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Nifker G, Grunwald A, Margalit S, Tulpova Z, Michaeli Y, Har-Gil H, Maimon N, Roichman E, Schütz L, Weinhold E, Ebenstein Y. Dam Assisted Fluorescent Tagging of Chromatin Accessibility (DAFCA) for Optical Genome Mapping in Nanochannel Arrays. ACS NANO 2023; 17:9178-9187. [PMID: 37154345 PMCID: PMC10210529 DOI: 10.1021/acsnano.2c12755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 05/03/2023] [Indexed: 05/10/2023]
Abstract
Proteins and enzymes in the cell nucleus require physical access to their DNA target sites in order to perform genomic tasks such as gene activation and transcription. Hence, chromatin accessibility is a central regulator of gene expression, and its genomic profile holds essential information on the cell type and state. We utilized the E. coli Dam methyltransferase in combination with a fluorescent cofactor analogue to generate fluorescent tags in accessible DNA regions within the cell nucleus. The accessible portions of the genome are then detected by single-molecule optical genome mapping in nanochannel arrays. This method allowed us to characterize long-range structural variations and their associated chromatin structure. We show the ability to create whole-genome, allele-specific chromatin accessibility maps composed of long DNA molecules extended in silicon nanochannels.
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Affiliation(s)
- Gil Nifker
- Department
of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Assaf Grunwald
- Department
of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Sapir Margalit
- Department
of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Zuzana Tulpova
- Department
of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Yael Michaeli
- Department
of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Hagai Har-Gil
- Department
of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Noy Maimon
- Department
of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Elad Roichman
- Department
of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Leonie Schütz
- Institute
of Organic Chemistry, RWTH Aachen University, D-52056 Aachen, Germany
| | - Elmar Weinhold
- Institute
of Organic Chemistry, RWTH Aachen University, D-52056 Aachen, Germany
| | - Yuval Ebenstein
- Department
of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
- Department
of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, 6997801 Tel Aviv, Israel
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Yin L, Zheng LJ, Jiang X, Liu WB, Han F, Cao J, Liu JY. Effects of Low-Dose Diethylstilbestrol Exposure on DNA Methylation in Mouse Spermatocytes. PLoS One 2015; 10:e0143143. [PMID: 26588706 PMCID: PMC4654501 DOI: 10.1371/journal.pone.0143143] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 10/30/2015] [Indexed: 12/31/2022] Open
Abstract
Evidence from previous studies suggests that the male reproductive system can be disrupted by fetal or neonatal exposure to diethylstilbestrol (DES). However, the molecular basis for this effect remains unclear. To evaluate the effects of DES on mouse spermatocytes and to explore its potential mechanism of action, the levels of DNA methyltransferases (DNMTs) and DNA methylation induced by DES were detected. The results showed that low doses of DES inhibited cell proliferation and cell cycle progression and induced apoptosis in GC-2 cells, an immortalized mouse pachytene spermatocyte-derived cell line, which reproduces primary cells responses to E2. Furthermore, global DNA methylation levels were increased and the expression levels of DNMTs were altered in DES-treated GC-2 cells. A total of 141 differentially methylated DNA sites were detected by microarray analysis. Rxra, an important component of the retinoic acid signaling pathway, and mybph, a RhoA pathway-related protein, were found to be hypermethylated, and Prkcd, an apoptosis-related protein, was hypomethylated. These results showed that low-dose DES was toxic to spermatocytes and that DNMT expression and DNA methylation were altered in DES-exposed cells. Taken together, these data demonstrate that DNA methylation likely plays an important role in mediating DES-induced spermatocyte toxicity in vitro.
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Affiliation(s)
- Li Yin
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, China
| | - Li-juan Zheng
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, China
- Gansu People’s Hospital, Lanzhou, China
| | - Xiao Jiang
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, China
| | - Wen-bin Liu
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, China
| | - Fei Han
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, China
| | - Jia Cao
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, China
| | - Jin-yi Liu
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, China
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3
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Cloning, purification and characterization of translationally fused protein DNA methyltransferase M•HhaI-EGFP. Process Biochem 2014. [DOI: 10.1016/j.procbio.2014.09.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Liu TJ, Sun LF, Shan XH, Wu Y, Su SZ, Li SP, Liu HK, Han JY, Yuan YP. Analysis of DNA methylation patterns and levels in maize hybrids and their parents. GENETICS AND MOLECULAR RESEARCH : GMR 2014. [PMID: 25366740 DOI: 10.1007/s10535-015-0490-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Heterosis is the superior performance of heterozygous individuals and has been widely exploited in plant breeding, although the underlying regulatory mechanisms still remain largely elusive. To understand the molecular basis of heterosis in maize, in this study, roots and leaves at the seedling stage and embryos and endosperm tissues 15 days after fertilization of 2 elite hybrids and their parental lines were used to estimate the levels and patterns of cytosine methylation by the methylation-sensitive amplification polymorphism method. The relative total methylation levels were lower in all the tissues of all hybrids than their corresponding mid-parent values, and the number of demethylation events was higher in the hybrids. These results implied that the decreasing trend and demethylation in hybrids relative to their parents may enable the derepression and possibly expression of many genes that were associated with the phenotypic variation in hybrids. To further analyze the observed methylation pattern changes, a total of 63 differentially displayed DNA fragments were successfully sequenced. Basic Local Alignment Search Tool analysis showed that 11 fragments shared similarity with known functional proteins in maize or other plant species, including metabolism, transposon/retrotransposon, development, stress response, and signal transduction, which indicated that these genes might play a significant role in maize hybrid vigor.
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Affiliation(s)
- T J Liu
- College of Plant Science, Jilin University, Changchun, China
| | - L F Sun
- College of Plant Science, Jilin University, Changchun, China
| | - X H Shan
- College of Plant Science, Jilin University, Changchun, China
| | - Y Wu
- College of Plant Science, Jilin University, Changchun, China
| | - S Z Su
- College of Plant Science, Jilin University, Changchun, China
| | - S P Li
- College of Plant Science, Jilin University, Changchun, China
| | - H K Liu
- College of Plant Science, Jilin University, Changchun, China
| | - J Y Han
- College of Plant Science, Jilin University, Changchun, China
| | - Y P Yuan
- College of Plant Science, Jilin University, Changchun, China
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Wu DH, Tai S. Molecular mechanism of hepatitis B virus X-associated hepatocarcinogenesis. Shijie Huaren Xiaohua Zazhi 2014; 22:3773-3779. [DOI: 10.11569/wcjd.v22.i25.3773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common malignant diseases and has the fourth highest mortality rate worldwide. Chronic hepatitis B virus (HBV) infection is one of the most important etiological factors for HCC. Current studies show that the hepatitis B virus X (HBX) gene plays an important role in the development of HBV-associated HCC. HBX protein is a multifunctional regulator. Though interacting with different host factors, HBX takes part in many cell physiological activities, such as signal transduction, gene transcription, cell cycle progression, apoptosis and autophagy. This review will discuss the biological role of HBX protein in the development of HCC based on the current state of knowledge on this protein.
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