nutrition, University of North Carolina at Chapel Hill , Chapel Hill, NC , USA
| | - Ashok N Hegde
- Department of Neurobiology and Anatomy, Wake Forest University School of Medicine, Winston-Salem, NC, USA; Department of Biological and Environmental Sciences, Georgia College and State University, Milledgeville, GA, USA
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Gardiner LJ, Quinton-Tulloch M, Olohan L, Price J, Hall N, Hall A. A genome-wide survey of DNA methylation in hexaploid wheat. Genome Biol 2015; 16:273. [PMID: 26653535 PMCID: PMC4674939 DOI: 10.1186/s13059-015-0838-3] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 11/17/2015] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND DNA methylation is an important mechanism of epigenetic gene expression control that can be passed between generations. Here, we use sodium bisulfite treatment and targeted gene enrichment to study genome-wide methylation across the three sub-genomes of allohexaploid wheat. RESULTS While the majority of methylation is conserved across all three genomes we demonstrate that differential methylation exists between the sub-genomes in approximately equal proportions. We correlate sub-genome-specific promoter methylation with decreased expression levels and show that altered growing temperature has a small effect on methylation state, identifying a small but functionally relevant set of methylated genes. Finally, we demonstrate long-term methylation maintenance using a comparison between the D sub-genome of hexaploid wheat and its progenitor Aegilops tauschii. CONCLUSIONS We show that tri-genome methylation is highly conserved with the diploid wheat progenitor while sub-genome-specific methylation shows more variation.
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Affiliation(s)
- Laura-Jayne Gardiner
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK.
| | - Mark Quinton-Tulloch
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK.
| | - Lisa Olohan
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK.
| | - Jonathan Price
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK.
| | - Neil Hall
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK.
| | - Anthony Hall
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK.
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MGMT testing allows for personalised therapy in the temozolomide era. Tumour Biol 2015; 37:87-96. [PMID: 26518768 DOI: 10.1007/s13277-015-4240-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 10/12/2015] [Indexed: 10/22/2022] Open
Abstract
Adjuvant temozolomide (TMZ)-based chemoradiation is the standard of care for most glioblastoma patients (GBMs); however, a large proportion of these patients do not respond to TMZ. Silencing of the O(6)-methylguanine-DNA methyltransferase (MGMT) promoter is thought to induce chemosensitivity, and testing for methylation may allow for patient stratification; however, this has yet to become routine clinical practice despite an abundance of literature on the subject. The databases PubMed, Embase, The Cochrane Library, Science Direct and Medline were searched for relevant articles published between 1999 and 2015. Articles utilising MGMT testing in glioblastomas, and treatment of glioblastomas with temozolomide were assessed. Immunohistochemistry, methylation-specific PCR (MSP), reverse transcriptase PCR, pyrosequencing and bisulphite sequencing were the main testing methods identified. Nested-MSP techniques produced poor correlation with survival, whilst bisulphite sequencing showed no evident benefit over MSP. Testing is limited by sample quality and contamination; however, efforts are made to minimise this. Strong evidence for MGMT-based personalised therapy was presented in the elderly but remains controversial in the entire GBM population. MGMT testing presents many obstacles yet to be overcome, and these warrant attention prior to the routine implementation of MGMT testing to aid decision making in GBMs. However, there is evidence to support its use, particularly in the elderly.
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Integrated DNA methylation and chromatin structural analysis at single-molecule resolution. Methods Mol Biol 2015; 1288:123-41. [PMID: 25827879 DOI: 10.1007/978-1-4939-2474-5_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Chromatin limits the accessibility of DNA to trans-acting factors in transcription, replication, and repair. Although transcriptional variation between cells in a population may contribute to survival and disease, most assays of chromatin structure recover only population averages. We have developed DNA methyltransferases (MTases) as probing agents of DNA accessibility in chromatin, either expressed in vivo in budding yeast or as recombinant enzymatic probes of nuclei isolated from mammalian cells. In this chapter, we focus on the use of recombinant MTase (M) M.CviPI to probe chromatin accessibility in nuclei isolated from mammalian cell lines and animal tissue. This technique, named methylation accessibility protocol for individual templates (MAPit), reports protein-DNA interactions at single-molecule resolution. The single-molecule readout allows identification of chromatin subpopulations and rare epigenetic variants within a cell population. Furthermore, the use of M.CviPI in mammalian systems gives a comprehensive view of both chromatin structure and endogenous DNA methylation in a single assay.
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Abstract
Steroid hormone receptors (SHR) are important transcription factors for regulating different physiological and pathological processes. Their altered expression has been strongly associated to cancer progression. Epigenetic marks such as DNA methylation have been proposed as one of the regulatory mechanisms for SHR expression in cancer. DNA methylation occurs at CpG dinucleotides, which form clusters known as CpG islands. These islands are mostly observed at promoter regions of housekeeping genes, and their aberrant methylation in cancer cells is associated with silencing of tumor-suppressor gene expression. SHR genes are characterized for presenting alternative promoters with different CpG island content, which are prone to be methylated. The method of choice for studying DNA methylation is bisulfite sequencing, since it provides information about the methylation pattern at single-nucleotide level. The method is based on the deamination of cytosine residues to uracil after treatment with sodium bisulfite. The converted DNA is amplified by a polymerase chain reaction, cloned, and sequenced. Here, we describe a protocol for bisulfite sequencing suitable for analyzing different CpG regions in SHR genes.
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Ai L, Kim WJ, Alpay M, Tang M, Pardo CE, Hatakeyama S, May WS, Kladde MP, Heldermon CD, Siegel EM, Brown KD. TRIM29 suppresses TWIST1 and invasive breast cancer behavior. Cancer Res 2014; 74:4875-87. [PMID: 24950909 DOI: 10.1158/0008-5472.can-13-3579] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
TRIM29 (ATDC) exhibits a contextual function in cancer, but seems to exert a tumor-suppressor role in breast cancer. Here, we show that TRIM29 is often silenced in primary breast tumors and cultured tumor cells as a result of aberrant gene hypermethylation. RNAi-mediated silencing of TRIM29 in breast tumor cells increased their motility, invasiveness, and proliferation in a manner associated with increased expression of mesenchymal markers (N-cadherin and vimentin), decreased expression of epithelial markers (E-cadherin and EpCAM), and increased expression and activity of the oncogenic transcription factor TWIST1, an important driver of the epithelial-mesenchymal transition (EMT). Functional investigations revealed an inverse relationship in the expression of TRIM29 and TWIST1, suggesting the existence of a negative regulatory feedback loop. In support of this relationship, we found that TWIST1 inhibited TRIM29 promoter activity through direct binding to a region containing a cluster of consensus E-box elements, arguing that TWIST1 transcriptionally represses TRIM29 expression. Analysis of a public breast cancer gene-expression database indicated that reduced TRIM29 expression was associated with reduced relapse-free survival, increased tumor size, grade, and metastatic characteristics. Taken together, our results suggest that TRIM29 acts as a tumor suppressor in breast cancer through its ability to inhibit TWIST1 and suppress EMT.
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Affiliation(s)
- Lingbao Ai
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida. UF-Health Cancer Center, University of Florida College of Medicine, Gainesville, Florida.
| | - Wan-Ju Kim
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida. UF-Health Cancer Center, University of Florida College of Medicine, Gainesville, Florida
| | - Merve Alpay
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida. UF-Health Cancer Center, University of Florida College of Medicine, Gainesville, Florida
| | - Ming Tang
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida. UF-Health Cancer Center, University of Florida College of Medicine, Gainesville, Florida
| | - Carolina E Pardo
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida. UF-Health Cancer Center, University of Florida College of Medicine, Gainesville, Florida
| | - Shigetsugu Hatakeyama
- Department of Biochemistry, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - W Stratford May
- UF-Health Cancer Center, University of Florida College of Medicine, Gainesville, Florida. Department of Medicine, University of Florida College of Medicine, Gainesville, Florida
| | - Michael P Kladde
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida. UF-Health Cancer Center, University of Florida College of Medicine, Gainesville, Florida
| | - Coy D Heldermon
- UF-Health Cancer Center, University of Florida College of Medicine, Gainesville, Florida. Department of Medicine, University of Florida College of Medicine, Gainesville, Florida
| | - Erin M Siegel
- Division of Population Sciences, Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida. Department of Anatomic Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Kevin D Brown
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida. UF-Health Cancer Center, University of Florida College of Medicine, Gainesville, Florida.
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Performance evaluation of kits for bisulfite-conversion of DNA from tissues, cell lines, FFPE tissues, aspirates, lavages, effusions, plasma, serum, and urine. PLoS One 2014; 9:e93933. [PMID: 24699908 PMCID: PMC3974851 DOI: 10.1371/journal.pone.0093933] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 03/08/2014] [Indexed: 12/31/2022] Open
Abstract
DNA methylation analyses usually require a preceding bisulfite conversion of the DNA. The choice of an appropriate kit for a specific application should be based on the specific performance requirements with regard to the respective sample material. In this study, the performance of nine kits was evaluated: EpiTect Fast FFPE Bisulfite Kit, EpiTect Bisulfite Kit, EpiTect Fast DNA Bisulfite Kit (Qiagen), EZ DNA Methylation-Gold Kit, EZ DNA Methylation-Direct Kit, EZ DNA Methylation-Lightning Kit (Zymo Research), innuCONVERT Bisulfite All-In-One Kit, innuCONVERT Bisulfite Basic Kit, innuCONVERT Bisulfite Body Fluids Kit (Analytik Jena). The kit performance was compared with regard to DNA yield, DNA degradation, DNA purity, conversion efficiency, stability and handling using qPCR, UV, clone sequencing, HPLC, and agarose gel electrophoresis. All kits yielded highly pure DNA suitable for PCR analyses without PCR inhibition. Significantly higher yields were obtained when using the EZ DNA Methylation-Gold Kit and the innuCONVERT Bisulfite kits. Conversion efficiency ranged from 98.7% (EpiTect Bisulfite Kit) to 99.9% (EZ DNA Methylation-Direct Kit). The inappropriate conversion of methylated cytosines to thymines varied between 0.9% (innuCONVERT Bisulfite kits) and 2.7% (EZ DNA Methylation-Direct Kit). Time-to-result ranged from 131 min (innuCONVERT kits) to 402 min (EpiTect Bisulfite Kit). Hands-on-time was between 66 min (EZ DNA Methylation-Lightning Kit) and 104 min (EpiTect Fast FFPE and Fast DNA Bisulfite kits). Highest yields from formalin-fixed and paraffin-embedded (FFPE) tissue sections without prior extraction were obtained using the innuCONVERT Bisulfite All-In-One Kit while the EZ DNA Methylation-Direct Kit yielded DNA with only low PCR-amplifiability. The innuCONVERT Bisulfite All-In-One Kit exhibited the highest versatility regarding different input sample materials (extracted DNA, tissue, FFPE tissue, cell lines, urine sediment, and cellular fractions of bronchial aspirates, pleural effusions, ascites). The innuCONVERT Bisulfite Body Fluids Kit allowed for the analysis of 3 ml plasma, serum, ascites, pleural effusions and urine.
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Mensaert K, Denil S, Trooskens G, Van Criekinge W, Thas O, De Meyer T. Next-generation technologies and data analytical approaches for epigenomics. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2014; 55:155-70. [PMID: 24327356 DOI: 10.1002/em.21841] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 11/27/2013] [Accepted: 11/27/2013] [Indexed: 05/18/2023]
Abstract
Epigenetics refers to the collection of heritable features that modulate the genome-environment interaction without being encoded in the actual DNA sequence. While being mitotically and sometimes even meiotically transmitted, epigenetic traits often demonstrate extensive flexibility. This allows cells to acquire diverse gene expression patterns during differentiation, but also to adapt to a changing environment. However, epigenetic alterations are not always beneficial to the organism, as they are, for example, frequently identified in human diseases such as cancer. Accurate and cost-efficient genome-scale profiling of epigenetic features is thus of major importance to pinpoint these "epimutations," for example, to monitor the epigenetic impact of environmental exposure. Over the last decade, the field of epigenetics has been revolutionized by several innovative "epigenomics" technologies exactly addressing this need. In this review, we discuss and compare widely used next-generation methods to assess DNA methylation and hydroxymethylation, noncoding RNA expression, histone modifications, and nucleosome positioning. Although recent methods are typically based on "second-generation" sequencing, we also pay attention to still commonly used array- and PCR-based methods, and look forward to the additional advantages of single-molecule sequencing. As the current bottleneck in epigenomics research is the analysis rather than generation of data, the basic difficulties and problem-solving strategies regarding data preprocessing and statistical analysis are introduced for the different technologies. Finally, we also consider the complications associated with epigenomic studies of species with yet unsequenced genomes and possible solutions.
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Affiliation(s)
- Klaas Mensaert
- Department of Mathematical Modelling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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Elhaik E, Pellegrini M, Tatarinova TV. Gene expression and nucleotide composition are associated with genic methylation level in Oryza sativa. BMC Bioinformatics 2014; 15:23. [PMID: 24447369 PMCID: PMC3903047 DOI: 10.1186/1471-2105-15-23] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 12/26/2013] [Indexed: 12/21/2022] Open
Abstract
Background The methylation of cytosines at CpG dinucleotides, which plays an important role in gene expression regulation, is one of the most studied epigenetic modifications. Thus far, the detection of DNA methylation has been determined mostly by experimental methods, which are not only prone to bench effects and artifacts but are also time-consuming, expensive, and cannot be easily scaled up to many samples. It is therefore useful to develop computational prediction methods for DNA methylation. Our previous studies highlighted the existence of correlations between the GC content of the third codon position (GC3), methylation, and gene expression. We thus designed a model to predict methylation in Oryza sativa based on genomic sequence features and gene expression data. Results We first derive equations to describe the relationship between gene methylation levels, GC3, expression, length, and other gene compositional features. We next assess gene compositional features involving sixmers and their association with methylation levels and other gene level properties. By applying our sixmer-based approach on rice gene expression data we show that it can accurately predict methylation (Pearson’s correlation coefficient r = 0.79) for the majority (79%) of the genes. Matlab code with our model is included. Conclusions Gene expression variation can be used as predictors of gene methylation levels.
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Affiliation(s)
| | | | - Tatiana V Tatarinova
- Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, 4650 Sunset Blvd, Los Angeles, CA 90027, USA.
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Johannsen MW, Gerrard SR, Melvin T, Brown T. Triplex-mediated analysis of cytosine methylation at CpA sites in DNA. Chem Commun (Camb) 2013; 50:551-3. [PMID: 24276836 DOI: 10.1039/c3cc45917a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Modified triplex-forming oligonucleotides distinguish 5-methyl cytosine from unmethylated cytosine in DNA duplexes by differences in triplex melting temperatures. The discrimination is sequence-specific; dramatic differences in stabilisation are seen for CpA methylation, whereas CpG methylation is not detected. This direct detection of DNA methylation constitutes a new approach for epigenetic analysis.
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Affiliation(s)
- Marie W Johannsen
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK.
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Bakkali M. A bird's-eye view on the modern genetics workflow and its potential applicability to the locust problem. C R Biol 2013; 336:375-83. [PMID: 24018194 DOI: 10.1016/j.crvi.2013.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 07/19/2013] [Accepted: 07/23/2013] [Indexed: 01/16/2023]
Abstract
Genetics is an immense science and the current developments in its methods and techniques as well as the fast emerging tools make it one of the most powerful biological sciences. Indeed, from taxonomy and ecology to physiology and molecular biology, every biological science makes use of genetics techniques and methods at one time or another. In fact, development in genetics is such that it is now possible to characterize and analyze the expression of the whole set of genes of virtually every living organism, even if it is a non-model one. Locusts are notorious for the damage they cause to the ecosystems and economies of the areas affected by their recurrent population outbreaks. To prevent and deal with these outbreaks, we now count on both biological as well as chemical agents that are proving to be successful in reducing the damage that otherwise locust population outbreaks might cause. However, a better, efficient and environmentally friendly solution is still a hoped-for target. In my opinion, the ideal future pesticide should be both environmentally friendly, risk free and species-specific. To reach the knowledge needed for the development of such species-specific anti-locust agent, deep and accurate knowledge of the locusts' genetics and molecular biology is a must. Since genes and their expression levels lie at the bottom of every biological phenomenon, any species-specific solution to the locust problem requires a good knowledge of these organisms' genes as well as the quantitative and spatio-temporal dynamics of their expression. To reach such knowledge, collaborative work is needed as well as a clear workflow that, given the fast development in the genetics tools, is not always clear to all research groups. For this reason, here I describe a genetics workflow that should allow taking advantage of the most recent genetics tools and techniques to answer question relating to locust biology. My hope is that the adoption of this and other work strategies by different research groups, especially when the work is a collaborative one, would provide precious information on the biology and the biological phenomena that these economically important organisms exhibit.
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Affiliation(s)
- Mohammed Bakkali
- Departamento de Genetica, Facultad de Ciencias, Universidad de Granada, Fuentenueva S/N, 18071 Granada, Spain.
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