1
|
N M, Kumar PS, Manna D. Chemical Methods to Identify Epigenetic Modifications in Cytosine Bases. Chem Asian J 2024; 19:e202301005. [PMID: 38206202 DOI: 10.1002/asia.202301005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/01/2024] [Accepted: 01/04/2024] [Indexed: 01/12/2024]
Abstract
Chemical modifications to Cytosine bases are among the most studied epigenetic markers and their detection in the human genome plays a crucial role in gaining more insights about gene regulation, prognosis of genetic disorders and unraveling genetic inheritance patterns. The Cytosine methylated at the 5th position and oxidized derivatives thereof generated in the demethylation pathways, perform separate and unique epigenetic functions in an organism. As the presence of various Cytosine modifications is associated with diverse diseases, including cancer, there has been a strong focus on developing methods, both chemical and alternative approaches, capable of detecting these modifications at a single-base resolution across the entire genome. In this comprehensive review, we aim to consolidate the various chemical methods and understanding their chemistry that have been established to date for the detection of various Cytosine modifications.
Collapse
Affiliation(s)
- Madhumitha N
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh, India
| | - Parvathy S Kumar
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh, India
| | - Debasish Manna
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh, India
| |
Collapse
|
2
|
Türkoğlu A, Haliloğlu K, Demirel F, Aydin M, Çiçek S, Yiğider E, Demirel S, Piekutowska M, Szulc P, Niedbała G. Machine Learning Analysis of the Impact of Silver Nitrate and Silver Nanoparticles on Wheat ( Triticum aestivum L.): Callus Induction, Plant Regeneration, and DNA Methylation. PLANTS (BASEL, SWITZERLAND) 2023; 12:4151. [PMID: 38140479 PMCID: PMC10747064 DOI: 10.3390/plants12244151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023]
Abstract
The objective of this study was to comprehend the efficiency of wheat regeneration, callus induction, and DNA methylation through the application of mathematical frameworks and artificial intelligence (AI)-based models. This research aimed to explore the impact of treatments with AgNO3 and Ag-NPs on various parameters. The study specifically concentrated on analyzing RAPD profiles and modeling regeneration parameters. The treatments and molecular findings served as input variables in the modeling process. It included the use of AgNO3 and Ag-NPs at different concentrations (0, 2, 4, 6, and 8 mg L-1). The in vitro and epigenetic characteristics were analyzed using several machine learning (ML) methods, including support vector machine (SVM), random forest (RF), extreme gradient boosting (XGBoost), k-nearest neighbor classifier (KNN), and Gaussian processes classifier (GP) methods. This study's results revealed that the highest values for callus induction (CI%) and embryogenic callus induction (EC%) occurred at a concentration of 2 mg L-1 of Ag-NPs. Additionally, the regeneration efficiency (RE) parameter reached its peak at a concentration of 8 mg L-1 of AgNO3. Taking an epigenetic approach, AgNO3 at a concentration of 2 mg L-1 demonstrated the highest levels of genomic template stability (GTS), at 79.3%. There was a positive correlation seen between increased levels of AgNO3 and DNA hypermethylation. Conversely, elevated levels of Ag-NPs were associated with DNA hypomethylation. The models were used to estimate the relationships between the input elements, including treatments, concentration, GTS rates, and Msp I and Hpa II polymorphism, and the in vitro output parameters. The findings suggested that the XGBoost model exhibited superior performance scores for callus induction (CI), as evidenced by an R2 score of 51.5%, which explained the variances. Additionally, the RF model explained 71.9% of the total variance and showed superior efficacy in terms of EC%. Furthermore, the GP model, which provided the most robust statistics for RE, yielded an R2 value of 52.5%, signifying its ability to account for a substantial portion of the total variance present in the data. This study exemplifies the application of various machine learning models in the cultivation of mature wheat embryos under the influence of treatments and concentrations involving AgNO3 and Ag-NPs.
Collapse
Affiliation(s)
- Aras Türkoğlu
- Department of Field Crops, Faculty of Agriculture, Necmettin Erbakan University, Konya 42310, Türkiye
| | - Kamil Haliloğlu
- Department of Field Crops, Faculty of Agriculture, Ataturk University, Erzurum 25240, Türkiye;
| | - Fatih Demirel
- Department of Agricultural Biotechnology, Faculty of Agriculture, Igdır University, Igdir 76000, Türkiye;
| | - Murat Aydin
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ataturk University, Erzurum 25240, Türkiye; (M.A.); (S.Ç.); (E.Y.)
| | - Semra Çiçek
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ataturk University, Erzurum 25240, Türkiye; (M.A.); (S.Ç.); (E.Y.)
| | - Esma Yiğider
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ataturk University, Erzurum 25240, Türkiye; (M.A.); (S.Ç.); (E.Y.)
| | - Serap Demirel
- Department of Molecular Biology and Genetics, Faculty of Science, Van Yüzüncü Yıl University, Van 65080, Türkiye;
| | - Magdalena Piekutowska
- Department of Geoecology and Geoinformation, Institute of Biology and Earth Sciences, Pomeranian University in Słupsk, 27 Partyzantów St., 76-200 Słupsk, Poland;
| | - Piotr Szulc
- Department of Agronomy, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland;
| | - Gniewko Niedbała
- Department of Biosystems Engineering, Faculty of Environmental and Mechanical Engineering, Poznań University of Life Sciences, Wojska Polskiego 50, 60-627 Poznań, Poland
| |
Collapse
|
3
|
Foley JW, Zhu SX, West RB. Cost-effective DNA methylation profiling by FML-seq. Life Sci Alliance 2023; 6:e202302326. [PMID: 37775270 PMCID: PMC10546043 DOI: 10.26508/lsa.202302326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/01/2023] Open
Abstract
Current methods for profiling DNA methylation require costly reagents, sequencing, and labor time. We introduce fragmentation at methylated loci and sequencing (FML-seq), a sequencing library protocol that greatly reduces all these costs. Relative to other techniques tested on the same human cell lines, FML-seq produces similar measurements of absolute and differential cytosine methylation at a fraction of the price. FML-seq enables inexpensive, high-throughput experimental designs for large-scale epigenetics research projects.
Collapse
Affiliation(s)
- Joseph W Foley
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Shirley X Zhu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Robert B West
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| |
Collapse
|
4
|
Liu F, Wang Y, Gu H, Wang X. Technologies and applications of single-cell DNA methylation sequencing. Theranostics 2023; 13:2439-2454. [PMID: 37215576 PMCID: PMC10196823 DOI: 10.7150/thno.82582] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/09/2023] [Indexed: 05/24/2023] Open
Abstract
DNA methylation is the most stable epigenetic modification. In mammals, it usually occurs at the cytosine of CpG dinucleotides. DNA methylation is essential for many physiological and pathological processes. Aberrant DNA methylation has been observed in human diseases, particularly cancer. Notably, conventional DNA methylation profiling technologies require a large amount of DNA, often from a heterogeneous cell population, and provide an average methylation level of many cells. It is often not realistic to collect sufficient numbers of cells, such as rare cells and circulating tumor cells in peripheral blood, for bulk sequencing assays. It is therefore essential to develop sequencing technologies that can accurately profile DNA methylation using small numbers of cells or even single cells. Excitingly, many single-cell DNA methylation sequencing and single-cell omics sequencing technologies have been developed, and applications of these methods have greatly expanded our understanding of the molecular mechanism of DNA methylation. Here, we summaries single-cell DNA methylation and multi-omics sequencing methods, delineate their applications in biomedical sciences, discuss technical challenges, and present our perspective on future research directions.
Collapse
Affiliation(s)
- Fang Liu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China
- University of Science and Technology of China, Hefei, 230026, China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, China
| | - Yunfei Wang
- Zhejiang ShengTing Biotech. Ltd, Hangzhou, 310000, China
| | - Hongcang Gu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China
- University of Science and Technology of China, Hefei, 230026, China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, China
| | - Xiaoxue Wang
- Department of Hematology, the First Hospital of China Medical University, Shenyang, 110001, China
| |
Collapse
|
5
|
Pereira WJ, de Castro Rodrigues Pappas M, Pappas GJ. Computational Protocol for DNA Methylation Profiling in Plants Using Restriction Enzyme-Based Genome Reduction. Methods Mol Biol 2023; 2638:23-36. [PMID: 36781633 DOI: 10.1007/978-1-0716-3024-2_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Epigenetics can be described as heritable phenotype changes that do not involve alterations in the underlying DNA sequence. Having widespread implications in fundamental biological phenomena, there is an increased interest in characterizing epigenetic modifications and studying their functional implications. DNA methylation, particularly 5-methylcytosine (5mC), stands out as the most studied epigenetic mark and several methodologies have been created to investigate it. With the development of next-generation sequencing technologies, several approaches to DNA methylation profiling were conceived, with differences in resolution and genomic scope. Besides the gold standard whole-genome bisulfite sequencing, which is costly for population-scale studies, genomic reduced representation methods emerged as viable alternatives to investigate methylation loci. Whole-genome bisulfite sequencing provides single-base methylation resolution but is costly for population-scale studies. Genomic reduction methods emerged as viable alternatives to investigate a fraction of methylated loci. One of such approaches uses double digestion with the restriction enzymes PstI and one of the isoschizomers, MspI and HpaII, with differential sensitivity to 5mC at the restriction site. Statistical comparison of sequencing reads counts obtained from the two libraries for each sample (PstI-MspI and PstI-HpaII) is used to infer the methylation status of thousands of cytosines. Here, we describe a general overview of the technique and a computational protocol to process the generated data to provide a medium-scale inventory of methylated sites in plant genomes. The software is available at https://github.com/wendelljpereira/DArTseqMet .
Collapse
Affiliation(s)
- Wendell Jacinto Pereira
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL, USA.,Department of Cell Biology, University of Brasilia, Brasilia, Distrito Federal, Brazil
| | | | | |
Collapse
|
6
|
Zhuo Z, Lin L, Miao L, Li M, He J. Advances in liquid biopsy in neuroblastoma. FUNDAMENTAL RESEARCH 2022; 2:903-917. [PMID: 38933377 PMCID: PMC11197818 DOI: 10.1016/j.fmre.2022.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/18/2022] [Accepted: 08/09/2022] [Indexed: 10/15/2022] Open
Abstract
Even with intensive treatment of high-risk neuroblastoma (NB) patients, half of high-risk NB patients still relapse. New therapies targeting the biological characteristics of NB have important clinical value for the personalized treatment of NB. However, the current biological markers for NB are mainly analyzed by tissue biopsy. In recent years, circulating biomarkers of NB based on liquid biopsy have attracted more and more attention. This review summarizes the analytes and methods for liquid biopsy of NB. We focus on the application of liquid biopsy in the diagnosis, prognosis assessment, and monitoring of NB. Finally, we discuss the prospects and challenges of liquid biopsy in NB.
Collapse
Affiliation(s)
- Zhenjian Zhuo
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
- Laboratory Animal Center, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Lei Lin
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
| | - Lei Miao
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
| | - Meng Li
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
| | - Jing He
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
| |
Collapse
|
7
|
Effects of Zinc, Copper and Iron Oxide Nanoparticles on Induced DNA Methylation, Genomic Instability and LTR Retrotransposon Polymorphism in Wheat (Triticum aestivum L.). PLANTS 2022; 11:plants11172193. [PMID: 36079574 PMCID: PMC9460560 DOI: 10.3390/plants11172193] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022]
Abstract
Nanomaterials with unique and diverse physico-chemical properties are used in plant science since they improve plant growth and development and offer protection against biotic and abiotic stressors. Previous studies have explored the effects of such nanomaterials on different plant mechanisms, but information about the effects of nanomaterials on induced DNA methylation, genomic instability and LTR retrotransposon polymorphism in wheat is lacking. Therefore, the present study highlights the key role of nanoparticles in DNA methylation and polymorphism in wheat by investigating the effects of ZnO, CuO and γ-Fe3O4 nanoparticles (NPs) on mature embryo cultures of wheat (Triticum aestivum L.). Nanoparticles were supplemented with Murashige and Skoog (MS) basal medium at normal (1X), double (2X) and triple (3X) concentrations. The findings revealed different responses to the polymorphism rate depending on the nanoparticle type and concentration. Genomic template stability (GTS) values were used to compare the changes encountered in iPBS profiles. ZnO, CuO and γ-Fe3O4 NPs increased the polymorphism rate and cytosine methylation compared to the positive control while reducing GTS values. Moreover, non-γ-Fe3O4 NPs treatments and 2X ZnO and CuO NP treatments yielded higher polymorphism percentages in both MspI- and HpaII-digested CRED-iPBS assays and were thus classified as hypermethylation when the average polymorphism percentage for MspI digestion was considered. On the other hand, the 3X concentrations of all nanoparticles decreased HpaII and MspI polymorphism percentages and were thus classified as hypomethylation. The findings revealed that MS medium supplemented with nanoparticles had epigenetic and genotoxic effects.
Collapse
|
8
|
Sikdar A, Sharma U, Barua R, Igamberdiev AU, Debnath SC. Epigenomic insight of lingonberry and health-promoting traits during micropropagation. Sci Rep 2022; 12:12487. [PMID: 35864145 PMCID: PMC9304418 DOI: 10.1038/s41598-022-16530-7] [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: 11/06/2021] [Accepted: 07/12/2022] [Indexed: 11/09/2022] Open
Abstract
Epigenetic variation plays a role in developmental gene regulation and responses to the environment. An efficient interaction of zeatin-induced cytosine methylation and secondary compounds has been displayed for the first time in tissue-culture shoots/plants of lingonberry (Vaccinium vitis-idaea L.) cultivar Erntedank in vitro (NC1, in a liquid medium; NC2, on a semi-solid medium), ex vitro (NC3, node culture-derived plants; LC1, leaf culture-derived plants) and its cutting-propagated (ED) plants. Through methylation-sensitive amplification polymorphism (MSAP) assay, we observed highest methylated sites in leaf regenerants (LC1) from all primer combinations (108 bands), along with the highest secondary metabolites. The four types of tissue culture-derived shoots/plants (NC1, NC2, NC3, LC1) showed higher methylation bands than cutting propagated donor plants (ED) that exhibited 79 bands of methylation, which is comparatively low. Our study showed more methylation in micropropagated shoots/plants than those derived from ED plants. On the contrary, we observed higher secondary metabolites in ED plants but comparatively less in micropropagated shoots (NC1, NC2) and plants (NC3, LC1).
Collapse
Affiliation(s)
- Arindam Sikdar
- St. John's Research and Development Centre, Agriculture and Agri-Food Canada, St. John's, Newfoundland and Labrador, Canada.,Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Umanath Sharma
- St. John's Research and Development Centre, Agriculture and Agri-Food Canada, St. John's, Newfoundland and Labrador, Canada.,Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Rajesh Barua
- St. John's Research and Development Centre, Agriculture and Agri-Food Canada, St. John's, Newfoundland and Labrador, Canada.,Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Abir U Igamberdiev
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Samir C Debnath
- St. John's Research and Development Centre, Agriculture and Agri-Food Canada, St. John's, Newfoundland and Labrador, Canada.
| |
Collapse
|
9
|
Qi H, Song S, Wang P. ImmuMethy, a database of DNA methylation plasticity at a single cytosine resolution in human blood and immune cells. Database (Oxford) 2022; 2022:6562126. [PMID: 35363305 PMCID: PMC9216548 DOI: 10.1093/database/baac020] [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: 08/02/2021] [Revised: 01/09/2022] [Accepted: 03/18/2022] [Indexed: 11/23/2022]
Abstract
Differential DNA methylation is a feature of numerous physiological and pathological processes. However, the extent to which single-base cytosine methylation modifies cellular responses to various stimuli has not been well characterized. In this study, we carried out a systematic analysis of methylome data derived from human blood and immune cells and constructed the ImmuMethy database. ImmuMethy allows interrogation of DNA methylation plasticity (MPL) at the single cytosine level. MPL, which refers to the variability of DNA methylation, is quantitatively measured in multiple ways, such as quartiles and standard deviations. ImmuMethy comprises over 36 000 samples from the Human Methylation450 and MethylationEPIC BeadChips platforms and provides multiple applications, such as an overview of methylation status and plasticity, differential methylation analysis, identification of methylation markers and sample stratification. An analysis of all datasets revealed that DNA methylation is generally stable, with minimal changes in beta values. This further supports the characteristics of DNA methylation homeostasis. Based on the beta value distribution, we identified three types of methylation sites: methylation tendency sites, unmethylation tendency sites and dual tendency or nonbiased methylation sites. These sites represent different methylation tendentiousness of DNA methylation across samples. The occurrence of multiple methylation tendencies in a site means split methylation, which generally corresponds to high MPL. Inverted methylation tendencies from methylation tendency sites to unmethylation tendency sites, or vice versa, represent strong differential methylation in response to conditions. All these sites can be identified in ImmuMethy, making it a useful tool for omics-based data-driven knowledge discovery. Database URL: http://immudb.bjmu.edu.cn/immumethy/
Collapse
Affiliation(s)
- Huiying Qi
- Department of Health Informatics and Management, Peking University Health Science Center, No. 38 Xueyuan Road, Beijing 100191, China
| | - Shibin Song
- Information Technology Center, Peking University Health Science Center, No. 38 Xueyuan Road, Beijing 100191, China
| | - Pingzhang Wang
- Department of Immunology, NHC Key Laboratory of Medical Immunology, School of Basic Medical Sciences, Peking University Health Science Center, No. 38 Xueyuan Road, Beijing 100191, China
- Peking University Center for Human Disease Genomics, No. 38 Xueyuan Road, Beijing 100191, China
| |
Collapse
|
10
|
Mair R, Mouliere F. Cell-free DNA technologies for the analysis of brain cancer. Br J Cancer 2022; 126:371-378. [PMID: 34811503 PMCID: PMC8811068 DOI: 10.1038/s41416-021-01594-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 09/07/2021] [Accepted: 10/06/2021] [Indexed: 11/08/2022] Open
Abstract
Survival for glioma patients has shown minimal improvement over the past 20 years. The ability to detect and monitor gliomas relies primarily upon imaging technologies that lack sensitivity and specificity, especially during the post-surgical treatment phase. Treatment-response monitoring with an effective liquid-biopsy paradigm may also provide the most facile clinical scenario for liquid-biopsy integration into brain-tumour care. Conceptually, liquid biopsy is advantageous when compared with both tissue sampling (less invasive) and imaging (more sensitive and specific), but is hampered by technical and biological problems. These problems predominantly relate to low concentrations of tumour-derived DNA in the bloodstream of glioma patients. In this review, we highlight methods by which the neuro-oncological scientific and clinical communities have attempted to circumvent this limitation. The use of novel biological, technological and computational approaches will be explored. The utility of alternate bio-fluids, tumour-guided sequencing, epigenomic and fragmentomic methods may eventually be leveraged to provide the biological and technological means to unlock a wide range of clinical applications for liquid biopsy in glioma.
Collapse
Affiliation(s)
- Richard Mair
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE, Cambridge, UK.
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE, Cambridge, UK.
- Division of Neurosurgery, Department of Clinical Neurosciences, University of Cambridge, CB2 0QQ, Cambridge, UK.
| | - Florent Mouliere
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Centre Amsterdam, 1081 HV, Amsterdam, The Netherlands.
| |
Collapse
|
11
|
Chiocchetti AG, Yousaf A, Waltes R, Bernhard A, Martinelli A, Ackermann K, Haslinger D, Rotter B, Krezdorn N, Konrad K, Kohls G, Vetro A, Hervas A, Fernández-Rivas A, Freitag CM. The methylome in females with adolescent Conduct Disorder: Neural pathomechanisms and environmental risk factors. PLoS One 2022; 17:e0261691. [PMID: 35089926 PMCID: PMC8797262 DOI: 10.1371/journal.pone.0261691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 12/07/2021] [Indexed: 11/24/2022] Open
Abstract
Conduct Disorder (CD) is an impairing psychiatric disorder of childhood and adolescence characterized by aggressive and dissocial behavior. Environmental factors such as maternal smoking during pregnancy, socio-economic status, trauma, or early life stress are associated with CD. Although the number of females with CD is rising in Western societies, CD is under-researched in female cohorts. We aimed at exploring the epigenetic signature of females with CD and its relation to psychosocial and environmental risk factors. We performed HpaII sensitive genome-wide methylation sequencing of 49 CD girls and 50 matched typically developing controls and linear regression models to identify differentially methylated CpG loci (tags) and regions. Significant tags and regions were mapped to the respective genes and tested for enrichment in pathways and brain developmental processes. Finally, epigenetic signatures were tested as mediators for CD-associated risk factors. We identified a 12% increased methylation 5’ of the neurite modulator SLITRK5 (FDR = 0.0046) in cases within a glucocorticoid receptor binding site. Functionally, methylation positively correlated with gene expression in lymphoblastoid cell lines. At systems-level, genes (uncorr. P < 0.01) were associated with development of neurons, neurite outgrowth or neuronal developmental processes. At gene expression level, the associated gene-networks are activated perinatally and during early childhood in neocortical regions, thalamus and striatum, and expressed in amygdala and hippocampus. Specifically, the epigenetic signatures of the gene network activated in the thalamus during early childhood correlated with the effect of parental education on CD status possibly mediating its protective effect. The differential methylation patterns identified in females with CD are likely to affect genes that are expressed in brain regions previously indicated in CD. We provide suggestive evidence that protective effects are likely mediated by epigenetic mechanisms impairing specific brain developmental networks and therefore exerting a long-term effect on neural functions in CD. Our results are exploratory and thus, further replication is needed.
Collapse
Affiliation(s)
- Andreas G. Chiocchetti
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Goethe University Frankfurt, Frankfurt am Main, Germany
- * E-mail: ;
| | - Afsheen Yousaf
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Regina Waltes
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Anka Bernhard
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Goethe University Frankfurt, Frankfurt am Main, Germany
- * E-mail: ;
| | - Anne Martinelli
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Katharina Ackermann
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Denise Haslinger
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Goethe University Frankfurt, Frankfurt am Main, Germany
| | | | | | - Kerstin Konrad
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Child Neuropsychology Section, University Hospital, RWTH Aachen, Aachen, Germany
- Molecular Neuroscience and Neuroimaging, Institute of Neuroscience and Medicine (INM-11) JARA BRAIN Institute II, Research Center Juelich, Juelich, Germany
| | - Gregor Kohls
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Child Neuropsychology Section, University Hospital, RWTH Aachen, Aachen, Germany
| | - Agnes Vetro
- Department of Pediatrics and Pediatrics Health Center, Child and Adolescent Psychiatry, Szeged, Szeged University, Szeged, Hungary
| | - Amaia Hervas
- Child and Adolescent Mental Health Service, Hospital Universitario Mutua de Terrassa, Barcelona, Spain
| | | | - Christine M. Freitag
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Goethe University Frankfurt, Frankfurt am Main, Germany
| |
Collapse
|
12
|
Bednarek PT, Orłowska R, Mańkowski DR, Zimny J, Kowalczyk K, Nowak M, Zebrowski J. Glutathione and copper ions as critical factors of green plant regeneration efficiency of triticale in vitro anther culture. FRONTIERS IN PLANT SCIENCE 2022; 13:926305. [PMID: 35982694 PMCID: PMC9379855 DOI: 10.3389/fpls.2022.926305] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/07/2022] [Indexed: 05/02/2023]
Abstract
Plant tissue culture techniques are handy tools for obtaining unique plant materials that are difficult to propagate or important for agriculture. Homozygous materials derived through in vitro cultures are invaluable and significantly accelerate the evaluation of new varieties, e.g., cereals. The induction of somatic embryogenesis/androgenesis and the regeneration and its efficiency can be influenced by the external conditions of tissue culture, such as the ingredients present in the induction or regeneration media. We have developed an approach based on biological system, molecular markers, Fourier Transform Infrared spectroscopy, and structural equation modeling technique to establish links between changes in sequence and DNA methylation at specific symmetric (CG, CHG) and asymmetric (CHH) sequences, glutathione, and green plant regeneration efficiency in the presence of variable supplementation of induction medium with copper ions. The methylation-sensitive Amplified Fragment Length Polymorphism was used to assess tissue culture-induced variation, Fourier Transform Infrared spectroscopy to describe the glutathione spectrum, and a structural equation model to develop the relationship between sequence variation, de novo DNA methylation within asymmetric sequence contexts, and copper ions in the induction medium, as well as, glutathione, and green plant efficiency. An essential aspect of the study is demonstrating the contribution of glutathione to green plant regeneration efficiency and indicating the critical role of copper ions in influencing tissue culture-induced variation, glutathione, and obtaining green regenerants. The model presented here also has practical implications, showing that manipulating the concentration of copper ions in the induction medium may influence cell function and increases green plant regeneration efficiency.
Collapse
Affiliation(s)
- Piotr T. Bednarek
- Plant Breeding and Acclimatization Institute-National Research Institute, Radzików, Poland
| | - Renata Orłowska
- Plant Breeding and Acclimatization Institute-National Research Institute, Radzików, Poland
- *Correspondence: Renata Orłowska,
| | - Dariusz R. Mańkowski
- Plant Breeding and Acclimatization Institute-National Research Institute, Radzików, Poland
| | - Janusz Zimny
- Plant Breeding and Acclimatization Institute-National Research Institute, Radzików, Poland
| | - Krzysztof Kowalczyk
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Lublin, Poland
| | - Michał Nowak
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Lublin, Poland
| | - Jacek Zebrowski
- Institute of Biology and Biotechnology, University of Rzeszow, Rzeszow, Poland
| |
Collapse
|
13
|
Z-DNA as a Tool for Nuclease-Free DNA Methyltransferase Assay. Int J Mol Sci 2021; 22:ijms222111990. [PMID: 34769422 PMCID: PMC8585049 DOI: 10.3390/ijms222111990] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/29/2021] [Accepted: 10/30/2021] [Indexed: 01/16/2023] Open
Abstract
Methylcytosines in mammalian genomes are the main epigenetic molecular codes that switch off the repertoire of genes in cell-type and cell-stage dependent manners. DNA methyltransferases (DMT) are dedicated to managing the status of cytosine methylation. DNA methylation is not only critical in normal development, but it is also implicated in cancers, degeneration, and senescence. Thus, the chemicals to control DMT have been suggested as anticancer drugs by reprogramming the gene expression profile in malignant cells. Here, we report a new optical technique to characterize the activity of DMT and the effect of inhibitors, utilizing the methylation-sensitive B-Z transition of DNA without bisulfite conversion, methylation-sensing proteins, and polymerase chain reaction amplification. With the high sensitivity of single-molecule FRET, this method detects the event of DNA methylation in a single DNA molecule and circumvents the need for amplification steps, permitting direct interpretation. This method also responds to hemi-methylated DNA. Dispensing with methylation-sensitive nucleases, this method preserves the molecular integrity and methylation state of target molecules. Sparing methylation-sensing nucleases and antibodies helps to avoid errors introduced by the antibody’s incomplete specificity or variable activity of nucleases. With this new method, we demonstrated the inhibitory effect of several natural bio-active compounds on DMT. All taken together, our method offers quantitative assays for DMT and DMT-related anticancer drugs.
Collapse
|
14
|
Nguyen K, Dobrowolski C, Shukla M, Cho WK, Luttge B, Karn J. Inhibition of the H3K27 demethylase UTX enhances the epigenetic silencing of HIV proviruses and induces HIV-1 DNA hypermethylation but fails to permanently block HIV reactivation. PLoS Pathog 2021; 17:e1010014. [PMID: 34673825 PMCID: PMC8562785 DOI: 10.1371/journal.ppat.1010014] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 11/02/2021] [Accepted: 10/07/2021] [Indexed: 01/09/2023] Open
Abstract
One strategy for a functional cure of HIV-1 is "block and lock", which seeks to permanently suppress the rebound of quiescent HIV-1 by epigenetic silencing. For the bivalent promoter in the HIV LTR, both histone 3 lysine 27 tri-methylation (H3K27me3) and DNA methylation are associated with viral suppression, while H3K4 tri-methylation (H3K4me3) is correlated with viral expression. However, H3K27me3 is readily reversed upon activation of T-cells through the T-cell receptor. In an attempt to suppress latent HIV-1 in a stable fashion, we knocked down the expression or inhibited the activity of UTX/KDM6A, the major H3K27 demethylase, and investigated its impact on latent HIV-1 reactivation in T cells. Inhibition of UTX dramatically enhanced H3K27me3 levels at the HIV LTR and was associated with increased DNA methylation. In latently infected cells from patients, GSK-J4, which is a potent dual inhibitor of the H3K27me3/me2-demethylases JMJD3/KDM6B and UTX/KDM6A, effectively suppressed the reactivation of latent HIV-1 and also induced DNA methylation at specific sites in the 5'LTR of latent HIV-1 by the enhanced recruitment of DNMT3A to HIV-1. Nonetheless, suppression of HIV-1 through epigenetic silencing required the continued treatment with GSK-J4 and was rapidly reversed after removal of the drug. DNA methylation was also rapidly lost after removal of drug, suggesting active and rapid DNA-demethylation of the HIV LTR. Thus, induction of epigenetic silencing by histone and DNA methylation appears to be insufficient to permanently silence HIV-1 proviral transcription.
Collapse
Affiliation(s)
- Kien Nguyen
- Department of Molecular Biology and Microbiology, Case Western Reserve University Medical School, Cleveland, Ohio, United States of America
| | - Curtis Dobrowolski
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory School of Medicine, Atlanta, Georgia, United States of America
| | - Meenakshi Shukla
- Department of Molecular Biology and Microbiology, Case Western Reserve University Medical School, Cleveland, Ohio, United States of America
| | - Won-Kyung Cho
- Korean Medicine (KM)-Application Center, Korea Institute of Oriental Medicine (KIOM), Dong-gu, Daegu, Republic of Korea
| | - Benjamin Luttge
- Department of Molecular Biology and Microbiology, Case Western Reserve University Medical School, Cleveland, Ohio, United States of America
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University Medical School, Cleveland, Ohio, United States of America
| |
Collapse
|
15
|
Lv H, Dao FY, Zhang D, Yang H, Lin H. Advances in mapping the epigenetic modifications of 5-methylcytosine (5mC), N6-methyladenine (6mA), and N4-methylcytosine (4mC). Biotechnol Bioeng 2021; 118:4204-4216. [PMID: 34370308 DOI: 10.1002/bit.27911] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 08/06/2021] [Indexed: 12/30/2022]
Abstract
DNA modification plays a pivotal role in regulating gene expression in cell development. As prevalent markers on DNA, 5-methylcytosine (5mC), N6-methyladenine (6mA), and N4-methylcytosine (4mC) can be recognized by specific methyltransferases, facilitating cellular defense and the versatile regulation of gene expression in eukaryotes and prokaryotes. Recent advances in DNA sequencing technology have permitted the positions of different modifications to be resolved at the genome-wide scale, which has led to the discovery of several novel insights into the complexity and functions of multiple methylations. In this review, we summarize differences in the various mapping approaches and discuss their pros and cons with respect to their relative read depths, speeds, and costs. We also discuss the development of future sequencing technologies and strategies for improving the detection resolution of current sequencing technologies. Lastly, we speculate on the potentially instrumental role that these sequencing technologies might play in future research.
Collapse
Affiliation(s)
- Hao Lv
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Fu-Ying Dao
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Dan Zhang
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Hui Yang
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Hao Lin
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| |
Collapse
|
16
|
Bednarek PT, Pachota KA, Dynkowska WM, Machczyńska J, Orłowska R. Understanding In Vitro Tissue Culture-Induced Variation Phenomenon in Microspore System. Int J Mol Sci 2021; 22:7546. [PMID: 34299165 PMCID: PMC8304781 DOI: 10.3390/ijms22147546] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/24/2021] [Accepted: 07/08/2021] [Indexed: 12/13/2022] Open
Abstract
In vitro tissue culture plant regeneration is a complicated process that requires stressful conditions affecting the cell functioning at multiple levels, including signaling pathways, transcriptome functioning, the interaction between cellular organelles (retro-, anterograde), compounds methylation, biochemical cycles, and DNA mutations. Unfortunately, the network linking all these aspects is not well understood, and the available knowledge is not systemized. Moreover, some aspects of the phenomenon are poorly studied. The present review attempts to present a broad range of aspects involved in the tissue culture-induced variation and hopefully would stimulate further investigations allowing a better understanding of the phenomenon and the cell functioning.
Collapse
Affiliation(s)
- Piotr Tomasz Bednarek
- Plant Breeding and Acclimatization Institute—National Research Institute, Radzików, 05-870 Błonie, Poland; (K.A.P.); (W.M.D.); (J.M.); (R.O.)
| | | | | | | | | |
Collapse
|
17
|
Ahn J, Heo S, Lee J, Bang D. Introduction to Single-Cell DNA Methylation Profiling Methods. Biomolecules 2021; 11:1013. [PMID: 34356635 PMCID: PMC8301785 DOI: 10.3390/biom11071013] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 02/06/2023] Open
Abstract
DNA methylation is an epigenetic mechanism that is related to mammalian cellular differentiation, gene expression regulation, and disease. In several studies, DNA methylation has been identified as an effective marker to identify differences between cells. In this review, we introduce single-cell DNA-methylation profiling methods, including experimental strategies and approaches to computational data analysis. Furthermore, the blind spots of the basic analysis and recent alternatives are briefly described. In addition, we introduce well-known applications and discuss future development.
Collapse
Affiliation(s)
- Jongseong Ahn
- Department of Chemistry, Yonsei University, Seoul 03722, Korea; (J.A.); (S.H.)
| | - Sunghoon Heo
- Department of Chemistry, Yonsei University, Seoul 03722, Korea; (J.A.); (S.H.)
| | - Jihyun Lee
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul 02447, Korea
- Department of Biomedical Science and Technology, Kyung Hee University, Seoul 02447, Korea
| | - Duhee Bang
- Department of Chemistry, Yonsei University, Seoul 03722, Korea; (J.A.); (S.H.)
| |
Collapse
|
18
|
Fridman H, Bormans C, Einhorn M, Au D, Bormans A, Porat Y, Sanchez LF, Manning B, Levy-Lahad E, Behar DM. Performance comparison: exome sequencing as a single test replacing Sanger sequencing. Mol Genet Genomics 2021; 296:653-663. [PMID: 33694043 DOI: 10.1007/s00438-021-01772-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/02/2021] [Indexed: 01/23/2023]
Abstract
Next generation sequencing tests are used routinely as first-choice tests in the clinic. However, systematic performance comparing the results of exome sequencing as a single test replacing Sanger sequencing of targeted gene(s) is still lacking. Performance comparison data are critically important for clinical case management. In this study, we compared Sanger-sequencing results of 258 genes to those obtained from next generation sequencing (NGS) using two exome-sequencing enrichment kits: Agilent-SureSelectQXT and Illumina-Nextera. Sequencing was performed on leukocytes and buccal-derived DNA from a single individual, and all 258 genes were sequenced a total of 11 times (using different sequencing methods and DNA sources). Sanger sequencing was completed for all exons, including flanking ± 8 bp regions. For the 258 genes, NGS mean coverage was > 20 × for > 98 and > 91% of the regions targeted by SureSelect and Nextera, respectively. Overall, 449 variants were identified in at least one experiment, and 407/449 (90.6%) were detected by all. Of the 42 discordant variants, 23 were determined as true calls, summing-up to a truth set of 430 variants. Sensitivity of true-variant detection was 99% for Sanger sequencing and 97-100% for the NGS experiments. Mean false-positive rates were 3.7E-6 for Sanger sequencing, 2.5E-6 for SureSelect-NGS and 5.2E-6 for Nextera-NGS. Our findings suggest a high overall concordance between Sanger sequencing and NGS performances. Both methods demonstrated false-positive and false-negative calls. High clinical suspicion for a specific diagnosis should, therefore, override negative results of either Sanger sequencing or NGS.
Collapse
Affiliation(s)
- Hila Fridman
- Medical Genetics Institute, Shaare Zedek Medical Center, 91031, Jerusalem, Israel. .,Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Jerusalem, Israel.
| | | | - Moshe Einhorn
- Data Analysis Group, 6688218, Genoox, Tel Aviv, Israel
| | - Daniel Au
- Genomic Research Center, Gene By Gene, Houston, TX, 77008, USA
| | - Arjan Bormans
- Genomic Research Center, Gene By Gene, Houston, TX, 77008, USA
| | - Yuval Porat
- Data Analysis Group, 6688218, Genoox, Tel Aviv, Israel
| | | | - Brent Manning
- Genomic Research Center, Gene By Gene, Houston, TX, 77008, USA
| | - Ephrat Levy-Lahad
- Medical Genetics Institute, Shaare Zedek Medical Center, 91031, Jerusalem, Israel.,Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Jerusalem, Israel
| | - Doron M Behar
- Genomic Research Center, Gene By Gene, Houston, TX, 77008, USA
| |
Collapse
|
19
|
Orłowska R, Zimny J, Bednarek PT. Copper Ions Induce DNA Sequence Variation in Zygotic Embryo Culture-Derived Barley Regenerants. FRONTIERS IN PLANT SCIENCE 2021; 11:614837. [PMID: 33613587 PMCID: PMC7889974 DOI: 10.3389/fpls.2020.614837] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 12/22/2020] [Indexed: 05/18/2023]
Abstract
In vitro tissue culture could be exploited to study cellular mechanisms that induce sequence variation. Altering the metal ion composition of tissue culture medium affects biochemical pathways involved in tissue culture-induced variation. Copper ions are involved in the mitochondrial respiratory chain and Yang cycle. Copper ions may participate in oxidative mutations, which may contribute to DNA sequence variation. Silver ions compete with copper ions to bind to the complex IV subunit of the respiratory chain, thus affecting the Yang cycle and DNA methylation. The mechanisms underlying somaclonal variation are unknown. In this study, we evaluated embryo-derived barley regenerants obtained from a single double-haploid plant via embryo culture under varying copper and silver ion concentrations and different durations of in vitro culture. Morphological variation among regenerants and the donor plant was not evaluated. Methylation-sensitive Amplified Fragment Length Polymorphism analysis of DNA samples showed DNA methylation pattern variation in CG and CHG (H = A, C, or T) sequence contexts. Furthermore, modification of in vitro culture conditions explained DNA sequence variation, demethylation, and de novo methylation in the CHG context, as indicated by analysis of variance. Linear regression indicated that DNA sequence variation was related to de novo DNA methylation in the CHG context. Mediation analysis showed the role of copper ions as a mediator of sequence variation in the CHG context. No other contexts showed a significant sequence variation in mediation analysis. Silver ions did not act as a mediator between any methylation contexts and sequence variation. Thus, incorporating copper ions in the induction medium should be treated with caution.
Collapse
Affiliation(s)
- Renata Orłowska
- Plant Breeding and Acclimatization Institute–National Research Institute, Błonie, Poland
| | | | | |
Collapse
|
20
|
Saha D, Norvil AB, Lanman NA, Gowher H. Simplified MethylRAD Sequencing to Detect Changes in DNA Methylation at Enhancer Elements in Differentiating Embryonic Stem Cells. EPIGENOMES 2020; 4:24. [PMID: 33828860 PMCID: PMC8023688 DOI: 10.3390/epigenomes4040024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 09/28/2020] [Indexed: 11/17/2022] Open
Abstract
Differential DNA methylation is characteristic of gene regulatory regions, such as enhancers, which mostly constitute low or intermediate CpG content in their DNA sequence. Consequently, quantification of changes in DNA methylation at these sites is challenging. Given that DNA methylation across most of the mammalian genome is maintained, the use of genome-wide bisulfite sequencing to measure fractional changes in DNA methylation at specific sites is an overexertion which is both expensive and cumbersome. Here, we developed a MethylRAD technique with an improved experimental plan and bioinformatic analysis tool to examine regional DNA methylation changes in embryonic stem cells (ESCs) during differentiation. The transcriptional silencing of pluripotency genes (PpGs) during ESC differentiation is accompanied by PpG enhancer (PpGe) silencing mediated by the demethylation of H3K4me1 by LSD1. Our MethylRAD data show that in the presence of LSD1 inhibitor, a significant fraction of LSD1-bound PpGe fails to gain DNA methylation. We further show that this effect is mostly observed in PpGes with low/intermediate CpG content. Underscoring the sensitivity and accuracy of MethylRAD sequencing, our study demonstrates that this method can detect small changes in DNA methylation in regulatory regions, including those with low/intermediate CpG content, thus asserting its use as a method of choice for diagnostic purposes.
Collapse
Affiliation(s)
- Debapriya Saha
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA; (D.S.); (A.B.N.)
| | - Allison B. Norvil
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA; (D.S.); (A.B.N.)
| | - Nadia A. Lanman
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA;
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, USA
| | - Humaira Gowher
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA; (D.S.); (A.B.N.)
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA;
| |
Collapse
|
21
|
Xiao M, Yang X, Yu J, Zhang L. CGIDLA:Developing the Web Server for CpG Island Related Density and LAUPs (Lineage-Associated Underrepresented Permutations) Study. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020; 17:2148-2154. [PMID: 31443042 DOI: 10.1109/tcbb.2019.2935971] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
It is well known that CpG island plays an important role in gene methylation. Since CpG island is closely related to human genetic characteristics such as TATA-box, tissue expression specificity, and LAUPs (Lineage-associated Underrepresented Permutations), it is important to investigate the sequence specificity of CpG island as well as the potential genetic characteristics related to CpG island to further understand the methylation related regulation mechanism. Therefore, this study develops such an online service website for CpG island related density and LAUPs analysis (CGIDLA, www.combio-lezhang.online/cgidla/index.html), that not only can investigate the relationship among the CpG island density, TATA-box feature, and expression breadth of human genes, but also deposit LAUPs of 32 representative species to help molecular biologists investigate the relationship between CpG island and LUAPs. Moreover, CGIDLA provides the source code download service and the related LAUPs counting functions.
Collapse
|
22
|
Wang M, Liang Y, Ibeagha-Awemu EM, Li M, Zhang H, Chen Z, Sun Y, Karrow NA, Yang Z, Mao Y. Genome-Wide DNA Methylation Analysis of Mammary Gland Tissues From Chinese Holstein Cows With Staphylococcus aureus Induced Mastitis. Front Genet 2020; 11:550515. [PMID: 33193625 PMCID: PMC7604493 DOI: 10.3389/fgene.2020.550515] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 09/29/2020] [Indexed: 12/17/2022] Open
Abstract
Staphylococcus aureus intramammary infection is one of the most common causes of chronic mastitis in dairy cows, whose development may be associated with epigenetic changes in the expression of important host defense genes. This study aimed to construct a genome-wide DNA methylation profile of the mammary gland of Chinese Holstein cows (n = 3) following experimentally induced S. aureus mastitis, and to explore the potential gene regulatory mechanisms affected by DNA methylation during S. aureus mastitis. DNA was extracted from S. aureus-positive (n = 3) and S. aureus-negative (n = 3) mammary gland quarters and subjected to methylation-dependent restriction-site associated DNA sequencing (Methyl-RAD Seq). Results showed that CmCGG/CmCWGG DNA methylation sites were unevenly distributed and concentrated on chromosomes 5, 11, and 19, and within intergenic regions and intron regions of genes. Compared with healthy control quarters, 9,181 significantly differentially methylated (DM) CmCGG sites and 1,790 DM CmCWGG sites were found in the S. aureus-positive quarters (P < 0.05, |log2FC| > 1). Furthermore, 363 CmCGG differently methylated genes (DMGs) and 301 CmCWGG DMGs (adjusted P < 0.05, |log2FC| > 1) were identified. Gene ontology and KEGG enrichment analysis indicated that CmCGG DMGs are involved in immune response pathways, while the CmCWGG DMGs were mainly enriched in gene ontology terms related to metabolism. The mRNAs of 526 differentially methylated CmCGG genes and 124 differentially methylated CmCWGG genes were also significantly differentially expressed (RNA-Seq data) in the same samples, herein denoted differentially methylated and expressed genes (DMEGs) (P < 0.05). Functional enrichment analysis of DMEGs revealed roles related to biological processes, especially the regulation of immune response to diseases. CmCGG DMEGs like IL6R, TNF, BTK, IL1R2, and TNFSF8 enriched in several immune-related GO terms and pathways indicated their important roles in host immune response and their potential as candidate genes for S. aureus mastitis. These results suggest potential regulatory roles for DNA methylation in bovine mammary gland processes during S. aureus mastitis and serves as a reference for future epigenetic regulation and mechanistic studies.
Collapse
Affiliation(s)
- Mengqi Wang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
| | - Yan Liang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Eveline M. Ibeagha-Awemu
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
| | - Mingxun Li
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Huimin Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Zhi Chen
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Yujia Sun
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Niel A. Karrow
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Zhangping Yang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Yongjiang Mao
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
| |
Collapse
|
23
|
Zeevaert K, Elsafi Mabrouk MH, Wagner W, Goetzke R. Cell Mechanics in Embryoid Bodies. Cells 2020; 9:E2270. [PMID: 33050550 PMCID: PMC7599659 DOI: 10.3390/cells9102270] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/06/2020] [Accepted: 10/09/2020] [Indexed: 12/14/2022] Open
Abstract
Embryoid bodies (EBs) resemble self-organizing aggregates of pluripotent stem cells that recapitulate some aspects of early embryogenesis. Within few days, the cells undergo a transition from rather homogeneous epithelial-like pluripotent stem cell colonies into a three-dimensional organization of various cell types with multifaceted cell-cell interactions and lumen formation-a process associated with repetitive epithelial-mesenchymal transitions. In the last few years, culture methods have further evolved to better control EB size, growth, cellular composition, and organization-e.g., by the addition of morphogens or different extracellular matrix molecules. There is a growing perception that the mechanical properties, cell mechanics, and cell signaling during EB development are also influenced by physical cues to better guide lineage specification; substrate elasticity and topography are relevant, as well as shear stress and mechanical strain. Epithelial structures outside and inside EBs support the integrity of the cell aggregates and counteract mechanical stress. Furthermore, hydrogels can be used to better control the organization and lineage-specific differentiation of EBs. In this review, we summarize how EB formation is accompanied by a variety of biomechanical parameters that need to be considered for the directed and reproducible self-organization of early cell fate decisions.
Collapse
Affiliation(s)
- Kira Zeevaert
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, 52074 Aachen, Germany; (K.Z.); (M.H.E.M.)
- Institute for Biomedical Engineering–Cell Biology, RWTH Aachen University Medical School, 52074 Aachen, Germany
| | - Mohamed H. Elsafi Mabrouk
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, 52074 Aachen, Germany; (K.Z.); (M.H.E.M.)
- Institute for Biomedical Engineering–Cell Biology, RWTH Aachen University Medical School, 52074 Aachen, Germany
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, 52074 Aachen, Germany; (K.Z.); (M.H.E.M.)
- Institute for Biomedical Engineering–Cell Biology, RWTH Aachen University Medical School, 52074 Aachen, Germany
| | - Roman Goetzke
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, 52074 Aachen, Germany; (K.Z.); (M.H.E.M.)
- Institute for Biomedical Engineering–Cell Biology, RWTH Aachen University Medical School, 52074 Aachen, Germany
| |
Collapse
|
24
|
Moudgil A, Wilkinson MN, Chen X, He J, Cammack AJ, Vasek MJ, Lagunas T, Qi Z, Lalli MA, Guo C, Morris SA, Dougherty JD, Mitra RD. Self-Reporting Transposons Enable Simultaneous Readout of Gene Expression and Transcription Factor Binding in Single Cells. Cell 2020; 182:992-1008.e21. [PMID: 32710817 PMCID: PMC7510185 DOI: 10.1016/j.cell.2020.06.037] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 04/14/2020] [Accepted: 06/23/2020] [Indexed: 12/13/2022]
Abstract
Cellular heterogeneity confounds in situ assays of transcription factor (TF) binding. Single-cell RNA sequencing (scRNA-seq) deconvolves cell types from gene expression, but no technology links cell identity to TF binding sites (TFBS) in those cell types. We present self-reporting transposons (SRTs) and use them in single-cell calling cards (scCC), a novel assay for simultaneously measuring gene expression and mapping TFBS in single cells. The genomic locations of SRTs are recovered from mRNA, and SRTs deposited by exogenous, TF-transposase fusions can be used to map TFBS. We then present scCC, which map SRTs from scRNA-seq libraries, simultaneously identifying cell types and TFBS in those same cells. We benchmark multiple TFs with this technique. Next, we use scCC to discover BRD4-mediated cell-state transitions in K562 cells. Finally, we map BRD4 binding sites in the mouse cortex at single-cell resolution, establishing a new method for studying TF biology in situ.
Collapse
Affiliation(s)
- Arnav Moudgil
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Medical Scientist Training Program, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Michael N Wilkinson
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Xuhua Chen
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - June He
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Alexander J Cammack
- Department of Neurology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Michael J Vasek
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Tomás Lagunas
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Zongtai Qi
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Matthew A Lalli
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Chuner Guo
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Medical Scientist Training Program, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Samantha A Morris
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Joseph D Dougherty
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Robi D Mitra
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA.
| |
Collapse
|
25
|
Bednarek PT, Orłowska R. CG Demethylation Leads to Sequence Mutations in an Anther Culture of Barley Due to the Presence of Cu, Ag Ions in the Medium and Culture Time. Int J Mol Sci 2020; 21:E4401. [PMID: 32575771 PMCID: PMC7353013 DOI: 10.3390/ijms21124401] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 12/13/2022] Open
Abstract
During plant tissue cultures the changes affecting regenerants have a broad range of genetic and epigenetic implications. These changes can be seen at the DNA methylation and sequence variation levels. In light of the latest studies, DNA methylation change plays an essential role in determining doubled haploid (DH) regenerants. The present study focuses on exploring the relationship between DNA methylation in CG and CHG contexts, and sequence variation, mediated by microelements (CuSO4 and AgNO3) supplemented during barley anther incubation on induction medium. To estimate such a relationship, a mediation analysis was used based on the results previously obtained through metAFLP method. Here, an interaction was observed between DNA demethylation in the context of CG and the time of culture. It was also noted that the reduction in DNA methylation was associated with a total decrease in the amount of Cu and Ag ions in the induction medium. Moreover, the total increase in Cu and Ag ions increased sequence variation. The importance of the time of tissue culture in the light of the observed changes resulted from the grouping of regenerants obtained after incubation on the induction medium for 28 days. The present study demonstrated that under a relatively short time of tissue culture (28 days), the multiplication of the Cu2+ and Ag+ ion concentrations ('Cu*Ag') acts as a mediator of demethylation in CG context. Change (increase) in the demethylation in CG sequence results in the decrease of 'Cu*Ag', and that change induces sequence variation equal to the value of the indirect effect. Thus, Cu and Ag ions mediate sequence variation. It seems that the observed changes at the level of methylation and DNA sequence may accompany the transition from direct to indirect embryogenesis.
Collapse
Affiliation(s)
- Piotr T. Bednarek
- Plant Breeding and Acclimatization Institute—National Research Institute, 05–870 Błonie, Radzików, Poland;
| | | |
Collapse
|
26
|
Pereira WJ, Pappas MDCR, Grattapaglia D, Pappas GJ. A cost-effective approach to DNA methylation detection by Methyl Sensitive DArT sequencing. PLoS One 2020; 15:e0233800. [PMID: 32497070 PMCID: PMC7272069 DOI: 10.1371/journal.pone.0233800] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 05/12/2020] [Indexed: 12/14/2022] Open
Abstract
Several studies suggest the relation of DNA methylation to diseases in humans and important phenotypes in plants drawing attention to this epigenetic mark as an important source of variability. In the last decades, several methodologies were developed to assess the methylation state of a genome. However, there is still a lack of affordable and precise methods for genome wide analysis in large sample size studies. Methyl sensitive double digestion MS-DArT sequencing method emerges as a promising alternative for methylation profiling. We developed a computational pipeline for the identification of DNA methylation using MS-DArT-seq data and carried out a pilot study using the Eucalyptus grandis tree sequenced for the species reference genome. Using a statistic framework as in differential expression analysis, 72,515 genomic sites were investigated and 5,846 methylated sites identified, several tissue specific, distributed along the species 11 chromosomes. We highlight a bias towards identification of DNA methylation in genic regions and the identification of 2,783 genes and 842 transposons containing methylated sites. Comparison with WGBS, DNA sequencing after treatment with bisulfite, data demonstrated a precision rate higher than 95% for our approach. The availability of a reference genome is useful for determining the genomic context of methylated sites but not imperative, making this approach suitable for any species. Our approach provides a cost effective, broad and reliable examination of DNA methylation profile on MspI/HpaII restriction sites, is fully reproducible and the source code is available on GitHub (https://github.com/wendelljpereira/ms-dart-seq).
Collapse
Affiliation(s)
| | | | - Dario Grattapaglia
- Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
- Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | - Georgios Joannis Pappas
- Department of Cell Biology, University of Brasília, Brasília, Distrito Federal, Brazil
- * E-mail:
| |
Collapse
|
27
|
Pereira WJ, Pappas MDCR, Grattapaglia D, Pappas GJ. A cost-effective approach to DNA methylation detection by Methyl Sensitive DArT sequencing. PLoS One 2020; 15:e0233800. [PMID: 32497070 DOI: 10.1371/journal.pone.00233800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 05/12/2020] [Indexed: 05/27/2023] Open
Abstract
Several studies suggest the relation of DNA methylation to diseases in humans and important phenotypes in plants drawing attention to this epigenetic mark as an important source of variability. In the last decades, several methodologies were developed to assess the methylation state of a genome. However, there is still a lack of affordable and precise methods for genome wide analysis in large sample size studies. Methyl sensitive double digestion MS-DArT sequencing method emerges as a promising alternative for methylation profiling. We developed a computational pipeline for the identification of DNA methylation using MS-DArT-seq data and carried out a pilot study using the Eucalyptus grandis tree sequenced for the species reference genome. Using a statistic framework as in differential expression analysis, 72,515 genomic sites were investigated and 5,846 methylated sites identified, several tissue specific, distributed along the species 11 chromosomes. We highlight a bias towards identification of DNA methylation in genic regions and the identification of 2,783 genes and 842 transposons containing methylated sites. Comparison with WGBS, DNA sequencing after treatment with bisulfite, data demonstrated a precision rate higher than 95% for our approach. The availability of a reference genome is useful for determining the genomic context of methylated sites but not imperative, making this approach suitable for any species. Our approach provides a cost effective, broad and reliable examination of DNA methylation profile on MspI/HpaII restriction sites, is fully reproducible and the source code is available on GitHub (https://github.com/wendelljpereira/ms-dart-seq).
Collapse
Affiliation(s)
| | | | - Dario Grattapaglia
- Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
- Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | | |
Collapse
|
28
|
Singer BD. A Practical Guide to the Measurement and Analysis of DNA Methylation. Am J Respir Cell Mol Biol 2020; 61:417-428. [PMID: 31264905 DOI: 10.1165/rcmb.2019-0150tr] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
DNA methylation represents a fundamental epigenetic mark that is associated with transcriptional repression during development, maintenance of homeostasis, and disease. In addition to methylation-sensitive PCR and targeted deep-amplicon bisulfite sequencing to measure DNA methylation at defined genomic loci, numerous unsupervised techniques exist to quantify DNA methylation on a genome-wide scale, including affinity enrichment strategies and methods involving bisulfite conversion. Both affinity-enriched and bisulfite-converted DNA can serve as input material for array hybridization or sequencing using next-generation technologies. In this practical guide to the measurement and analysis of DNA methylation, the goal is to convey basic concepts in DNA methylation biology and explore genome-scale bisulfite sequencing as the current gold standard for assessment of DNA methylation. Bisulfite conversion chemistry and library preparation are discussed in addition to a bioinformatics approach to quality assessment, trimming, alignment, and methylation calling of individual cytosine residues. Bisulfite-converted DNA presents challenges for standard next-generation sequencing library preparation protocols and data-processing pipelines, but these challenges can be met with elegant solutions that leverage the power of high-performance computing systems. Quantification of DNA methylation, data visualization, statistical approaches to compare DNA methylation between sample groups, and examples of integrating DNA methylation data with other -omics data sets are also discussed. The reader is encouraged to use this article as a foundation to pursue advanced topics in DNA methylation measurement and data analysis, particularly the application of bioinformatics and computational biology principles to generate a deeper understanding of mechanisms linking DNA methylation to cellular function.
Collapse
Affiliation(s)
- Benjamin D Singer
- Division of Pulmonary and Critical Care Medicine, Department of Biochemistry and Molecular Genetics, and Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| |
Collapse
|
29
|
Weiser DA, West-Szymanski DC, Fraint E, Weiner S, Rivas MA, Zhao CWT, He C, Applebaum MA. Progress toward liquid biopsies in pediatric solid tumors. Cancer Metastasis Rev 2020; 38:553-571. [PMID: 31836951 DOI: 10.1007/s10555-019-09825-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Pediatric solid tumors have long been known to shed tumor cells, DNA, RNA, and proteins into the blood. Recent technological advances have allowed for improved capture and analysis of these typically scant circulating materials. Efforts are ongoing to develop "liquid biopsy" assays as minimally invasive tools to address diagnostic, prognostic, and disease monitoring needs in childhood cancer care. Applying these highly sensitive technologies to serial liquid biopsies is expected to advance understanding of tumor biology, heterogeneity, and evolution over the course of therapy, thus opening new avenues for personalized therapy. In this review, we outline the latest technologies available for liquid biopsies and describe the methods, pitfalls, and benefits of the assays that are being developed for children with extracranial solid tumors. We discuss what has been learned in several of the most common pediatric solid tumors including neuroblastoma, sarcoma, Wilms tumor, and hepatoblastoma and highlight promising future directions for the field.
Collapse
Affiliation(s)
- Daniel A Weiser
- Department of Pediatrics, Albert Einstein College of Medicine and Children's Hospital at Montefiore, Bronx, NY, USA
| | | | - Ellen Fraint
- Department of Pediatrics, Albert Einstein College of Medicine and Children's Hospital at Montefiore, Bronx, NY, USA
| | - Shoshana Weiner
- Department of Pediatrics, Weill Cornell Medical Center, New York, NY, USA
| | - Marco A Rivas
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Carolyn W T Zhao
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Mark A Applebaum
- Department of Pediatrics, The University of Chicago, 900 E. 57th St., KCBD 5116, Chicago, IL, 60637, USA.
| |
Collapse
|
30
|
Lee HJ, Hou Y, Chen Y, Dailey ZZ, Riddihough A, Jang HS, Wang T, Johnson SL. Regenerating zebrafish fin epigenome is characterized by stable lineage-specific DNA methylation and dynamic chromatin accessibility. Genome Biol 2020; 21:52. [PMID: 32106888 PMCID: PMC7047409 DOI: 10.1186/s13059-020-1948-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 01/28/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Zebrafish can faithfully regenerate injured fins through the formation of a blastema, a mass of proliferative cells that can grow and develop into the lost body part. After amputation, various cell types contribute to blastema formation, where each cell type retains fate restriction and exclusively contributes to regeneration of its own lineage. Epigenetic changes that are associated with lineage restriction during regeneration remain underexplored. RESULTS We produce epigenome maps, including DNA methylation and chromatin accessibility, as well as transcriptomes, of osteoblasts and other cells in uninjured and regenerating fins. This effort reveals regeneration as a process of highly dynamic and orchestrated transcriptomic and chromatin accessibility changes, coupled with stably maintained lineage-specific DNA methylation. The epigenetic signatures also reveal many novel regeneration-specific enhancers, which are experimentally validated. Regulatory networks important for regeneration are constructed through integrative analysis of the epigenome map, and a knockout of a predicted upstream regulator disrupts normal regeneration, validating our prediction. CONCLUSION Our study shows that lineage-specific DNA methylation signatures are stably maintained during regeneration, and regeneration enhancers are preset as hypomethylated before injury. In contrast, chromatin accessibility is dynamically changed during regeneration. Many enhancers driving regeneration gene expression as well as upstream regulators of regeneration are identified and validated through integrative epigenome analysis.
Collapse
Affiliation(s)
- Hyung Joo Lee
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
| | - Yiran Hou
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Yujie Chen
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Zea Z Dailey
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Aiyana Riddihough
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Hyo Sik Jang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA.
| | - Stephen L Johnson
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| |
Collapse
|
31
|
Antwi EB, Olins A, Teif VB, Bieg M, Bauer T, Gu Z, Brors B, Eils R, Olins D, Ishaque N. Whole-genome fingerprint of the DNA methylome during chemically induced differentiation of the human AML cell line HL-60/S4. Biol Open 2020; 9:bio044222. [PMID: 31988093 PMCID: PMC7044446 DOI: 10.1242/bio.044222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Accepted: 01/13/2020] [Indexed: 12/22/2022] Open
Abstract
Epigenomic regulation plays a vital role in cell differentiation. The leukemic HL-60/S4 [human myeloid leukemic cell line HL-60/S4 (ATCC CRL-3306)] promyelocytic cell can be easily differentiated from its undifferentiated promyelocyte state into neutrophil- and macrophage-like cell states. In this study, we present the underlying genome and epigenome architecture of HL-60/S4 through its differentiation. We performed whole-genome bisulphite sequencing of HL-60/S4 cells and their differentiated counterparts. With the support of karyotyping, we show that HL-60/S4 maintains a stable genome throughout differentiation. Analysis of differential Cytosine-phosphate-Guanine dinucleotide methylation reveals that most methylation changes occur in the macrophage-like state. Differential methylation of promoters was associated with immune-related terms. Key immune genes, CEBPA, GFI1, MAFB and GATA1 showed differential expression and methylation. However, we observed the strongest enrichment of methylation changes in enhancers and CTCF binding sites, implying that methylation plays a major role in large-scale transcriptional reprogramming and chromatin reorganisation during differentiation. Correlation of differential expression and distal methylation with support from chromatin capture experiments allowed us to identify putative proximal and long-range enhancers for a number of immune cell differentiation genes, including CEBPA and CCNF Integrating expression data, we present a model of HL-60/S4 differentiation in relation to the wider scope of myeloid differentiation.
Collapse
Affiliation(s)
- Enoch B Antwi
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular and Cellular Engineering, Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
- Heidelberg Biosciences International Graduate School (HBIGS), Heidelberg, Germany
| | - Ada Olins
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New England, Portland, ME, USA
| | - Vladimir B Teif
- School of Life Sciences, University of Essex, Colchester, UK
| | - Matthias Bieg
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Center for Personalized Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health
- Digital Health Centre, Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Str. 2, 10178 Berlin, Germany
| | - Tobias Bauer
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Center for Personalized Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Zuguang Gu
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Center for Personalized Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Benedikt Brors
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Core Center, Heidelberg, Germany
| | - Roland Eils
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Center for Personalized Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health
- Digital Health Centre, Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Str. 2, 10178 Berlin, Germany
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), University of Heidelberg, Heidelberg, Germany
| | - Donald Olins
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New England, Portland, ME, USA
| | - Naveed Ishaque
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Center for Personalized Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health
- Digital Health Centre, Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Str. 2, 10178 Berlin, Germany
| |
Collapse
|
32
|
Zhang L, Dai Z, Yu J, Xiao M. CpG-island-based annotation and analysis of human housekeeping genes. Brief Bioinform 2020; 22:515-525. [PMID: 31982909 DOI: 10.1093/bib/bbz134] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 08/27/2019] [Accepted: 10/03/2019] [Indexed: 11/14/2022] Open
Abstract
By reviewing previous CpG-related studies, we consider that the transcription regulation of about half of the human genes, mostly housekeeping (HK) genes, involves CpG islands (CGIs), their methylation states, CpG spacing and other chromosomal parameters. However, the precise CGI definition and positioning of CGIs within gene structures, as well as specific CGI-associated regulatory mechanisms, all remain to be explained at individual gene and gene-family levels, together with consideration of species and lineage specificity. Although previous studies have already classified CGIs into high-CpG (HCGI), intermediate-CpG (ICGI) and low-CpG (LCGI) densities based on CpG density variation, the correlation between CGI density and gene expression regulation, such as co-regulation of CGIs and TATA box on HK genes, remains to be elucidated. First, this study introduces such a problem-solving protocol for human-genome annotation, which is based on a combination of GTEx, JBLA and Gene Ontology (GO) analysis. Next, we discuss why CGI-associated genes are most likely regulated by HCGI and tend to be HK genes; the HCGI/TATA± and LCGI/TATA± combinations show different GO enrichment, whereas the ICGI/TATA± combination is less characteristic based on GO enrichment analysis. Finally, we demonstrate that Hadoop MapReduce-based MR-JBLA algorithm is more efficient than the original JBLA in k-mer counting and CGI-associated gene analysis.
Collapse
Affiliation(s)
- Le Zhang
- College of Computer Science, Sichuan University, Chengdu, 610065, PR China
| | - Zichun Dai
- Medical Big Data Center of Sichuan University, Sichuan University, Chengdu, 610065, PR China
| | - Jun Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Ming Xiao
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| |
Collapse
|
33
|
Lim JH, Kang YJ, Lee BY, Han YJ, Chung JH, Kim MY, Kim MH, Kim JW, Cho YH, Ryu HM. Epigenome-wide base-resolution profiling of DNA methylation in chorionic villi of fetuses with Down syndrome by methyl-capture sequencing. Clin Epigenetics 2019; 11:180. [PMID: 31801612 PMCID: PMC6894197 DOI: 10.1186/s13148-019-0756-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 10/06/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Epigenetic mechanisms provide an interface between environmental factors and the genome and are influential in various diseases. These mechanisms, including DNA methylation, influence the regulation of development, differentiation, and establishment of cellular identity. Here, we performed high-throughput methylome profiling to determine whether differential patterns of DNA methylation correlate with Down syndrome (DS). MATERIALS AND METHODS We extracted DNA from the chorionic villi cells of five normal and five DS fetuses at the early developmental stage (12-13 weeks of gestation). Methyl-capture sequencing (MC-Seq) was used to investigate the methylation levels of CpG sites distributed across the whole genome to identify differentially methylated CpG sites (DMCs) and regions (DMRs) in DS. New functional annotations of DMR genes using bioinformatics tools were predicted. RESULTS DNA hypermethylation was observed in DS fetal chorionic villi cells. Significant differences were evident for 4,439 DMCs, including hypermethylation (n = 4,261) and hypomethylation (n = 178). Among them, 140 hypermethylated DMRs and only 1 hypomethylated DMR were located on 121 genes and 1 gene, respectively. One hundred twenty-two genes, including 141 DMRs, were associated with heart morphogenesis and development of the ear, thyroid gland, and nervous systems. The genes were significantly associated with DS and various diseases, including hepatopulmonary syndrome, conductive hearing loss, holoprosencephaly, heart diseases, glaucoma, and musculoskeletal abnormalities. CONCLUSIONS This is the first study to compare the whole-epigenome DNA methylation pattern of the chorionic villi cells from normal and DS fetuses at the early developmental-stage using MC-seq. Overall, our results indicate that the chorionic villi cells of DS fetuses are hypermethylated in all autosomes and suggested that altered DNA methylation may be a recurrent and functionally relevant downstream response to DS in human cells. This study provides basic information for future research focused on the pathophysiology of the DS and its potential effects, as well as the role DNA methylation plays in the early developmental stage of DS fetuses.
Collapse
Affiliation(s)
- Ji Hyae Lim
- Center for Biomarker Research and Precision Medicine, CHA Advanced Research Institute, Gyeonggi-do, Republic of Korea.,Department of Medical Genetics, College of Medicine, Hanyang University, 222, Wangsimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Yu-Jung Kang
- Center for Biomarker Research and Precision Medicine, CHA Advanced Research Institute, Gyeonggi-do, Republic of Korea
| | - Bom Yi Lee
- SD Genomics Co., Ltd., Seoul, Republic of Korea
| | - You Jung Han
- Department of Obstetrics and Gynecology, CHA Gangnam Medical Center, CHA University, Seoul, Republic of Korea
| | - Jin Hoon Chung
- Department of Obstetrics and Gynecology, CHA Gangnam Medical Center, CHA University, Seoul, Republic of Korea
| | - Moon Young Kim
- Department of Obstetrics and Gynecology, CHA Gangnam Medical Center, CHA University, Seoul, Republic of Korea
| | - Min Hyoung Kim
- Department of Obstetrics Gynecology, Mizmedi Hospital, Seoul, Republic of Korea
| | - Jin Woo Kim
- Laboratory of Medical Genetics, Medical Research Institute, Cheil General Hospital and Women's Healthcare Center, Seoul, Republic of Korea
| | - Youl-Hee Cho
- Department of Medical Genetics, College of Medicine, Hanyang University, 222, Wangsimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea.
| | - Hyun Mee Ryu
- Center for Biomarker Research and Precision Medicine, CHA Advanced Research Institute, Gyeonggi-do, Republic of Korea. .,Department of Obstetrics and Gynecology, CHA Bundang Medical Center, CHA University, 59, Yatap-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, 13496, Republic of Korea.
| |
Collapse
|
34
|
Tahir RA, Zheng DA, Nazir A, Qing H. A review of computational algorithms for CpG islands detection. J Biosci 2019; 44:143. [PMID: 31894124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
CpG islands are generally known as the epigenetic regulatory regions in accordance with histone modifications, methylation, and promoter activity. There is a significant need for the exact mapping of DNA methylation in CpG islands to understand the diverse biological functions. However, the precise identification of CpG islands from the whole genome through experimental and computational approaches is still challenging. Numerous computational methods are being developed to detect the CpG-enriched regions, effectively, to reduce the time and cost of the experiments. Here, we review some of the latest computational CpG detection methods that utilize clustering, patterns and physical-distance like parameters for CpG island detection. The comparative analyses of the methods relying on different principles and parameters allow prioritizing the algorithms for specific CpG associated datasets to achieve higher accuracy and sensitivity. A number of computational tools based on the window, Hidden Markov Model, density and distance-/length-based algorithms are being applied on human or mammalian genomes for accurate CpG detection. Comparative analyses of CpG island detection algorithms facilitate to prefer the method according to the target genome and required parameters to attain higher accuracy, specificity, and performance. There is still a need for efficient computational CpG detection methods with lower false-positive results. This review provides a better understanding about the principles of tools that will assist to prioritize and develop the algorithms for accurate CpG islands detection.
Collapse
|
35
|
Huang J, Wang L. Cell-Free DNA Methylation Profiling Analysis-Technologies and Bioinformatics. Cancers (Basel) 2019; 11:cancers11111741. [PMID: 31698791 PMCID: PMC6896050 DOI: 10.3390/cancers11111741] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/01/2019] [Accepted: 11/04/2019] [Indexed: 12/24/2022] Open
Abstract
Analysis of circulating nucleic acids in bodily fluids, referred to as “liquid biopsies”, is rapidly gaining prominence. Studies have shown that cell-free DNA (cfDNA) has great potential in characterizing tumor status and heterogeneity, as well as the response to therapy and tumor recurrence. DNA methylation is an epigenetic modification that plays an important role in a broad range of biological processes and diseases. It is well known that aberrant DNA methylation is generalizable across various samples and occurs early during the pathogenesis of cancer. Methylation patterns of cfDNA are also consistent with their originated cells or tissues. Systemic analysis of cfDNA methylation profiles has emerged as a promising approach for cancer detection and origin determination. In this review, we will summarize the technologies for DNA methylation analysis and discuss their feasibility for liquid biopsy applications. We will also provide a brief overview of the bioinformatic approaches for analysis of DNA methylation sequencing data. Overall, this review provides informative guidance for the selection of experimental and computational methods in cfDNA methylation-based studies.
Collapse
|
36
|
Tahir RA, Zheng D, Nazir A, Qing H. A review of computational algorithms for CpG islands detection. J Biosci 2019. [DOI: 10.1007/s12038-019-9961-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
37
|
Sun X, Johnson J, St John JC. Global DNA methylation synergistically regulates the nuclear and mitochondrial genomes in glioblastoma cells. Nucleic Acids Res 2019; 46:5977-5995. [PMID: 29722878 PMCID: PMC6158714 DOI: 10.1093/nar/gky339] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 04/19/2018] [Indexed: 12/12/2022] Open
Abstract
Replication of mitochondrial DNA is strictly regulated during differentiation and development allowing each cell type to acquire its required mtDNA copy number to meet its specific needs for energy. Undifferentiated cells establish the mtDNA set point, which provides low numbers of mtDNA copy but sufficient template for replication once cells commit to specific lineages. However, cancer cells, such as those from the human glioblastoma multiforme cell line, HSR-GBM1, cannot complete differentiation as they fail to enforce the mtDNA set point and are trapped in a ‘pseudo-differentiated’ state. Global DNA methylation is likely to be a major contributing factor, as DNA demethylation treatments promote differentiation of HSR-GBM1 cells. To determine the relationship between DNA methylation and mtDNA copy number in cancer cells, we applied whole genome MeDIP-Seq and RNA-Seq to HSR-GBM1 cells and following their treatment with the DNA demethylation agents 5-azacytidine and vitamin C. We identified key methylated regions modulated by the DNA demethylation agents that also induced synchronous changes to mtDNA copy number and nuclear gene expression. Our findings highlight the control exerted by DNA methylation on the expression of key genes, the regulation of mtDNA copy number and establishment of the mtDNA set point, which collectively contribute to tumorigenesis.
Collapse
Affiliation(s)
- Xin Sun
- Centre for Genetic Diseases, Hudson Institute of Medical Research, 27-31 Wright Street, Clayton, VIC 3168, Australia.,Department of Molecular and Translational Sciences, Monash University, 27-31 Wright Street, Clayton, VIC 3168, Australia
| | - Jacqueline Johnson
- Centre for Genetic Diseases, Hudson Institute of Medical Research, 27-31 Wright Street, Clayton, VIC 3168, Australia
| | - Justin C St John
- Centre for Genetic Diseases, Hudson Institute of Medical Research, 27-31 Wright Street, Clayton, VIC 3168, Australia.,Department of Molecular and Translational Sciences, Monash University, 27-31 Wright Street, Clayton, VIC 3168, Australia
| |
Collapse
|
38
|
Sina AAI, Carrascosa LG, Trau M. DNA Methylation-Based Point-of-Care Cancer Detection: Challenges and Possibilities. Trends Mol Med 2019; 25:955-966. [PMID: 31253589 DOI: 10.1016/j.molmed.2019.05.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 05/28/2019] [Accepted: 05/29/2019] [Indexed: 12/31/2022]
Abstract
Eukaryotic cell DNA conserves a distinct genomic methylation pattern, which acts as a molecular switch to control the transcriptional machinery of the cell. However, pathological processes can alter this methylation pattern, leading to the onset of diseases such as cancer. Recent advances in methylation analysis provide a more precise understanding of the consequence of DNA methylation changes towards cancer progression. Consequently, the discoveries of numerous methylation-based biomarkers have inspired the development of simple tests for cancer detection. In this opinion article, we systematically discuss the benefits and challenges associated with the promising methylation-based approaches and develop a point-of-care index to evaluate their potential in terms of point-of-care cancer diagnostics.
Collapse
Affiliation(s)
- Abu Ali Ibn Sina
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), Corner College and Cooper Roads (Bldg 75), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Laura G Carrascosa
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), Corner College and Cooper Roads (Bldg 75), The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Matt Trau
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), Corner College and Cooper Roads (Bldg 75), The University of Queensland, Brisbane, QLD 4072, Australia; School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia.
| |
Collapse
|
39
|
Abstract
Treatment outcomes for acute lymphoblastic leukemia (ALL), especially pediatric ALL, have greatly improved due to the risk-adapted therapy. Combination of drug development, clinical practice, as well as basic genetic researches has brought the survival rate of ALL from less than 10% to more than 90% today, not only increasing the treatment efficacy but also limiting adverse drug reactions (ADRs). In this review, we summarized the landscape identification of ALL genetic alterations, which provided the opportunity to increase the survival rate and especially minimize the relapse risk of ALL, and highlighted the importance of the development of new technologies of genomic investigation for translational medicine.
Collapse
|
40
|
An integrated chromatin accessibility and transcriptome landscape of human pre-implantation embryos. Nat Commun 2019; 10:364. [PMID: 30664750 PMCID: PMC6341076 DOI: 10.1038/s41467-018-08244-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 12/21/2018] [Indexed: 12/22/2022] Open
Abstract
Human pre-implantation embryonic development involves extensive changes in chromatin structure and transcriptional activity. Here, we report on LiCAT-seq, a technique that enables simultaneous profiling of chromatin accessibility and gene expression with ultra-low input of cells, and map the chromatin accessibility and transcriptome landscapes for human pre-implantation embryos. We observed global difference in chromatin accessibility between sperm and all stages of embryos, finding that the accessible regions in sperm tend to occur in gene-poor genomic regions. Integrative analyses between the two datasets reveals strong association between the establishment of accessible chromatin and embryonic genome activation (EGA), and uncovers transcription factors and endogenous retrovirus (ERVs) specific to EGA. In particular, a large proportion of the early activated genes and ERVs are bound by DUX4 and become accessible as early as the 2- to 4-cell stages. Our results thus offer mechanistic insights into the molecular events inherent to human pre-implantation development.
Collapse
|
41
|
Liu Z, Wang Z, Jia E, Ouyang T, Pan M, Lu J, Ge Q, Bai Y. Analysis of genome-wide in cell free DNA methylation: progress and prospect. Analyst 2019; 144:5912-5922. [DOI: 10.1039/c9an00935c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In this work, we focus on the detection methods of cfDNA methylation based on NGS and the latest progress.
Collapse
Affiliation(s)
- Zhiyu Liu
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing
- China
| | - Zexin Wang
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing
- China
| | - Erteng Jia
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing
- China
| | - Tinglan Ouyang
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing
- China
| | - Min Pan
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing
- China
| | - Jiafeng Lu
- Center of Reproduction and Genetics
- Affiliated Suzhou Hospital of Nanjing Medical University
- Suzhou Municipal Hospital
- Suzhou 215002
- China
| | - Qinyu Ge
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing
- China
| | - Yunfei Bai
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing
- China
| |
Collapse
|
42
|
Cañadas-Garre M, Anderson K, McGoldrick J, Maxwell AP, McKnight AJ. Genomic approaches in the search for molecular biomarkers in chronic kidney disease. J Transl Med 2018; 16:292. [PMID: 30359254 PMCID: PMC6203198 DOI: 10.1186/s12967-018-1664-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 10/14/2018] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Chronic kidney disease (CKD) is recognised as a global public health problem, more prevalent in older persons and associated with multiple co-morbidities. Diabetes mellitus and hypertension are common aetiologies for CKD, but IgA glomerulonephritis, membranous glomerulonephritis, lupus nephritis and autosomal dominant polycystic kidney disease are also common causes of CKD. MAIN BODY Conventional biomarkers for CKD involving the use of estimated glomerular filtration rate (eGFR) derived from four variables (serum creatinine, age, gender and ethnicity) are recommended by clinical guidelines for the evaluation, classification, and stratification of CKD. However, these clinical biomarkers present some limitations, especially for early stages of CKD, elderly individuals, extreme body mass index values (serum creatinine), or are influenced by inflammation, steroid treatment and thyroid dysfunction (serum cystatin C). There is therefore a need to identify additional non-invasive biomarkers that are useful in clinical practice to help improve CKD diagnosis, inform prognosis and guide therapeutic management. CONCLUSION CKD is a multifactorial disease with associated genetic and environmental risk factors. Hence, many studies have employed genetic, epigenetic and transcriptomic approaches to identify biomarkers for kidney disease. In this review, we have summarised the most important studies in humans investigating genomic biomarkers for CKD in the last decade. Several genes, including UMOD, SHROOM3 and ELMO1 have been strongly associated with renal diseases, and some of their traits, such as eGFR and serum creatinine. The role of epigenetic and transcriptomic biomarkers in CKD and related diseases is still unclear. The combination of multiple biomarkers into classifiers, including genomic, and/or epigenomic, may give a more complete picture of kidney diseases.
Collapse
Affiliation(s)
- M. Cañadas-Garre
- Epidemiology and Public Health Research Group, Centre for Public Health, Belfast City Hospital, Queen’s University of Belfast, c/o University Floor, Level A, Tower Block, Lisburn Road, Belfast, BT9 7AB Northern Ireland UK
| | - K. Anderson
- Epidemiology and Public Health Research Group, Centre for Public Health, Belfast City Hospital, Queen’s University of Belfast, c/o University Floor, Level A, Tower Block, Lisburn Road, Belfast, BT9 7AB Northern Ireland UK
| | - J. McGoldrick
- Epidemiology and Public Health Research Group, Centre for Public Health, Belfast City Hospital, Queen’s University of Belfast, c/o University Floor, Level A, Tower Block, Lisburn Road, Belfast, BT9 7AB Northern Ireland UK
| | - A. P. Maxwell
- Epidemiology and Public Health Research Group, Centre for Public Health, Belfast City Hospital, Queen’s University of Belfast, c/o University Floor, Level A, Tower Block, Lisburn Road, Belfast, BT9 7AB Northern Ireland UK
- Regional Nephrology Unit, Belfast City Hospital, Belfast, UK
| | - A. J. McKnight
- Epidemiology and Public Health Research Group, Centre for Public Health, Belfast City Hospital, Queen’s University of Belfast, c/o University Floor, Level A, Tower Block, Lisburn Road, Belfast, BT9 7AB Northern Ireland UK
| |
Collapse
|
43
|
Sun X, St John JC. Modulation of mitochondrial DNA copy number in a model of glioblastoma induces changes to DNA methylation and gene expression of the nuclear genome in tumours. Epigenetics Chromatin 2018; 11:53. [PMID: 30208958 PMCID: PMC6136172 DOI: 10.1186/s13072-018-0223-z] [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] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 09/06/2018] [Indexed: 01/23/2023] Open
Abstract
Background There are multiple copies of mitochondrial DNA (mtDNA) present in each cell type, and they are strictly regulated in a cell-specific manner by a group of nuclear-encoded mtDNA-specific replication factors. This strict regulation of mtDNA copy number is mediated by cell-specific DNA methylation of these replication factors. Glioblastoma multiforme, HSR-GBM1, cells are hyper-methylated and maintain low mtDNA copy number to support their tumorigenic status. We have previously shown that when HSR-GBM1 cells with 50% of their original mtDNA content were inoculated into mice, tumours grew more aggressively than non-depleted cells. However, when the cells possessed only 3% and 0.2% of their original mtDNA content, tumour formation was less frequent and the initiation of tumorigenesis was significantly delayed. Importantly, the process of tumorigenesis was dependent on mtDNA copy number being restored to pre-depletion levels. Results By performing whole genome MeDIP-Seq and RNA-Seq on tumours generated from cells possessing 100%, 50%, 0.3% and 0.2% of their original mtDNA content, we determined that restoration of mtDNA copy number caused significant changes to both the nuclear methylome and its transcriptome for each tumour type. The affected genes were specifically associated with gene networks and pathways involving behaviour, nervous system development, cell differentiation and regulation of transcription and cellular processes. The mtDNA-specific replication factors were also modulated. Conclusions Our results highlight the bidirectional control of the nuclear and mitochondrial genomes through modulation of DNA methylation to control mtDNA copy number, which, in turn, modulates nuclear gene expression during tumorigenesis. Electronic supplementary material The online version of this article (10.1186/s13072-018-0223-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Xin Sun
- Mitochondrial Genetics Group, Hudson Institute of Medical Research, 27-31 Wright Street, Clayton, VIC, 3168, Australia.,Department of Molecular and Translational Sciences, Monash University, 27-31 Wright Street, Clayton, VIC, 3168, Australia
| | - Justin C St John
- Mitochondrial Genetics Group, Hudson Institute of Medical Research, 27-31 Wright Street, Clayton, VIC, 3168, Australia. .,Department of Molecular and Translational Sciences, Monash University, 27-31 Wright Street, Clayton, VIC, 3168, Australia.
| |
Collapse
|
44
|
Next-generation sequencing approaches for the study of genome and epigenome toxicity induced by sulfur mustard. Arch Toxicol 2018; 92:3443-3457. [PMID: 30155719 DOI: 10.1007/s00204-018-2294-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 08/20/2018] [Indexed: 12/19/2022]
Abstract
Sulfur mustard (SM) is an extensive nucleophilic and alkylating agent that targets different tissues. The genotoxic property of SM is the most threatening effect, because it is associated with detrimental inflammations and susceptibility to several kinds of cancer. Moreover, SM causes a wide variety of adverse effects on DNA which result in accumulation of DNA adducts, multiple mutations, aneuploidies, and epigenetic aberrations in the genome. However, these adverse effects are still not known well, possibly because no valid biomarkers have been developed for detecting them. The advent of next-generation sequencing (NGS) has provided opportunities for the characterization of these alterations with a higher level of molecular detail and cost-effectivity. The present review introduces NGS approaches for the detection of SM-induced DNA adducts, mutations, chromosomal structural variation, and epigenetic aberrations, and also comparing and contrasting them with regard to which might be most advantageous.
Collapse
|
45
|
Corso-Díaz X, Jaeger C, Chaitankar V, Swaroop A. Epigenetic control of gene regulation during development and disease: A view from the retina. Prog Retin Eye Res 2018; 65:1-27. [PMID: 29544768 PMCID: PMC6054546 DOI: 10.1016/j.preteyeres.2018.03.002] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 02/01/2018] [Accepted: 03/08/2018] [Indexed: 12/20/2022]
Abstract
Complex biological processes, such as organogenesis and homeostasis, are stringently regulated by genetic programs that are fine-tuned by epigenetic factors to establish cell fates and/or to respond to the microenvironment. Gene regulatory networks that guide cell differentiation and function are modulated and stabilized by modifications to DNA, RNA and proteins. In this review, we focus on two key epigenetic changes - DNA methylation and histone modifications - and discuss their contribution to retinal development, aging and disease, especially in the context of age-related macular degeneration (AMD) and diabetic retinopathy. We highlight less-studied roles of DNA methylation and provide the RNA expression profiles of epigenetic enzymes in human and mouse retina in comparison to other tissues. We also review computational tools and emergent technologies to profile, analyze and integrate epigenetic information. We suggest implementation of editing tools and single-cell technologies to trace and perturb the epigenome for delineating its role in transcriptional regulation. Finally, we present our thoughts on exciting avenues for exploring epigenome in retinal metabolism, disease modeling, and regeneration.
Collapse
Affiliation(s)
- Ximena Corso-Díaz
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Catherine Jaeger
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Vijender Chaitankar
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Anand Swaroop
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
| |
Collapse
|
46
|
Lyu G, Zhang C, Ling T, Liu R, Zong L, Guan Y, Huang X, Sun L, Zhang L, Li C, Nie Y, Tao W. Genome and epigenome analysis of monozygotic twins discordant for congenital heart disease. BMC Genomics 2018; 19:428. [PMID: 29866040 PMCID: PMC5987557 DOI: 10.1186/s12864-018-4814-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 05/22/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Congenital heart disease (CHD) is the leading non-infectious cause of death in infants. Monozygotic (MZ) twins share nearly all of their genetic variants before and after birth. Nevertheless, MZ twins are sometimes discordant for common complex diseases. The goal of this study is to identify genomic and epigenomic differences between a pair of twins discordant for a form of congenital heart disease, double outlet right ventricle (DORV). RESULTS A monoamniotic monozygotic (MZ) twin pair discordant for DORV were subjected to genome-wide sequencing and methylation analysis. We identified few genomic differences but 1566 differentially methylated regions (DMRs) between the MZ twins. Twenty percent (312/1566) of the DMRs are located within 2 kb upstream of transcription start sites (TSS), containing 121 binding sites of transcription factors. Particularly, ZIC3 and NR2F2 are found to have hypermethylated promoters in both the diseased twin and additional patients suffering from DORV. CONCLUSIONS The results showed a high correlation between hypermethylated promoters at ZIC3 and NR2F2 and down-regulated gene expression levels of these two genes in patients with DORV compared to normal controls, providing new insight into the potential mechanism of this rare form of CHD.
Collapse
Affiliation(s)
- Guoliang Lyu
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Chao Zhang
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
- Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Te Ling
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Rui Liu
- Department of Cardiovascular Surgery, Center for Cardiovascular Regenerative Medicine, Fuwai Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100871 China
| | - Le Zong
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Yiting Guan
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Xiaoke Huang
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Lei Sun
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Lijun Zhang
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Cheng Li
- Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Yu Nie
- Department of Cardiovascular Surgery, Center for Cardiovascular Regenerative Medicine, Fuwai Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100871 China
| | - Wei Tao
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
| |
Collapse
|
47
|
Nair SS, Luu PL, Qu W, Maddugoda M, Huschtscha L, Reddel R, Chenevix-Trench G, Toso M, Kench JG, Horvath LG, Hayes VM, Stricker PD, Hughes TP, White DL, Rasko JEJ, Wong JJL, Clark SJ. Guidelines for whole genome bisulphite sequencing of intact and FFPET DNA on the Illumina HiSeq X Ten. Epigenetics Chromatin 2018; 11:24. [PMID: 29807544 PMCID: PMC5971424 DOI: 10.1186/s13072-018-0194-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 05/21/2018] [Indexed: 12/24/2022] Open
Abstract
Background Comprehensive genome-wide DNA methylation profiling is critical to gain insights into epigenetic reprogramming during development and disease processes. Among the different genome-wide DNA methylation technologies, whole genome bisulphite sequencing (WGBS) is considered the gold standard for assaying genome-wide DNA methylation at single base resolution. However, the high sequencing cost to achieve the optimal depth of coverage limits its application in both basic and clinical research. To achieve 15× coverage of the human methylome, using WGBS, requires approximately three lanes of 100-bp-paired-end Illumina HiSeq 2500 sequencing. It is important, therefore, for advances in sequencing technologies to be developed to enable cost-effective high-coverage sequencing. Results In this study, we provide an optimised WGBS methodology, from library preparation to sequencing and data processing, to enable 16–20× genome-wide coverage per single lane of HiSeq X Ten, HCS 3.3.76. To process and analyse the data, we developed a WGBS pipeline (METH10X) that is fast and can call SNPs. We performed WGBS on both high-quality intact DNA and degraded DNA from formalin-fixed paraffin-embedded tissue. First, we compared different library preparation methods on the HiSeq 2500 platform to identify the best method for sequencing on the HiSeq X Ten. Second, we optimised the PhiX and genome spike-ins to achieve higher quality and coverage of WGBS data on the HiSeq X Ten. Third, we performed integrated whole genome sequencing (WGS) and WGBS of the same DNA sample in a single lane of HiSeq X Ten to improve data output. Finally, we compared methylation data from the HiSeq 2500 and HiSeq X Ten and found high concordance (Pearson r > 0.9×). Conclusions Together we provide a systematic, efficient and complete approach to perform and analyse WGBS on the HiSeq X Ten. Our protocol allows for large-scale WGBS studies at reasonable processing time and cost on the HiSeq X Ten platform. Electronic supplementary material The online version of this article (10.1186/s13072-018-0194-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Shalima S Nair
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.,St Vincent's Clinical School, UNSW, Sydney, NSW, 2010, Australia
| | - Phuc-Loi Luu
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.,St Vincent's Clinical School, UNSW, Sydney, NSW, 2010, Australia
| | - Wenjia Qu
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
| | - Madhavi Maddugoda
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.,St Vincent's Clinical School, UNSW, Sydney, NSW, 2010, Australia
| | - Lily Huschtscha
- Cancer Research Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia
| | - Roger Reddel
- Cancer Research Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia
| | | | | | - James G Kench
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia.,Central Clinical School, Sydney Medical School, University of Sydney, Camperdown, NSW, Australia
| | - Lisa G Horvath
- Central Clinical School, Sydney Medical School, University of Sydney, Camperdown, NSW, Australia.,Clinical Prostate Cancer Research, The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,Chris O'Brien Lifehouse, Camperdown, NSW, Australia
| | - Vanessa M Hayes
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.,St Vincent's Clinical School, UNSW, Sydney, NSW, 2010, Australia.,Central Clinical School, Sydney Medical School, University of Sydney, Camperdown, NSW, Australia
| | - Phillip D Stricker
- Department of Urology, St. Vincent's Hospital, Darlinghurst, NSW, Australia
| | - Timothy P Hughes
- Cancer Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia.,Australian Leukaemia and Lymphoma Group, Melbourne, Australia.,Discipline of Medicine, University of Adelaide, Adelaide, SA, Australia.,Department of Haematology, SA Pathology, Adelaide, SA, Australia
| | - Deborah L White
- Cancer Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia.,Australian Leukaemia and Lymphoma Group, Melbourne, Australia.,Faculty of Health Science and Faculty of Science, University of Adelaide, Adelaide, SA, Australia.,Australian Genomic Health Alliance, Melbourne, Australia
| | - John E J Rasko
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, NSW, 2050, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia.,Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, 2050, Australia
| | - Justin J-L Wong
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, NSW, 2050, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia.,Gene Regulation in Cancer Laboratory, Centenary Institute, University of Sydney, Camperdown, NSW, 2050, Australia
| | - Susan J Clark
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia. .,St Vincent's Clinical School, UNSW, Sydney, NSW, 2010, Australia. .,Epigenetics Research Program, The Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, NSW, 2010, Australia.
| |
Collapse
|
48
|
Abdalla M, Khairy E, Louka ML, Ali-Labib R, Ibrahim EAS. Vitamin D receptor gene methylation in hepatocellular carcinoma. Gene 2018; 653:65-71. [PMID: 29432829 DOI: 10.1016/j.gene.2018.02.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 01/31/2018] [Accepted: 02/08/2018] [Indexed: 01/19/2023]
Abstract
Worldwide, hepatocellular carcinoma (HCC) is the major subtype of primary liver cancers. HCC is typically diagnosed late in its course. With respect to cancer, the genomic actions of vitamin D are mediated through binding to the Vitamin D Receptor (VDR), which allows it to modulate the expression of genes in a cell-and tissue-specific manner. Epigenetics is a rapidly evolving field of genetic study applicable to HCC. Changes in DNA methylation patterns are thought to be early events in hepatocarcinogenesis. Curcumin has great potential as an epigenetic agent. Accordingly, the current study has been designed to study the methylation status of VDR gene promoter for the first time in HCC aiming to find its clinical significance and potential screening role in chronic Liver Disease (CLD). Additionally, we aimed to investigate, the effect of Curcumin on HCC cell line, aiming to discover new therapeutic targets through epigenetics. This study was conducted on 45 formalin-fixed, paraffin-embedded liver tissue blocks including 15 HCC samples (group A), 15 CLD samples (group B) and 15 apparently normal tissue taken from around benign lesions (group C). Methylation Specific Restriction Digestion and qPCR were done on all samples after DNA extraction. The percentage of VDR gene promoter methylation was significantly higher in the HCC group compared to both CLD and control groups (p < 0.01). VDR promoter methylation by (MS-qPCR) was decreased and the relative expression of VDR by (qRT-PCR) was markedly increased in a dose-dependent fashion in cells grown in Curcumin-adequate medium. In conclusion, this study may open a new gate for the use of VDR promoter methylation as a potential biomarker in HCC.
Collapse
Affiliation(s)
- Mai Abdalla
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Ain Shams University, Abbassia, Cairo, P.O. box 11381, Egypt
| | - Eman Khairy
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Ain Shams University, Abbassia, Cairo, P.O. box 11381, Egypt.
| | - Manal L Louka
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Ain Shams University, Abbassia, Cairo, P.O. box 11381, Egypt
| | - Randa Ali-Labib
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Ain Shams University, Abbassia, Cairo, P.O. box 11381, Egypt
| | | |
Collapse
|
49
|
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
|
50
|
Ravichandran M, Jurkowska RZ, Jurkowski TP. Target specificity of mammalian DNA methylation and demethylation machinery. Org Biomol Chem 2018; 16:1419-1435. [DOI: 10.1039/c7ob02574b] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We review here the molecular mechanisms employed by DNMTs and TET enzymes that are responsible for shaping the DNA methylation pattern of a mammalian cell.
Collapse
Affiliation(s)
| | | | - T. P. Jurkowski
- Universität Stuttgart
- Abteilung Biochemie
- Institute für Biochemie und Technische Biochemie
- Stuttgart D-70569
- Germany
| |
Collapse
|