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Wang Z, Jiang C, Jin Y, Yang J, Zhao Y, Huang L, Yuan Y. Cationic Conjugated Polymer Fluorescence Resonance Energy Transfer for DNA Methylation Assessment to Discriminate the Geographical Origins of Lonicerae japonicae flos. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:12346-12356. [PMID: 37539957 DOI: 10.1021/acs.jafc.3c02646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
The flavor and taste of Lonicerae japonicae flos (LJF) products are heavily influenced by geographical origin. Tracing the geographical origin is an important aspect of LJF quality assessment. Here, DNA methylation analysis coupled with chemometrics revealed that, in 10 CpG islands upstream of genes in the chlorogenic acid and iridoid biosynthetic pathways, DNA methylation differences appear close association with LJF geographical origin. DNA methylation status in these CpG islands was determined using the cationic conjugated polymer fluorescence resonance energy transfer method. As a result, LJFs from 39 geographical origins were classified into four groups corresponding to Northern China, Central Plain of China, Southeast China, and Western China, according to cluster analysis and principal component analysis. Our findings contribute to an understanding of the modulation of LJF taste and can assist in understanding how DNA methylation in LJF varies with geographical origin.
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Affiliation(s)
- Zhengpeng Wang
- National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing 100700, People's Republic of China
- School of Pharmacy, Jiangsu University, Zhenjiang, Jiangsu 212013, People's Republic of China
| | - Chao Jiang
- National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing 100700, People's Republic of China
| | - Yan Jin
- National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing 100700, People's Republic of China
| | - Jian Yang
- National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing 100700, People's Republic of China
| | - Yuyang Zhao
- National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing 100700, People's Republic of China
| | - Luqi Huang
- National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing 100700, People's Republic of China
| | - Yuan Yuan
- National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing 100700, People's Republic of China
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2
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Volná A, Bartas M, Nezval J, Pech R, Pečinka P, Špunda V, Červeň J. Beyond the Primary Structure of Nucleic Acids: Potential Roles of Epigenetics and Noncanonical Structures in the Regulations of Plant Growth and Stress Responses. Methods Mol Biol 2023; 2642:331-361. [PMID: 36944887 DOI: 10.1007/978-1-0716-3044-0_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Epigenetics deals with changes in gene expression that are not caused by modifications in the primary sequence of nucleic acids. These changes beyond primary structures of nucleic acids not only include DNA/RNA methylation, but also other reversible conversions, together with histone modifications or RNA interference. In addition, under particular conditions (such as specific ion concentrations or protein-induced stabilization), the right-handed double-stranded DNA helix (B-DNA) can form noncanonical structures commonly described as "non-B DNA" structures. These structures comprise, for example, cruciforms, i-motifs, triplexes, and G-quadruplexes. Their formation often leads to significant differences in replication and transcription rates. Noncanonical RNA structures have also been documented to play important roles in translation regulation and the biology of noncoding RNAs. In human and animal studies, the frequency and dynamics of noncanonical DNA and RNA structures are intensively investigated, especially in the field of cancer research and neurodegenerative diseases. In contrast, noncanonical DNA and RNA structures in plants have been on the fringes of interest for a long time and only a few studies deal with their formation, regulation, and physiological importance for plant stress responses. Herein, we present a review focused on the main fields of epigenetics in plants and their possible roles in stress responses and signaling, with special attention dedicated to noncanonical DNA and RNA structures.
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Affiliation(s)
- Adriana Volná
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Martin Bartas
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Jakub Nezval
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Radomír Pech
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Petr Pečinka
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Vladimír Špunda
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- Global Change Research Institute, Czech Academy of Sciences, Brno, Czech Republic
| | - Jiří Červeň
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic.
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Harvey KE, LaVigne EK, Dar MS, Salyer AE, Pratt EPS, Sample PA, Aryal UK, Gowher H, Hockerman GH. RyR2/IRBIT regulates insulin gene transcript, insulin content, and secretion in the insulinoma cell line INS-1. Sci Rep 2022; 12:7713. [PMID: 35562179 PMCID: PMC9095623 DOI: 10.1038/s41598-022-11276-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/31/2022] [Indexed: 12/01/2022] Open
Abstract
The role of ER Ca2+ release via ryanodine receptors (RyR) in pancreatic β-cell function is not well defined. Deletion of RyR2 from the rat insulinoma INS-1 (RyR2KO) enhanced IP3 receptor activity stimulated by 7.5 mM glucose, coincident with reduced levels of the protein IP3 Receptor Binding protein released with Inositol 1,4,5 Trisphosphate (IRBIT). Insulin content, basal (2.5 mM glucose) and 7.5 mM glucose-stimulated insulin secretion were reduced in RyR2KO and IRBITKO cells compared to controls. INS2 mRNA levels were reduced in both RyR2KO and IRBITKO cells, but INS1 mRNA levels were specifically decreased in RyR2KO cells. Nuclear localization of S-adenosylhomocysteinase (AHCY) was increased in RyR2KO and IRBITKO cells. DNA methylation of the INS1 and INS2 gene promotor regions was very low, and not different among RyR2KO, IRBITKO, and controls, but exon 2 of the INS1 and INS2 genes was more extensively methylated in RyR2KO and IRBITKO cells. Exploratory proteomic analysis revealed that deletion of RyR2 or IRBIT resulted in differential regulation of 314 and 137 proteins, respectively, with 41 in common. These results suggest that RyR2 regulates IRBIT levels and activity in INS-1 cells, and together maintain insulin content and secretion, and regulate the proteome, perhaps via DNA methylation.
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Affiliation(s)
- Kyle E Harvey
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Emily K LaVigne
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
- Interdisciplinary Life Sciences Program, Purdue University, West Lafayette, IN, USA
| | - Mohd Saleem Dar
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Amy E Salyer
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Evan P S Pratt
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
- Interdisciplinary Life Sciences Program, Purdue University, West Lafayette, IN, USA
| | - Paxton A Sample
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Uma K Aryal
- Proteomics Facility, Bindley Bioscience Center, Purdue University, West Lafayette, IN, USA
| | - Humaira Gowher
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Gregory H Hockerman
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA.
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4
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A novel methyl-dependent DNA endonuclease GlaI coupling with double cascaded strand displacement amplification and CRISPR/Cas12a for ultra-sensitive detection of DNA methylation. Anal Chim Acta 2022; 1212:339914. [DOI: 10.1016/j.aca.2022.339914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 12/26/2022]
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Anton BP, Fomenkov A, Wu V, Roberts RJ. Genome-wide identification of 5-methylcytosine sites in bacterial genomes by high-throughput sequencing of MspJI restriction fragments. PLoS One 2021; 16:e0247541. [PMID: 33974631 PMCID: PMC8112702 DOI: 10.1371/journal.pone.0247541] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/26/2021] [Indexed: 11/19/2022] Open
Abstract
Single-molecule Real-Time (SMRT) sequencing can easily identify sites of N6-methyladenine and N4-methylcytosine within DNA sequences, but similar identification of 5-methylcytosine sites is not as straightforward. In prokaryotic DNA, methylation typically occurs within specific sequence contexts, or motifs, that are a property of the methyltransferases that "write" these epigenetic marks. We present here a straightforward, cost-effective alternative to both SMRT and bisulfite sequencing for the determination of prokaryotic 5-methylcytosine methylation motifs. The method, called MFRE-Seq, relies on excision and isolation of fully methylated fragments of predictable size using MspJI-Family Restriction Enzymes (MFREs), which depend on the presence of 5-methylcytosine for cleavage. We demonstrate that MFRE-Seq is compatible with both Illumina and Ion Torrent sequencing platforms and requires only a digestion step and simple column purification of size-selected digest fragments prior to standard library preparation procedures. We applied MFRE-Seq to numerous bacterial and archaeal genomic DNA preparations and successfully confirmed known motifs and identified novel ones. This method should be a useful complement to existing methodologies for studying prokaryotic methylomes and characterizing the contributing methyltransferases.
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Affiliation(s)
- Brian P. Anton
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
- * E-mail:
| | - Alexey Fomenkov
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Victoria Wu
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
- Wellesley College, Wellesley, Massachusetts, United States of America
| | - Richard J. Roberts
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
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Current Advances in DNA Methylation Analysis Methods. BIOMED RESEARCH INTERNATIONAL 2021; 2021:8827516. [PMID: 33824878 PMCID: PMC8007345 DOI: 10.1155/2021/8827516] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 02/04/2021] [Accepted: 03/01/2021] [Indexed: 12/18/2022]
Abstract
DNA methylation is one of the epigenetic changes, which plays a major role in regulating gene expression and, thus, many biological processes and diseases. There are several methods for determining the methylation of DNA samples. However, selecting the most appropriate method for answering biological questions appears to be a challenging task. The primary methods in DNA methylation focused on identifying the state of methylation of the examined genes and determining the total amount of 5-methyl cytosine. The study of DNA methylation at a large scale of genomic levels became possible following the use of microarray hybridization technology. The new generation of sequencing platforms now allows the preparation of genomic maps of DNA methylation at the single-open level. This review includes the majority of methods available to date, introducing the most widely used methods, the bisulfite treatment, biological identification, and chemical cutting along with their advantages and disadvantages. The techniques are then scrutinized according to their robustness, high throughput capabilities, and cost.
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Bourges AC, Torres Montaguth OE, Tadesse W, Labesse G, Aertsen A, Royer CA, Declerck N. An oligomeric switch controls the Mrr-induced SOS response in E. coli. DNA Repair (Amst) 2020; 97:103009. [PMID: 33220536 DOI: 10.1016/j.dnarep.2020.103009] [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: 07/21/2020] [Revised: 10/05/2020] [Accepted: 11/01/2020] [Indexed: 11/26/2022]
Abstract
Mrr from Escherichia coli K12 is a type IV restriction endonuclease whose role is to recognize and cleave foreign methylated DNA. Beyond this protective role, Mrr can inflict chromosomal DNA damage that elicits the SOS response in the host cell upon heterologous expression of specific methyltransferases such as M.HhaII, or after exposure to high pressure (HP). Activation of Mrr in response to these perturbations involves an oligomeric switch that dissociates inactive homo-tetramers into active dimers. Here we used scanning number and brightness (sN&B) analysis to determine in vivo the stoichiometry of a constitutively active Mrr mutant predicted to be dimeric and examine other GFP-Mrr mutants compromised in their response to either M.HhaII activity or HP shock. We also observed in vitro the direct pressure-induced tetramer dissociation by HP fluorescence correlation spectroscopy of purified GFP-Mrr. To shed light on the linkages between subunit interactions and activity of Mrr and its variants, we built a structural model of the full-length tetramer bound to DNA. Similar to functionally related endonucleases, the conserved DNA cleavage domain would be sequestered by the DNA recognition domain in the Mrr inactive tetramer, dissociating into an enzymatically active dimer upon interaction with multiple DNA sites.
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Affiliation(s)
- Anaïs C Bourges
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA; Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, 34090, Montpellier, France
| | | | - Wubishet Tadesse
- Department of Microbial and Molecular Systems, KU Leuven, B-3001, Leuven, Belgium
| | - Gilles Labesse
- Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, 34090, Montpellier, France
| | - Abram Aertsen
- Department of Microbial and Molecular Systems, KU Leuven, B-3001, Leuven, Belgium
| | - Catherine A Royer
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Nathalie Declerck
- Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, 34090, Montpellier, France; Département MICA, INRA, 78350 Jouy-en-Josas, France.
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Pan G, Jiang L, Tang J, Guo F. A Novel Computational Method for Detecting DNA Methylation Sites with DNA Sequence Information and Physicochemical Properties. Int J Mol Sci 2018; 19:ijms19020511. [PMID: 29419752 PMCID: PMC5855733 DOI: 10.3390/ijms19020511] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 02/01/2018] [Accepted: 02/02/2018] [Indexed: 02/06/2023] Open
Abstract
DNA methylation is an important biochemical process, and it has a close connection with many types of cancer. Research about DNA methylation can help us to understand the regulation mechanism and epigenetic reprogramming. Therefore, it becomes very important to recognize the methylation sites in the DNA sequence. In the past several decades, many computational methods—especially machine learning methods—have been developed since the high-throughout sequencing technology became widely used in research and industry. In order to accurately identify whether or not a nucleotide residue is methylated under the specific DNA sequence context, we propose a novel method that overcomes the shortcomings of previous methods for predicting methylation sites. We use k-gram, multivariate mutual information, discrete wavelet transform, and pseudo amino acid composition to extract features, and train a sparse Bayesian learning model to do DNA methylation prediction. Five criteria—area under the receiver operating characteristic curve (AUC), Matthew’s correlation coefficient (MCC), accuracy (ACC), sensitivity (SN), and specificity—are used to evaluate the prediction results of our method. On the benchmark dataset, we could reach 0.8632 on AUC, 0.8017 on ACC, 0.5558 on MCC, and 0.7268 on SN. Additionally, the best results on two scBS-seq profiled mouse embryonic stem cells datasets were 0.8896 and 0.9511 by AUC, respectively. When compared with other outstanding methods, our method surpassed them on the accuracy of prediction. The improvement of AUC by our method compared to other methods was at least 0.0399. For the convenience of other researchers, our code has been uploaded to a file hosting service, and can be downloaded from: https://figshare.com/s/0697b692d802861282d3.
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Affiliation(s)
- Gaofeng Pan
- School of Computer Science and Technology, Tianjin University, Tianjin 300350, China.
- Tianjin University Institute of Computational Biology, Tianjin University, Tianjin 300350, China.
| | - Limin Jiang
- School of Computer Science and Technology, Tianjin University, Tianjin 300350, China.
- Tianjin University Institute of Computational Biology, Tianjin University, Tianjin 300350, China.
| | - Jijun Tang
- School of Computer Science and Technology, Tianjin University, Tianjin 300350, China.
- Tianjin University Institute of Computational Biology, Tianjin University, Tianjin 300350, China.
- Department of Computer Science and Engineering, University of South Carolina, Columbia, SC 29208, USA.
| | - Fei Guo
- School of Computer Science and Technology, Tianjin University, Tianjin 300350, China.
- Tianjin University Institute of Computational Biology, Tianjin University, Tianjin 300350, China.
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