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Naue J. Getting the chronological age out of DNA: using insights of age-dependent DNA methylation for forensic DNA applications. Genes Genomics 2023; 45:1239-1261. [PMID: 37253906 PMCID: PMC10504122 DOI: 10.1007/s13258-023-01392-8] [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: 02/28/2023] [Accepted: 04/15/2023] [Indexed: 06/01/2023]
Abstract
BACKGROUND DNA analysis for forensic investigations has a long tradition with important developments and optimizations since its first application. Traditionally, short tandem repeats analysis has been the most powerful method for the identification of individuals. However, in addition, epigenetic changes, i.e., DNA methylation, came into focus of forensic DNA research. Chronological age prediction is one promising application to allow for narrowing the pool of possible individuals who caused a trace, as well as to support the identification of unknown bodies and for age verification of living individuals. OBJECTIVE This review aims to provide an overview of the current knowledge, possibilities, and (current) limitations about DNA methylation-based chronological age prediction with emphasis on forensic application. METHODS The development, implementation and application of age prediction tools requires a deep understanding about the biological background, the analysis methods, the age-dependent DNA methylation markers, as well as the mathematical models for age prediction and their evaluation. Furthermore, additional influences can have an impact. Therefore, the literature was evaluated in respect to these diverse topics. CONCLUSION The numerous research efforts in recent years have led to a rapid change in our understanding of the application of DNA methylation for chronological age prediction, which is now on the way to implementation and validation. Knowledge of the various aspects leads to a better understanding and allows a more informed interpretation of DNAm quantification results, as well as the obtained results by the age prediction tools.
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Affiliation(s)
- Jana Naue
- Institute of Forensic Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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Tukek T, Pehlivan S, Medetalibeyoglu A, Serin I, Oyacı Y, Arıcı H, Senkal N, Pehlivan M, Isoglu-Alkac U, Kose M. The suppressor of cytokine signaling-1 ( SOCS1) gene polymorphism and promoter methylation correlate with the course of COVID-19. Pathog Glob Health 2023; 117:392-400. [PMID: 36448222 PMCID: PMC10177741 DOI: 10.1080/20477724.2022.2151861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
The suppressor of the cytokine signaling-1 (SOCS1) gene is a short sequence located on chromosome 16 that functions to induce an appropriate immune response and is an essential physiological regulator of interferon (IFN) signaling. In addition to comparing the global DNA and SOCS1 gene promoter methylation status between our patients with coronavirus disease 2019 (COVID-19) and healthy controls, this study demonstrates the effect of the SOCS1 rs33989964 polymorphism on patients with COVID-19. The study group included 139 patients diagnosed with COVID-19 in our hospital's clinics between June and December 2020, and the control group included 78 healthy individuals. After comparing the initial gene polymorphisms of the patients with the healthy control group, three separate clinical subgroups were formed. The gene polymorphism distribution and the methylation status of SOCS1 were examined in these clinical subgroups. Hypomethylation of the SOCS1 gene was observed in the COVID-19 patient group compared to the healthy control group (p = 0.001). Between the patients divided into two separate clinical subgroups, those with severe and mild infections, the Del/Del genotype of the SOCS1 gene was more common in patients with severe infection than in patients with mild infection (p = 0.018). Patients with the CA/CA and CA/Del genotypes were 0.201 times more likely to have a severe infection (95% CI: 0.057-0.716, p = 0.007). Having a non-Del/Del genotype was a protective factor against severe infection. The effect of the SOCS1 rs33989964 polymorphism and methylation status of the SOCS1 gene throughout the COVID-19 pandemic could be significant contributions to the literature.
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Affiliation(s)
- Tufan Tukek
- Department of Internal Medicine, Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Sacide Pehlivan
- Department of Medical Biology, Faculty of Medicine, Institute of Health Sciences, Istanbul University, Istanbul, Turkey
| | - Alpay Medetalibeyoglu
- Department of Internal Medicine, Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Istemi Serin
- Department of Hematology, Istanbul Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Yasemin Oyacı
- Department of Medical Biology, Faculty of Medicine, Institute of Health Sciences, Istanbul University, Istanbul, Turkey
| | - Huzeyfe Arıcı
- Department of Internal Medicine, Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Naci Senkal
- Department of Internal Medicine, Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Mustafa Pehlivan
- Department of Hematology, Faculty of Medicine, Gaziantep University, Gaziantep, Turkey
| | - Ummuhan Isoglu-Alkac
- Department of Physiology, Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Murat Kose
- Department of Internal Medicine, Faculty of Medicine, Istanbul University, Istanbul, Turkey
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Tuncel FC, Serin I, Pehlivan S, Oyaci Y, Pehlivan M. Epigenetic and genetic investigation of SOCS-1 gene in patients with multiple myeloma. Blood Res 2022; 57:250-255. [PMID: 36289192 PMCID: PMC9812727 DOI: 10.5045/br.2022.2022097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/17/2022] [Accepted: 09/08/2022] [Indexed: 02/01/2023] Open
Abstract
Background The suppressor of cytokine signaling-1 (SOCS-1) functions to induce an appropriate immune response and is an essential physiological regulator of interferon signaling. DNA methylation involves adding a methyl group to the carbon 5 position of cytosine. Besides comparing SOCS-1 gene methylation status between patients with multiple myeloma (MM) and healthy controls, this study also aimed to demonstrate the effect of SOCS-1 gene distribution and the effect of methylation of SOCS-1 on progression-free survival (PFS) and overall survival (OS). Methods This study included 120 patients diagnosed with MM between January 2018 and 2020 and 80 healthy individuals. The distribution of the SOCS-1 genotypes was statistically compared between MM patients and healthy controls. Additionally, the statistically significant effects of these genotypes on survival were examined. Results The CA/CA genotype of SOCS-1 was significantly higher in healthy controls (P=0.001), while the Del/Del genotype was significantly higher in patients with MM (P=0.034). The percent methylated reference (PMR) value of the SOCS-1 gene was significantly higher in the healthy controls (median, 43.48; range, 2.76‒247.75; P=0.001). Patients with a PMR value of ≥43.48 were 3.125 times more likely to develop progression than those with a PMR value of <43.48. Conclusion The effects of SOCS-1 polymorphisms on the pathogenesis of.
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Affiliation(s)
- Fatıma Ceren Tuncel
- Department of Medical Biology, Faculty of Medicine, Institute of Health Sciences, Istanbul University, Istanbul, Turkey
| | - Istemi Serin
- Department of Hematology, Istanbul Training and Research Hospital, University of Health Sciences, Istanbul, Turkey,Correspondence to Istemi Serin, M.D., Department of Hematology, Istanbul Training and Research Hospital, University of Health Sciences, Org. Nafiz Gurman Cad. Fatih 34098, Istanbul, Turkey, E-mail:
| | - Sacide Pehlivan
- Department of Medical Biology, Faculty of Medicine, Institute of Health Sciences, Istanbul University, Istanbul, Turkey
| | - Yasemin Oyaci
- Department of Medical Biology, Faculty of Medicine, Institute of Health Sciences, Istanbul University, Istanbul, Turkey
| | - Mustafa Pehlivan
- Department of Hematology, Faculty of Medicine, Gaziantep University, Gaziantep, Turkey
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Pharmacological Approaches to Decelerate Aging: A Promising Path. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:4201533. [PMID: 35860429 PMCID: PMC9293537 DOI: 10.1155/2022/4201533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 05/24/2022] [Accepted: 06/26/2022] [Indexed: 11/17/2022]
Abstract
Biological aging or senescence is a course in which cellular function decreases over a period of time and is a consequence of altered signaling mechanisms that are triggered in stressed cells leading to cell damage. Aging is among the principal risk factors for many chronic illnesses such as cancer, cardiovascular disorders, and neurodegenerative diseases. Taking this into account, targeting fundamental aging mechanisms therapeutically may effectively impact numerous chronic illnesses. Selecting ideal therapeutic options in order to hinder the process of aging and decelerate the progression of age-related diseases is valuable. Along therapeutic options, life style modifications may well render the process of aging. The process of aging is affected by alteration in many cellular and signaling pathways amid which mTOR, SIRT1, and AMPK pathways are the most emphasized. Herein, we have discussed the mechanisms of aging focusing mainly on the mentioned pathways as well as the role of inflammation and autophagy in aging. Moreover, drugs and natural products with antiaging properties are discussed in detail.
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Chen Z, Fan Y, Liu X, Shang X, Qi K, Zhang S. Clinicopathological significance of DAPK gene promoter hypermethylation in non-small cell lung cancer: A meta-analysis. Int J Biol Markers 2022; 37:47-57. [PMID: 34935548 DOI: 10.1177/17246008211067552] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND Death-associated protein kinase (DAPK) has a strong function of tumor suppression involving apoptosis regulation, autophagy, and metastasis inhibition. Hypermethylation of CpG islands in DAPK gene promoter region is one of the important ways to inactivate this tumor suppressor gene, which might promote lung carcinogenesis. However, the clinicopathological significance of the DAPK promoter hypermethylation in lung cancer remains unclear. In this study, we performed a meta-analysis trying to estimate the clinicopathological significance of DAPK promoter hypermethylation in non-small cell lung cancer (NSCLC). METHODS A detailed literature search for publications relevant to DAPK gene promoter methylation and NSCLC was made in PubMed, Embase, Cochrane Library, Web of Science, China National Knowledge Infrastructure, CSTJ, Wanfang databases, and SinoMed (CBM). The random-effects model and fixed-effects model were utilized to pool the relative ratio based on the heterogeneity test in the meta-analysis. RESULTS A total of 41 studies with 3348 patients were included. The frequency of DAPK methylation was significantly higher in NSCLC than in non-malignant control (odds ratio (OR) = 6.88, 95% confidence interval (CI): 4.17-11.35, P < 0.00001). The pooled results also showed that DAPK gene promoter hypermethylation was significantly associated with poor prognosis for overall survival in patients with NSCLC (hazard ratio: 1.23, 95% CI:1.01-1.52, P = 0.04). Moreover, DAPK gene promoter hypermethylation was significantly associated with squamous cell carcinoma (OR: 1.25, 95% CI: 1.01-1.54, P = 0.04) and smoking behavior (OR: 1.42, 95% CI: 1.04-1.93, P = 0.03) but not with TNM stage, tumor differentiation, age, or gender. CONCLUSION DAPK promoter hypermethylation might be a candidate diagnostic and prognostic tumor marker for NSCLC.
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Affiliation(s)
- Zhimao Chen
- Department of Thoracic Surgery, 26447Peking University First Hospital, Beijing, China
| | - Yu Fan
- Department of Pathology, 571674Shantou University Medical College, Shantou, Guangdong, China
| | - Xiangzheng Liu
- Department of Thoracic Surgery, 26447Peking University First Hospital, Beijing, China
| | - Xueqian Shang
- Department of Thoracic Surgery, 26447Peking University First Hospital, Beijing, China
| | - Kang Qi
- Department of Thoracic Surgery, 26447Peking University First Hospital, Beijing, China
| | - Shijie Zhang
- Department of Thoracic Surgery, 26447Peking University First Hospital, Beijing, China
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Rissone P, Bizarro CV, Ritort F. Stem-loop formation drives RNA folding in mechanical unzipping experiments. Proc Natl Acad Sci U S A 2022; 119:e2025575119. [PMID: 35022230 PMCID: PMC8784153 DOI: 10.1073/pnas.2025575119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 11/29/2021] [Indexed: 12/22/2022] Open
Abstract
Accurate knowledge of RNA hybridization is essential for understanding RNA structure and function. Here we mechanically unzip and rezip a 2-kbp RNA hairpin and derive the 10 nearest-neighbor base pair (NNBP) RNA free energies in sodium and magnesium with 0.1 kcal/mol precision using optical tweezers. Notably, force-distance curves (FDCs) exhibit strong irreversible effects with hysteresis and several intermediates, precluding the extraction of the NNBP energies with currently available methods. The combination of a suitable RNA synthesis with a tailored pulling protocol allowed us to obtain the fully reversible FDCs necessary to derive the NNBP energies. We demonstrate the equivalence of sodium and magnesium free-energy salt corrections at the level of individual NNBP. To characterize the irreversibility of the unzipping-rezipping process, we introduce a barrier energy landscape of the stem-loop structures forming along the complementary strands, which compete against the formation of the native hairpin. This landscape correlates with the hysteresis observed along the FDCs. RNA sequence analysis shows that base stacking and base pairing stabilize the stem-loops that kinetically trap the long-lived intermediates observed in the FDC. Stem-loops formation appears as a general mechanism to explain a wide range of behaviors observed in RNA folding.
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Affiliation(s)
- Paolo Rissone
- Small Biosystems Laboratory, Condensed Matter Physics Department, University of Barcelona, Barcelona 08028, Spain
| | - Cristiano V Bizarro
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul, 90616-900 Porto Alegre, Brazil
| | - Felix Ritort
- Small Biosystems Laboratory, Condensed Matter Physics Department, University of Barcelona, Barcelona 08028, Spain;
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Zhang M, Jia C, Li F, Li C, Zhu Y, Akutsu T, Webb GI, Zou Q, Coin LJM, Song J. Critical assessment of computational tools for prokaryotic and eukaryotic promoter prediction. Brief Bioinform 2022; 23:6502561. [PMID: 35021193 PMCID: PMC8921625 DOI: 10.1093/bib/bbab551] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 11/12/2021] [Accepted: 11/30/2021] [Indexed: 01/13/2023] Open
Abstract
Promoters are crucial regulatory DNA regions for gene transcriptional activation. Rapid advances in next-generation sequencing technologies have accelerated the accumulation of genome sequences, providing increased training data to inform computational approaches for both prokaryotic and eukaryotic promoter prediction. However, it remains a significant challenge to accurately identify species-specific promoter sequences using computational approaches. To advance computational support for promoter prediction, in this study, we curated 58 comprehensive, up-to-date, benchmark datasets for 7 different species (i.e. Escherichia coli, Bacillus subtilis, Homo sapiens, Mus musculus, Arabidopsis thaliana, Zea mays and Drosophila melanogaster) to assist the research community to assess the relative functionality of alternative approaches and support future research on both prokaryotic and eukaryotic promoters. We revisited 106 predictors published since 2000 for promoter identification (40 for prokaryotic promoter, 61 for eukaryotic promoter, and 5 for both). We systematically evaluated their training datasets, computational methodologies, calculated features, performance and software usability. On the basis of these benchmark datasets, we benchmarked 19 predictors with functioning webservers/local tools and assessed their prediction performance. We found that deep learning and traditional machine learning-based approaches generally outperformed scoring function-based approaches. Taken together, the curated benchmark dataset repository and the benchmarking analysis in this study serve to inform the design and implementation of computational approaches for promoter prediction and facilitate more rigorous comparison of new techniques in the future.
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Affiliation(s)
| | - Cangzhi Jia
- Corresponding authors: Jiangning Song, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia. E-mail: ; Lachlan J.M. Coin, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, 792 Elizabeth Street, Melbourne, Victoria 3000, Australia. E-mail: ; Quan Zou, Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China. E-mail: ; Cangzhi Jia, School of Science, Dalian Maritime University, Dalian 116026, China. E-mail:
| | | | | | | | | | - Geoffrey I Webb
- Department of Data Science and Artificial Intelligence, Monash University, Melbourne, VIC 3800, Australia,Monash Data Futures Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Quan Zou
- Corresponding authors: Jiangning Song, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia. E-mail: ; Lachlan J.M. Coin, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, 792 Elizabeth Street, Melbourne, Victoria 3000, Australia. E-mail: ; Quan Zou, Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China. E-mail: ; Cangzhi Jia, School of Science, Dalian Maritime University, Dalian 116026, China. E-mail:
| | - Lachlan J M Coin
- Corresponding authors: Jiangning Song, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia. E-mail: ; Lachlan J.M. Coin, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, 792 Elizabeth Street, Melbourne, Victoria 3000, Australia. E-mail: ; Quan Zou, Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China. E-mail: ; Cangzhi Jia, School of Science, Dalian Maritime University, Dalian 116026, China. E-mail:
| | - Jiangning Song
- Corresponding authors: Jiangning Song, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia. E-mail: ; Lachlan J.M. Coin, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, 792 Elizabeth Street, Melbourne, Victoria 3000, Australia. E-mail: ; Quan Zou, Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China. E-mail: ; Cangzhi Jia, School of Science, Dalian Maritime University, Dalian 116026, China. E-mail:
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Shcherbak N, Suchkova I, Patkin E, Voznyuk I. DNA methylation in experimental ischemic brain injury. Zh Nevrol Psikhiatr Im S S Korsakova 2022; 122:32-40. [DOI: 10.17116/jnevro202212208232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Use of Average Mutual Information and Derived Measures to Find Coding Regions. ENTROPY 2021; 23:e23101324. [PMID: 34682048 PMCID: PMC8534840 DOI: 10.3390/e23101324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/09/2021] [Accepted: 09/16/2021] [Indexed: 11/17/2022]
Abstract
One of the important steps in the annotation of genomes is the identification of regions in the genome which code for proteins. One of the tools used by most annotation approaches is the use of signals extracted from genomic regions that can be used to identify whether the region is a protein coding region. Motivated by the fact that these regions are information bearing structures we propose signals based on measures motivated by the average mutual information for use in this task. We show that these signals can be used to identify coding and noncoding sequences with high accuracy. We also show that these signals are robust across species, phyla, and kingdom and can, therefore, be used in species agnostic genome annotation algorithms for identifying protein coding regions. These in turn could be used for gene identification.
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Tschirley AM, Stockwell PA, Rodger EJ, Eltherington O, Morison IM, Christensen N, Chatterjee A, Hibma M. The Mouse Papillomavirus Epigenetic Signature Is Characterised by DNA Hypermethylation after Lesion Regression. Viruses 2021; 13:v13102045. [PMID: 34696474 PMCID: PMC8539022 DOI: 10.3390/v13102045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 10/07/2021] [Indexed: 12/17/2022] Open
Abstract
Papillomaviruses (PVs) are double-stranded DNA tumour viruses that can infect cutaneous and mucosal epidermis. Human papillomavirus (HPV) types have been linked to the causality of cutaneous squamous cell carcinoma (cSCC); however, HPV DNA is not always detected in the resultant tumour. DNA methylation is an epigenetic change that can contribute to carcinogenesis. We hypothesise that the DNA methylation pattern in cells is altered following PV infection. We tested if DNA methylation was altered by PV infection in the mouse papillomavirus (MmuPV1) model. Immunosuppressed mice were infected with MmuPV1 on cutaneous tail skin. Immunosuppression was withdrawn for some mice, causing lesions to spontaneously regress. Reduced representation bisulphite sequencing was carried out on DNA from the actively infected lesions, visibly regressed lesions, and mock-infected control mice. DNA methylation libraries were generated and analysed for differentially methylated regions throughout the genome. The presence of MmuPV1 sequences was also assessed. We identified 834 predominantly differentially hypermethylated fragments in regressed lesions, and no methylation differences in actively infected lesions. The promoter regions of genes associated with tumorigenicity, including the tumour suppressor protein DAPK1 and mismatch repair proteins MSH6 and PAPD7, were hypermethylated. Viral DNA was detected in active lesions and in some lesions that had regressed. This is the first description of the genome-wide DNA methylation landscape for active and regressed MmuPV1 lesions. We propose that the DNA hypermethylation in the regressed lesions that we report here may increase the susceptibility of cells to ultraviolet-induced cSCC.
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Affiliation(s)
- Allison M. Tschirley
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9054, New Zealand; (A.M.T.); (P.A.S.); (E.J.R.); (O.E.); (I.M.M.); (A.C.)
| | - Peter A. Stockwell
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9054, New Zealand; (A.M.T.); (P.A.S.); (E.J.R.); (O.E.); (I.M.M.); (A.C.)
| | - Euan J. Rodger
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9054, New Zealand; (A.M.T.); (P.A.S.); (E.J.R.); (O.E.); (I.M.M.); (A.C.)
| | - Oliver Eltherington
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9054, New Zealand; (A.M.T.); (P.A.S.); (E.J.R.); (O.E.); (I.M.M.); (A.C.)
| | - Ian M. Morison
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9054, New Zealand; (A.M.T.); (P.A.S.); (E.J.R.); (O.E.); (I.M.M.); (A.C.)
| | - Neil Christensen
- Department of Pathology, Pennsylvania State University, State College, PA 16802, USA;
| | - Aniruddha Chatterjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9054, New Zealand; (A.M.T.); (P.A.S.); (E.J.R.); (O.E.); (I.M.M.); (A.C.)
| | - Merilyn Hibma
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9054, New Zealand; (A.M.T.); (P.A.S.); (E.J.R.); (O.E.); (I.M.M.); (A.C.)
- Correspondence: ; Tel.: +64-3479-7726
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11
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Walsh AD, Johnson LJ, Harvey AJ, Kilpatrick TJ, Binder MD. Identification and Characterisation of cis-Regulatory Elements Upstream of the Human Receptor Tyrosine Kinase Gene MERTK. Brain Plast 2021; 7:3-16. [PMID: 34631417 PMCID: PMC8461731 DOI: 10.3233/bpl-200102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND: MERTK encodes a receptor tyrosine kinase that regulates immune homeostasis via phagocytosis of apoptotic cells and cytokine-mediated immunosuppression. MERTK is highly expressed in the central nervous system (CNS), specifically in myeloid derived innate immune cells and its dysregulation is implicated in CNS pathologies including the autoimmune disease multiple sclerosis (MS). OBJECTIVE: While the cell types and tissues that express MERTK have been well described, the genetic elements that define the gene’s promoter and regulate specific transcription domains remain unknown. The primary objective of this study was to define and characterise the human MERTK promoter region. METHODS: We cloned and characterized the 5’ upstream region of MERTK to identify cis-acting DNA elements that promote gene transcription in luciferase reporter assays. In addition, promoter regions were tested for sensitivity to the anti-inflammatory glucocorticoid dexamethasone. RESULTS: This study identified identified both proximal and distal-acting DNA elements that promote transcription. The strongest promoter activity was identified in an ∼850 bp region situated 3 kb upstream of the MERTK transcription start site. Serial deletions of this putative enhancer revealed that the entire region is essential for expression activity. Using in silico analysis, we identified several candidate transcription factor binding sites. Despite a well-established upregulation of MERTK in response to anti-inflammatory glucocorticoids, no DNA region within the 5 kb putative promoter was found to directly respond to dexamethasone treatment. CONCLUSIONS: Elucidating the genetic mechanisms that regulate MERTK expression gives insights into gene regulation during homeostasis and disease, providing potential targets for therapeutic modulation of MERTK transcription.
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Affiliation(s)
- Alexander D. Walsh
- The Florey Institute of Neuroscience and Mental Health, Parkville, Melbourne, Australia
| | - Laura J. Johnson
- The Florey Institute of Neuroscience and Mental Health, Parkville, Melbourne, Australia
| | - Alexandra J. Harvey
- School of BioSciences, University of Melbourne, Parkville, Melbourne, Australia
| | - Trevor J. Kilpatrick
- The Florey Institute of Neuroscience and Mental Health, Parkville, Melbourne, Australia
- The Florey Department of Neuroscience and Mental Health, University of Melbourne, Parkville, Melbourne, Australia
| | - Michele D. Binder
- The Florey Institute of Neuroscience and Mental Health, Parkville, Melbourne, Australia
- Department of Anatomy and Neuroscience, University of Melbourne, Parkville, Melbourne, Australia
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Chiara VD, Daxinger L, Staal FJT. The Route of Early T Cell Development: Crosstalk between Epigenetic and Transcription Factors. Cells 2021; 10:1074. [PMID: 33946533 PMCID: PMC8147249 DOI: 10.3390/cells10051074] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/25/2021] [Accepted: 04/26/2021] [Indexed: 12/21/2022] Open
Abstract
Hematopoietic multipotent progenitors seed the thymus and then follow consecutive developmental stages until the formation of mature T cells. During this process, phenotypic changes of T cells entail stage-specific transcriptional programs that underlie the dynamic progression towards mature lymphocytes. Lineage-specific transcription factors are key drivers of T cell specification and act in conjunction with epigenetic regulators that have also been elucidated as crucial players in the establishment of regulatory networks necessary for proper T cell development. In this review, we summarize the activity of transcription factors and epigenetic regulators that together orchestrate the intricacies of early T cell development with a focus on regulation of T cell lineage commitment.
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Affiliation(s)
- Veronica Della Chiara
- Department of Human Genetics, Leiden University Medical Centre (LUMC), 2300 RC Leiden, The Netherlands; (V.D.C.); (L.D.)
| | - Lucia Daxinger
- Department of Human Genetics, Leiden University Medical Centre (LUMC), 2300 RC Leiden, The Netherlands; (V.D.C.); (L.D.)
| | - Frank J. T. Staal
- Department of Immunology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
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Ansari I, Chaturvedi A, Chitkara D, Singh S. CRISPR/Cas mediated epigenome editing for cancer therapy. Semin Cancer Biol 2021; 83:570-583. [PMID: 33421620 DOI: 10.1016/j.semcancer.2020.12.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/26/2020] [Accepted: 12/28/2020] [Indexed: 02/07/2023]
Abstract
The understanding of the relationship between epigenetic alterations, their effects on gene expression and the knowledge that these epigenetic alterations are reversible, have opened up new therapeutic pathways for treating various diseases, including cancer. This has led the research for a better understanding of the mechanism and pathways of carcinogenesis and provided the opportunity to develop the therapeutic approaches by targeting such pathways. Epi-drugs, DNA methyl transferase (DNMT) inhibitors and histone deacetylase (HDAC) inhibitors are the best examples of epigenetic therapies with clinical applicability. Moreover, precise genome editing technologies such as CRISPR/Cas has proven their efficacy in epigenome editing, including the alteration of epigenetic markers, such as DNA methylation or histone modification. The main disadvantage with DNA gene editing technologies is off-target DNA sequence alteration, which is not an issue with epigenetic editing. It is known that cancer is linked with epigenetic alteration, and thus CRISPR/Cas system shows potential for cancer therapy via epigenome editing. This review outlines the epigenetic therapeutic approach for cancer therapy using CRISPR/Cas, from the basic understanding of cancer epigenetics to potential applications of CRISPR/Cas in treating cancer.
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Affiliation(s)
- Imran Ansari
- Department of Pharmacy, Birla Institute of Technology and Science (BITS)-Pilani, Pilani Campus, Vidya Vihar, Pilani, 333 031, Rajasthan, India
| | | | - Deepak Chitkara
- Department of Pharmacy, Birla Institute of Technology and Science (BITS)-Pilani, Pilani Campus, Vidya Vihar, Pilani, 333 031, Rajasthan, India.
| | - Saurabh Singh
- Novartis Healthcare Pvt Ltd., Hyderabad 500032, Telangana, India.
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Arévalo L, Gardner S, Campbell P. Haldane's rule in the placenta: Sex-biased misregulation of the Kcnq1 imprinting cluster in hybrid mice. Evolution 2020; 75:86-100. [PMID: 33215684 DOI: 10.1111/evo.14132] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 10/08/2020] [Accepted: 10/25/2020] [Indexed: 12/15/2022]
Abstract
Hybrid phenotypes that contribute to postzygotic reproductive isolation often exhibit pronounced asymmetry, both between reciprocal crosses and between the sexes in accordance with Haldane's rule. Inviability in mammalian hybrids is associated with parent-of-origin placental growth abnormalities for which misregulation of imprinted gene (IGs) is the leading candidate mechanism. However, direct evidence for the involvement of IGs in hybrid growth dysplasia is limited. We used transcriptome and reduced representation bisulfite sequencing to conduct the first genome-scale assessment of the contribution of IGs to parent-of-origin placental growth dysplasia in the cross between the house mouse (Mus musculus domesticus) and the Algerian mouse (Mus spretus). IGs with transgressive expression and methylation were concentrated in the Kcnq1 cluster, which contains causal genes for prenatal growth abnormalities in mice and humans. Hypermethylation of the cluster's imprinting control region, and consequent misexpression of the genes Phlda2 and Ascl2, is a strong candidate mechanism for transgressive placental undergrowth. Transgressive placental and gene regulatory phenotypes, including expression and methylation in the Kcnq1 cluster, were more extreme in hybrid males. Although consistent with Haldane's rule, male-biased defects are unexpected in rodent placenta because the X-chromosome is effectively hemizygous in both sexes. In search of an explanation, we found evidence of leaky imprinted (paternal) X-chromosome inactivation in hybrid female placenta, an epigenetic disturbance that may buffer females from the effects of X-linked incompatibilities to which males are fully exposed. Sex differences in chromatin structure on the X and sex-biased maternal effects are nonmutually exclusive alternative explanations for adherence to Haldane's rule in hybrid placenta. The results of this study contribute to understanding the genetic basis of hybrid inviability in mammals, and the role of IGs in speciation.
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Affiliation(s)
- Lena Arévalo
- Department of Integrative Biology, Oklahoma State University, Stillwater, Oklahoma, 74078.,Current Address: Department of Developmental Pathology, University of Bonn Medical School, Bonn, DE-53127, Germany
| | - Sarah Gardner
- Department of Integrative Biology, Oklahoma State University, Stillwater, Oklahoma, 74078.,Current Address: Department of Evolution, Ecology, and Organismal Biology, University of California Riverside, Riverside, California, 92521
| | - Polly Campbell
- Department of Integrative Biology, Oklahoma State University, Stillwater, Oklahoma, 74078.,Current Address: Department of Evolution, Ecology, and Organismal Biology, University of California Riverside, Riverside, California, 92521
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15
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Detect differentially methylated regions using non-homogeneous hidden Markov model for bisulfite sequencing data. Methods 2020; 189:34-43. [PMID: 32949692 DOI: 10.1016/j.ymeth.2020.09.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 06/11/2020] [Accepted: 09/11/2020] [Indexed: 11/22/2022] Open
Abstract
DNA methylation plays an important role in many biological processes and diseases. With the rise of the whole genome bisulfite sequencing technique, aberrant methylation patterns can now be detected by comparing paired normal and disease samples at the single nucleotide level. We develop a novel Bayesian method for detecting differentially methylated regions from paired bisulfite sequencing data, and implement it as a R package called BSDMR. Based on a non-homogeneous hidden Markov model, BSDMR provides a better modeling strategy for the spatial correlation between CpG sites and takes into consideration the relationship between methylation signals from normal and disease samples. Simulations show that BSDMR performs well even under low read depth and has a smaller false discovery rates than existing methods. We also apply BSDMR to the colon cancer data from Gene Expression Omnibus. The detected DMRs are well supported by existing biomedical literatures.
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16
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Ferapontova EE. Electron Transfer in DNA at Electrified Interfaces. Chem Asian J 2019; 14:3773-3781. [PMID: 31545875 DOI: 10.1002/asia.201901024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/22/2019] [Indexed: 12/24/2022]
Abstract
The ability of the DNA double helix to transport electrons underlies many life-centered biological processes and bio-electronic applications. However, there is little consensus on how efficiently the base pair π-stacks of DNA mediate electron transport. This minireview scrutinizes the current state-of-the-art knowledge on electron transfer (ET) properties of DNA and its long-range ability to transfer (mediate) electrical signals at electrified interfaces, without being oxidized or reduced. Complex changes an electric field induces in the DNA structure and its electronic properties govern the efficiency of DNA-mediated ET at electrodes and allow addressing the existing phenomenological riddles, while recently discovered rectifying properties of DNA contribute both to our understanding of DNA's ET in living systems and to advances in molecular bioelectronics.
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Affiliation(s)
- Elena E Ferapontova
- Interdisciplinary Nanoscience Center, Science and Technology, Aarhus University, Gustav Wieds Vej 1590-14, 8000, Aarhus C, Denmark
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17
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Chen C, Chen Y, Huang W, Jiang Y, Zhang H, Wu W. Mining of simple sequence repeats (SSRs) loci and development of novel transferability-across EST-SSR markers from de novo transcriptome assembly of Angelica dahurica. PLoS One 2019; 14:e0221040. [PMID: 31437239 PMCID: PMC6706007 DOI: 10.1371/journal.pone.0221040] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 07/29/2019] [Indexed: 11/18/2022] Open
Abstract
Angelica dahurica is a widely grown plant species with multiple uses, especially in the medical field. However, the frequent introduction of A. dahurica to new areas has made it difficult to distinguish between varieties. Simple sequence repeats (SSRs) detected based on transcriptome analyses are very useful for constructing genetic maps and analyzing genetic diversity. They are also relevant for the molecular marker-assisted breeding of A. dahurica. We identified 33,724 genic SSR loci based on transcriptome sequencing data. A total of 114 primer pairs were designed for the SSR loci and were tested for their specificity and diversity. Ten SSR loci in untranslated regions were ultimately selected. Subsequently, 56 A. dahurica ecotypes collected from different regions were analyzed. The SSR loci comprised 2–8 alleles, with a mean of 5.2 alleles per locus. The polymorphic information content value and Shannon’s information index were 0.6274–0.2702 (average of 0.4091) and 1.3040–0.5618 (average of 0.8475), respectively. Thus, the 10 novel SSRs identified in this study were almost in accordance with Harvey-Weinberg equilibrium and will be useful for analyzing A. dahurica genetic relationships. The results of this study confirm the potential value of transcriptome databases for the development of new SSR markers.
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Affiliation(s)
- Chen Chen
- Agronomy College, Sichuan Agricultural University, Chengdu, Sichuan Province, China
| | - Youjun Chen
- Key Laborary of Superior Forage Germplasm in the Qinghai-Tibetan Plateau (2017-ZJ-Y12), Qinghai University, Xining, Qinghai Province, China
| | - Wenjuan Huang
- Agronomy College, Sichuan Agricultural University, Chengdu, Sichuan Province, China
| | - Yijie Jiang
- Agronomy College, Sichuan Agricultural University, Chengdu, Sichuan Province, China
| | - Huihui Zhang
- Agronomy College, Sichuan Agricultural University, Chengdu, Sichuan Province, China
| | - Wei Wu
- Agronomy College, Sichuan Agricultural University, Chengdu, Sichuan Province, China
- * E-mail:
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18
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Lyu X, Chastain M, Chai W. Genome-wide mapping and profiling of γH2AX binding hotspots in response to different replication stress inducers. BMC Genomics 2019; 20:579. [PMID: 31299901 PMCID: PMC6625122 DOI: 10.1186/s12864-019-5934-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 06/25/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Replication stress (RS) gives rise to DNA damage that threatens genome stability. RS can originate from different sources that stall replication by diverse mechanisms. However, the mechanism underlying how different types of RS contribute to genome instability is unclear, in part due to the poor understanding of the distribution and characteristics of damage sites induced by different RS mechanisms. RESULTS We use ChIP-seq to map γH2AX binding sites genome-wide caused by aphidicolin (APH), hydroxyurea (HU), and methyl methanesulfonate (MMS) treatments in human lymphocyte cells. Mapping of γH2AX ChIP-seq reveals that APH, HU, and MMS treatments induce non-random γH2AX chromatin binding at discrete regions, suggesting that there are γH2AX binding hotspots in the genome. Characterization of the distribution and sequence/epigenetic features of γH2AX binding sites reveals that the three treatments induce γH2AX binding at largely non-overlapping regions, suggesting that RS may cause damage at specific genomic loci in a manner dependent on the fork stalling mechanism. Nonetheless, γH2AX binding sites induced by the three treatments share common features including compact chromatin, coinciding with larger-than-average genes, and depletion of CpG islands and transcription start sites. Moreover, we observe significant enrichment of SINEs in γH2AX sites in all treatments, indicating that SINEs may be a common barrier for replication polymerases. CONCLUSIONS Our results identify the location and common features of genome instability hotspots induced by different types of RS, and help in deciphering the mechanisms underlying RS-induced genetic diseases and carcinogenesis.
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Affiliation(s)
- Xinxing Lyu
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine, Washington State University, Spokane, Washington, USA
| | - Megan Chastain
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine, Washington State University, Spokane, Washington, USA
| | - Weihang Chai
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine, Washington State University, Spokane, Washington, USA.
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19
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Gu HF. Genetic and Epigenetic Studies in Diabetic Kidney Disease. Front Genet 2019; 10:507. [PMID: 31231424 PMCID: PMC6566106 DOI: 10.3389/fgene.2019.00507] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 05/08/2019] [Indexed: 01/19/2023] Open
Abstract
Chronic kidney disease is a worldwide health crisis, while diabetic kidney disease (DKD) has become the leading cause of end-stage renal disease (ESRD). DKD is a microvascular complication and occurs in 30–40% of diabetes patients. Epidemiological investigations and clinical observations on the familial clustering and heritability in DKD have highlighted an underlying genetic susceptibility. Furthermore, DKD is a progressive and long-term diabetic complication, in which epigenetic effects and environmental factors interact with an individual’s genetic background. In recent years, researchers have undertaken genetic and epigenetic studies of DKD in order to better understand its molecular mechanisms. In this review, clinical material, research approaches and experimental designs that have been used for genetic and epigenetic studies of DKD are described. Current information from genetic and epigenetic studies of DKD and ESRD in patients with diabetes, including the approaches of genome-wide association study (GWAS) or epigenome-wide association study (EWAS) and candidate gene association analyses, are summarized. Further investigation of molecular defects in DKD with new approaches such as next generation sequencing analysis and phenome-wide association study (PheWAS) is also discussed.
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Affiliation(s)
- Harvest F Gu
- Center for Pathophysiology, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
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20
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Feng W, Zhou L, Wang H, Hu Z, Wang X, Fu J, Wang A, Liu JF. Functional analysis of DNA methylation of the PACSIN1 promoter in pig peripheral blood mononuclear cells. J Cell Biochem 2018; 120:10118-10127. [PMID: 30537176 DOI: 10.1002/jcb.28295] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 10/22/2018] [Indexed: 12/19/2022]
Abstract
DNA methylation plays essential roles in regulating the activity of genes and may contribute to understanding the potential epigenetic biomarkers response to viruses. To explore the function of DNA methylation of protein kinase C and casein kinase substrate in neurons 1 (PACSNI1) promoter, herein we performed the bisulfite sequencing polymerase chain reaction and Western blot analysis to verify hypermethylation and downregulation of PACSIN1 expression in peripheral blood mononuclear cells of pig as the vitro model. Promoter methylation could reduce the transcriptional activity of the PACSIN1 gene potentially by affecting the binding of transcription factor Sp1. In addition, downregulation of the PACSIN1 gene expression could facilitate the production of interleukin-6 (IL-6), IL-8, tumor necrosis factor α, and NECAP2. The comprehensive analysis of PACSIN1 methylation and its function will help us to understand the gene to be served as an important candidate gene in pig for disease resistance breeding and aid in the identification of potential epigenetic biomarkers associated with responsiveness to viruses.
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Affiliation(s)
- Wen Feng
- National Engineering Laboratory for Animal Breeding; Department of Animal genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lei Zhou
- National Engineering Laboratory for Animal Breeding; Department of Animal genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Haifei Wang
- National Engineering Laboratory for Animal Breeding; Department of Animal genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, China.,Department of Animal Genetics, Breeding and Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Zhengzheng Hu
- National Engineering Laboratory for Animal Breeding; Department of Animal genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xiaomei Wang
- National Engineering Laboratory for Animal Breeding; Department of Animal genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jianlian Fu
- National Engineering Laboratory for Animal Breeding; Department of Animal genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Aiguo Wang
- National Engineering Laboratory for Animal Breeding; Department of Animal genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jian-Feng Liu
- National Engineering Laboratory for Animal Breeding; Department of Animal genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, China
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21
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Kékedy-Nagy L, Ferapontova EE. Sequence-Specific Electron Transfer Mediated by DNA Duplexes Attached to Gold through the Alkanethiol Linker. J Phys Chem B 2018; 122:10077-10085. [DOI: 10.1021/acs.jpcb.8b07505] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- László Kékedy-Nagy
- Interdisciplinary Nanoscience Center (iNANO), Science and Technology, Aarhus University, Gustav Wieds Vej 1590-14, DK-8000 Aarhus C, Denmark
| | - Elena E. Ferapontova
- Interdisciplinary Nanoscience Center (iNANO), Science and Technology, Aarhus University, Gustav Wieds Vej 1590-14, DK-8000 Aarhus C, Denmark
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22
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Abu‐Toamih Atamni HJ, Botzman M, Mott R, Gat‐Viks I, Iraqi FA. Mapping novel genetic loci associated with female liver weight variations using Collaborative Cross mice. Animal Model Exp Med 2018; 1:212-220. [PMID: 30891567 PMCID: PMC6388055 DOI: 10.1002/ame2.12036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 09/03/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Liver weight is a complex trait, controlled by polygenic factors and differs within populations. Dissecting the genetic architecture underlying these variations will facilitate the search for key role candidate genes involved directly in the hepatomegaly process and indirectly involved in related diseases etiology. METHODS Liver weight of 506 mice generated from 39 different Collaborative Cross (CC) lines with both sexes at age 20 weeks old was determined using an electronic balance. Genomic DNA of the CC lines was genotyped with high-density single nucleotide polymorphic markers. RESULTS Statistical analysis revealed a significant (P < 0.05) variation of liver weight between the CC lines, with broad sense heritability (H 2) of 0.32 and genetic coefficient of variation (CVG) of 0.28. Subsequently, quantitative trait locus (QTL) mapping was performed, and results showed a significant QTL only for females on chromosome 8 at genomic interval 88.61-93.38 Mb (4.77 Mb). Three suggestive QTL were mapped at chromosomes 4, 12 and 13. The four QTL were designated as LWL1-LWL4 referring to liver weight loci 1-4 on chromosomes 8, 4, 12 and 13, respectively. CONCLUSION To our knowledge, this report presents, for the first time, the utilization of the CC for mapping QTL associated with baseline liver weight in mice. Our findings demonstrate that liver weight is a complex trait controlled by multiple genetic factors that differ significantly between sexes.
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Affiliation(s)
| | - Maya Botzman
- Faculty of Life SciencesTel‐Aviv UniversityTel‐AvivIsrael
| | - Richard Mott
- Department of GeneticsUniversity College of LondonLondonUK
| | - Irit Gat‐Viks
- Faculty of Life SciencesTel‐Aviv UniversityTel‐AvivIsrael
| | - Fuad A. Iraqi
- Sackler Faculty of MedicineTel‐Aviv UniversityTel‐AvivIsrael
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Larsen K, Kristensen KK, Callesen H. DNA methyltransferases and tRNA methyltransferase DNMT2 in developing pig brain - expression and promoter methylation. GENE REPORTS 2018. [DOI: 10.1016/j.genrep.2018.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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24
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D'Addario C, Micale V, Di Bartolomeo M, Stark T, Pucci M, Sulcova A, Palazzo M, Babinska Z, Cremaschi L, Drago F, Carlo Altamura A, Maccarrone M, Dell'Osso B. A preliminary study of endocannabinoid system regulation in psychosis: Distinct alterations of CNR1 promoter DNA methylation in patients with schizophrenia. Schizophr Res 2017; 188:132-140. [PMID: 28108228 DOI: 10.1016/j.schres.2017.01.022] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 01/10/2017] [Accepted: 01/10/2017] [Indexed: 12/21/2022]
Abstract
Compelling evidence supports the involvement of the endocannabinoid system (ECS) in psychosis vulnerability. We here evaluated the transcriptional regulation of ECS components in human peripheral blood mononuclear cells (PBMCs) obtained from subjects suffering from bipolar disorder, major depressive disorder and schizophrenia, focusing in particular on the effects of DNA methylation. We observed selective alterations of DNA methylation at the promoter of CNR1, the gene coding for the type-1 cannabinoid receptor, in schizophrenic patients (N=25) with no changes in any other disorder. We confirmed the regulation of CNR1 in a well-validated animal model of schizophrenia, induced by prenatal methylazoxymethanol (MAM) acetate exposure (N=7 per group) where we found, in the prefrontal cortex, a significant increase in CNR1 expression and a consistent reduction in DNA methylation at specific CpG sites of gene promoter. Overall, our findings suggest a selective dysregulation of ECS in psychosis, and highlight the evaluation of CNR1 DNA methylation levels in PBMCs as a potential biomarker for schizophrenia.
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Affiliation(s)
- Claudio D'Addario
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Italy; Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden.
| | - Vincenzo Micale
- CEITEC/Masaryk University, Brno, Czech Republic; Department of Biomedical and Biotechnological Sciences, Section of Pharmacology, University of Catania, Catania, Italy
| | - Martina Di Bartolomeo
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Italy
| | - Tibor Stark
- Masaryk University, Faculty of Medicine, Department of Pharmacology, Brno, Czech Republic
| | - Mariangela Pucci
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Italy
| | | | - Mariacarlotta Palazzo
- Centro Sant'Ambrogio, Ordine Ospedaliero San Giovanni di Dio-Fatebenefratelli, Cernusco sul Naviglio, Italy
| | - Zuzana Babinska
- Masaryk University, Faculty of Medicine, Department of Pharmacology, Brno, Czech Republic
| | - Laura Cremaschi
- Department of Neuroscience, University of Milan, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Filippo Drago
- Department of Biomedical and Biotechnological Sciences, Section of Pharmacology, University of Catania, Catania, Italy
| | - A Carlo Altamura
- Department of Neuroscience, University of Milan, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Mauro Maccarrone
- Department of Medicine, Campus Bio-Medico University of Rome, Rome, Italy; European Center for Brain Research, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Bernardo Dell'Osso
- Department of Neuroscience, University of Milan, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy; Department of Psychiatry and Behavioral Sciences, Bipolar Disorders Clinic, Stanford University, CA, USA.
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Van Tongelen A, Loriot A, De Smet C. Oncogenic roles of DNA hypomethylation through the activation of cancer-germline genes. Cancer Lett 2017; 396:130-137. [DOI: 10.1016/j.canlet.2017.03.029] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 03/16/2017] [Accepted: 03/16/2017] [Indexed: 12/19/2022]
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Nishihara H, Yoshida S, Kanno N, Nishimura N, Ueharu H, Ohgane J, Kato T, Kato Y. Involvement of DNA methylation in regulating rat Prop1 gene expression during pituitary organogenesis. J Reprod Dev 2017; 63:37-44. [PMID: 27773885 PMCID: PMC5320428 DOI: 10.1262/jrd.2016-102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
PROP1 is a pituitary specific transcription factor that plays a crucial role in pituitary organogenesis. The Prop1 shows varied expression
patterns that promptly emerge and then fade during the early embryonic period. However, the regulatory mechanisms governing Prop1 expression
remain unclear. Here, we investigated whether Prop1 was under epigenetic regulation by DNA methylation. Bisulfite sequencing was performed on
DNA obtained from the pituitary glands and livers of rats on embryonic days (E) 13.5 and E14.5, and postnatal days (P) 4 and P30. The methylation of CpG sites
in seven regions from 3-kb upstream of the Prop1 transcription start site through to its second intron were examined. Certain differences in
CpG-methylation levels were observed in Region-1 (–2772 b to –2355 b), Region-4 (–198 b to +286 b), Region-5 (+671 b to +990 b), and Region-6 (+1113 b to +1273
b) based on comparisons between pituitary and liver DNA on E13.5. DNA methylation in pituitary glands on E14.5, P4, and P30 was generally similar to that
observed in in the pituitary gland on E13.5, whereas the anterior and intermediate lobes of the pituitary gland on P4 and P30 showed only small differences.
These results indicate that Prop1 is under regulation by CpG methylation during the early period of pituitary primordium development around
E13.5.
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Affiliation(s)
- Hiroto Nishihara
- Laboratory of Molecular Biology and Gene Regulation, Division of Life Science, Graduate School of Agriculture, Meiji University, Kanagawa 214-8571, Japan
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Gao Y, Kobayashi H, Ganss B. The Human KROX-26/ZNF22 Gene is Expressed at Sites of Tooth Formation and Maps to the Locus for Permanent Tooth Agenesis (He-Zhao Deficiency). J Dent Res 2016; 82:1002-7. [PMID: 14630903 DOI: 10.1177/154405910308201213] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Tooth development is mediated by sequential and reciprocal interactions between dental epithelium and mesenchyme under the molecular control of secreted growth factors and responsive transcription factors. We have previously identified the transcription factor Krox-26 as a potential regulator of tooth formation in mice. The purpose of this study was to investigate a potentially similar role for the human KROX-26 orthologue. We cloned the KROX-26 gene and found its single mRNA transcript (2.4 kb) to be expressed in multiple adult tissues. During fetal development, KROX-26 is expressed in the epithelial component of the developing tooth organ during early bud and cap stages as well as in osteoblasts of craniofacial bone and the developing tongue. The KROX-26 gene was mapped to chromosome 10q11.21, a locus that has been associated with permanent tooth agenesis (He-Zhao deficiency). These results indicate a potential function for KROX-26 in the molecular regulation of tooth formation in humans.
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Affiliation(s)
- Y Gao
- Canadian Institutes for Health Research Group in Matrix Dynamics, University of Toronto, Faculty of Dentistry, Fitzgerald Building, Room 239, 150 College Street, Toronto, ON M5S 3E2, Canada
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Corwin EJ. The Concept of Epigenetics and Its Role in the Development of Cardiovascular Disease: Commentary on “New and Emerging Theories of Cardiovascular Disease”. Biol Res Nurs 2016; 6:11-6; discussion 21-3. [PMID: 15186703 DOI: 10.1177/1099800404264779] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Elizabeth J Corwin
- School of Nursing and Intercollege Physiology Program, Pennsylvania State University, 307C Health and Human Development East, University Park, PA 16802, USA.
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Kuo LT, Lu HY, Lee CC, Tsai JC, Lai HS, Tseng HM, Kuo MF, Tu YK. Multiplexed methylation profiles of tumor suppressor genes and clinical outcome in oligodendroglial tumors. Cancer Med 2016; 5:1830-9. [PMID: 27367901 PMCID: PMC4971911 DOI: 10.1002/cam4.762] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 04/07/2016] [Accepted: 04/15/2016] [Indexed: 01/03/2023] Open
Abstract
Aberrant methylation has been associated with transcriptional inactivation of tumor‐related genes in a wide spectrum of human neoplasms. The influence of DNA methylation in oligodendroglial tumors is not fully understood. Genomic DNA was isolated from 61 oligodendroglial tumors for analysis of methylation using methylation‐specific multiplex ligation‐dependent probe amplification assay (MS‐MLPA). We correlated methylation status with clinicopathological findings and outcome. The genes found to be most frequently methylated in oligodendroglial tumors were RASSF1A (80.3%), CASP8 (70.5%), and CDKN2A (52.5%). Kaplan–Meier survival curve analysis demonstrated longer duration of progression‐free survival in patients with 19q loss, aged less than 38 years, and with a proliferative index of less than 5%. Methylation of the ESR1 promoter is significantly associated with shorter duration of overall survival and progression‐free survival, and that methylation of IGSF4 and RASSF1A is significantly associated with shorter duration of progression‐free survival. However, none of the methylation status of ESR1, IGSF4, and RASSF1A was of prognostic value for survival in a multivariate Cox model. A number of novel and interesting epigenetic alterations were identified in this study. The findings highlight the importance of methylation profiles in oligodendroglial tumors and their possible involvement in tumorigenesis.
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Affiliation(s)
- Lu-Ting Kuo
- Division of Neurosurgery, Department of Surgery, National Taiwan University Hospital, Taipei 100, Taiwan
| | - Hsueh-Yi Lu
- Department of Industrial Engineering and Management, National Yunlin University of Science and Technology, Douliu, Yunlin county, 640, Taiwan
| | - Chien-Chang Lee
- Department of Emergency Medicine, National Taiwan University Hospital, Yun-Lin branch, Yun-Lin county, 640, Taiwan
| | - Jui-Chang Tsai
- Division of Neurosurgery, Department of Surgery, National Taiwan University Hospital, Taipei 100, Taiwan
| | - Hong-Shiee Lai
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Ham-Min Tseng
- Division of Neurosurgery, Department of Surgery, National Taiwan University Hospital, Taipei 100, Taiwan
| | - Meng-Fai Kuo
- Division of Neurosurgery, Department of Surgery, National Taiwan University Hospital, Taipei 100, Taiwan
| | - Yong-Kwang Tu
- Division of Neurosurgery, Department of Surgery, National Taiwan University Hospital, Taipei 100, Taiwan
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Patel V, Patel AM, McArdle JJ. Synaptic abnormalities of mice lacking toll-like receptor (TLR)-9. Neuroscience 2016; 324:1-10. [PMID: 26955780 DOI: 10.1016/j.neuroscience.2016.03.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 02/23/2016] [Accepted: 03/01/2016] [Indexed: 02/07/2023]
Abstract
Motor, sensory, and autonomic abnormalities are reported for toll-like receptor 9 (TLR9) knock-out (KO) mice. However, a physiological role of TLR9 in the nervous system is largely unknown. Since altered synaptic transmission can contribute to sensory and motor abnormalities, we evaluated neuromuscular junction (NMJ) function and morphology of TLR9 KO mice. Triangularis sterni nerve-muscle preparations were dissected from TLR9 KO and age-matched control mice. Two-electrode voltage clamp of the motor endplate revealed that the amplitude and frequency of miniature end plate currents (mEPCs) for TLR9 KO NMJs were significantly greater than control. In contrast, mean endplate current (EPC, 1Hz) amplitude was equivalent to control. The ratio of mean EPC to mean mEPC amplitude indicated a decline of quantal content (m) for TLR9 KO NMJs. Furthermore, m declined more rapidly than control in response to 50-Hz stimulus trains. A rightward shift of the mEPC amplitude distribution suggested formation of vesicles containing larger amounts of acetylcholine (ACh). Staining with rhodamine α-bungarotoxin revealed a significant decline of endplate size in TLR9 KO mice. This alteration may result from ACh-induced decline of acetylcholine receptor (AChR) expression resulting from increased frequency and amplitude of mEPCs. At the same time, excessive spontaneous vesicular ACh release may initiate retrograde suppression of excitation-secretion coupling. These data suggest a novel role of TLR9 in the development of the NMJ.
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Affiliation(s)
- V Patel
- Department of Pharmacology, Physiology, and Neuroscience, New Jersey Medical School-Rutgers University, Newark, NJ 07103, USA.
| | - A M Patel
- Department of Pharmacology, Physiology, and Neuroscience, New Jersey Medical School-Rutgers University, Newark, NJ 07103, USA
| | - J J McArdle
- Department of Pharmacology, Physiology, and Neuroscience, New Jersey Medical School-Rutgers University, Newark, NJ 07103, USA
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Fan H, Zhao Z, Cheng Y, Cui H, Qiao F, Wang L, Hu J, Wu H, Song W. Genome-wide profiling of DNA methylation reveals preferred sequences of DNMTs in hepatocellular carcinoma cells. Tumour Biol 2016; 37:877-85. [PMID: 26254611 DOI: 10.1007/s13277-015-3202-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Accepted: 02/03/2015] [Indexed: 02/03/2023] Open
Abstract
Aberrant DNA methylation of CpG site is among the earliest and most frequent alterations in developmental process and diseases including cancer. To elucidate the functional preferred site of DNMTs, we analyzed the feature of distinct methylated sequences and established the defined relationship between DNMTs and preference genomic DNA sequences. Small interfering RNA (siRNA) construct of DNTM1, DNMT3A, and DNMT3B was transfected into the human hepatocellular carcinoma cell line SMMC-7721, respectively. Distinguishing methylated fragments pool was enriched by SHH method in cells which is knocked down DNMT1, DNMT3A, DNMT3B, separately. The defined binding transcription factors (TFs) containing of 5'CpG islands were obtained with bioinformatics software and website. In SMMC-7721 hepatocellular carcinoma (HCC) cell line, DNMT1, DNMT3A, and DNMT3B were specific suppressed by their corresponding siRNA construct, separately. A 46, 42, 67 distinctive methylated fragments from three different DNMTs were evaluated according to genomic DNA database. Those separated fragments were distributed among genomic DNA regions of all chromosome complements, including coding genes, repeat sequences, and genes with unknown function. The majority of coding genes contain CpG islands in their promoter region. Cluster analysis demonstrated all of preference sequences identified by three DNMTs shares their own conserved sequences. In depleting of different DNMTs cells, 80 % of 103 upregulation genes induced by DNMT1 knock-down contain CpG sites; 76 % of 25 upregulation genes induced by DNMT3A knock-down contain CpG sites; 63 % of 126 upregulation genes induced by DNMT3B knock-down contain CpG sites. Our findings suggested that distinctive DNMTs targeted DNA methylation site to their preference sequences, and this targeting might be associated with diverse roles of DNMTs in tumorigenesis. Meanwhile, the analysis of preference sequences provides an alternative way to find out the individual function of DNMTs.
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Affiliation(s)
- Hong Fan
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, 87 Ding JiaQiao Road, Nanjing, 210009, China.
- The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, China.
| | - Zhujiang Zhao
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, 87 Ding JiaQiao Road, Nanjing, 210009, China
- The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, China
| | - Yuchao Cheng
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, 87 Ding JiaQiao Road, Nanjing, 210009, China
- The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, China
| | - He Cui
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, 87 Ding JiaQiao Road, Nanjing, 210009, China
- The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, China
| | - Fengchang Qiao
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, 87 Ding JiaQiao Road, Nanjing, 210009, China
- The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, China
| | - Ling Wang
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, 87 Ding JiaQiao Road, Nanjing, 210009, China
- The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, China
| | - Jiaojiao Hu
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, 87 Ding JiaQiao Road, Nanjing, 210009, China
- The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, China
| | - Huzhang Wu
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, 87 Ding JiaQiao Road, Nanjing, 210009, China
- The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, China
| | - Wei Song
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, 87 Ding JiaQiao Road, Nanjing, 210009, China
- The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, China
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Parham DM. Immunohistochemical Markers of Soft Tissue Tumors: Pathologic Diagnosis, Genetic Contributions, and Therapeutic Options. ANALYTICAL CHEMISTRY INSIGHTS 2015; 10:1-10. [PMID: 26549970 PMCID: PMC4627416 DOI: 10.4137/aci.s32730] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Accepted: 09/16/2015] [Indexed: 12/18/2022]
Abstract
After ~30 years of widespread usage, immunohistochemistry (IHC) has become a standard method of diagnosis for surgical pathology. Because of the plethora of diagnoses and often subtle nature of diagnostic criteria, IHC finds particular utility in soft tissue tumors. The use of progressively small amounts of tissue for diagnosis highlights the importance of this method. The sensitivity and crispness of IHC stains have progressively improved with the advent of new techniques. Traditionally, IHC detects cell-typic markers that characterize cell phenotypes, such as chromogranin for neuroectodermal tissue, myogenin for skeletal muscle, and cytokeratin for epithelium. However, the advent of genetic discoveries have led to IHC testing for detection of fusion gene products or overexpressed oncogenes associated with deletions and mutations. Proliferation-based markers such as Ki-67 can also be used for prognosis and grading, but more standardization is needed. Development of monoclonal antibody-based pharmaceuticals, such as imatinib or crizotinib, holds the promise of tailored anticancer therapy. IHC thus has assumed importance not only for diagnosis but also for guidance of personalized medicine.
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Affiliation(s)
- David M Parham
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA. ; Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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Maggi N, Ruggiero C, Arrigo P. Prediction of potential barcoding sites on ITS1 by wavelet transform. J Biomol Struct Dyn 2015; 34:814-23. [PMID: 26183584 DOI: 10.1080/07391102.2015.1056550] [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: 10/23/2022]
Abstract
For sustainable development, biodiversity conservation and life-quality improvement must be simultaneously considered. Molecular techniques have greatly impacted biotechnology. These methods have, in particular, improved the capability to investigate the fine differences among organisms and, as a consequence, to better investigate the effects on environmental factors on them. We propose an approach to support the optimal selection of molecular probes for barcoding application in many biotechnological fields. The aim of our work is specificity maximization. To this purpose, we have integrated a filter system based on wavelet transforms with biological knowledge about the sequence proneness to mutation and post-translational modification. Specifically, we have tested the proposed method on ITS1 sequences that are a region of the rRNA locus. Our analysis has shown the presence of other local relative stable conformations in addition to known cleavage site. Their characteristics differ within the group of mammals selected for our analysis. These variations could be used to design new species-specific barcoding probes or other quick molecular screening tools.
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Affiliation(s)
| | | | - Patrizio Arrigo
- b ISMAC - National Research Council (CNR) , via de Marini, 6, Genoa , Italy
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Héninger E, Krueger TEG, Lang JM. Augmenting antitumor immune responses with epigenetic modifying agents. Front Immunol 2015; 6:29. [PMID: 25699047 PMCID: PMC4316783 DOI: 10.3389/fimmu.2015.00029] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 01/14/2015] [Indexed: 12/31/2022] Open
Abstract
Epigenetic silencing of immune-related genes is a striking feature of the cancer genome that occurs in the process of tumorigenesis. This phenomena impacts antigen processing and antigen presentation by tumor cells and facilitates evasion of immunosurveillance. Further modulation of the tumor microenvironment by altered expression of immunosuppressive cytokines impairs antigen-presenting cells and cytolytic T-cell function. The potential reversal of immunosuppression by epigenetic modulation is therefore a promising and versatile therapeutic approach to reinstate endogenous immune recognition and tumor lysis. Pre-clinical studies have identified multiple elements of the immune system that can be modulated by epigenetic mechanisms and result in improved antigen presentation, effector T-cell function, and breakdown of suppressor mechanisms. Recent clinical studies are utilizing epigenetic therapies prior to, or in combination with, immune therapies to improve clinical outcomes.
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Affiliation(s)
- Erika Héninger
- University of Wisconsin Carbone Cancer Center , Madison, WI , USA
| | | | - Joshua M Lang
- University of Wisconsin Carbone Cancer Center , Madison, WI , USA ; Department of Medicine, University of Wisconsin , Madison, WI , USA
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35
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Komori HK, Hart T, LaMere SA, Chew PV, Salomon DR. Defining CD4 T cell memory by the epigenetic landscape of CpG DNA methylation. THE JOURNAL OF IMMUNOLOGY 2015; 194:1565-79. [PMID: 25576597 DOI: 10.4049/jimmunol.1401162] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Memory T cells are primed for rapid responses to Ag; however, the molecular mechanisms responsible for priming remain incompletely defined. CpG methylation in promoters is an epigenetic modification, which regulates gene transcription. Using targeted bisulfite sequencing, we examined methylation of 2100 genes (56,000 CpGs) mapped by deep sequencing of T cell activation in human naive and memory CD4 T cells. Four hundred sixty-six CpGs (132 genes) displayed differential methylation between naive and memory cells. Twenty-one genes exhibited both differential methylation and gene expression before activation, linking promoter DNA methylation states to gene regulation; 6 of 21 genes encode proteins closely studied in T cells, whereas 15 genes represent novel targets for further study. Eighty-four genes demonstrated differential methylation between memory and naive cells that correlated to differential gene expression following activation, of which 39 exhibited reduced methylation in memory cells coupled with increased gene expression upon activation compared with naive cells. These reveal a class of primed genes more rapidly expressed in memory compared with naive cells and putatively regulated by DNA methylation. These findings define a DNA methylation signature unique to memory CD4 T cells that correlates with activation-induced gene expression.
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Affiliation(s)
- H Kiyomi Komori
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Traver Hart
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Sarah A LaMere
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Pamela V Chew
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Daniel R Salomon
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037
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36
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Jensik PJ, Vargas JD, Reardon SN, Rajamanickam S, Huggenvik JI, Collard MW. DEAF1 binds unmethylated and variably spaced CpG dinucleotide motifs. PLoS One 2014; 9:e115908. [PMID: 25531106 PMCID: PMC4274154 DOI: 10.1371/journal.pone.0115908] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 11/28/2014] [Indexed: 11/19/2022] Open
Abstract
DEAF1 is a transcriptional regulator associated with autoimmune and neurological disorders and is known to bind TTCG motifs. To further ascertain preferred DEAF1 DNA ligands, we screened a random oligonucleotide library containing an "anchored" CpG motif. We identified a binding consensus that generally conformed to a repeated TTCGGG motif, with the two invariant CpG dinucleotides separated by 6-11 nucleotides. Alteration of the consensus surrounding the dual CpG dinucleotides, or cytosine methylation of a single CpG half-site, eliminated DEAF1 binding. A sequence within the Htr1a promoter that resembles the binding consensus but contains a single CpG motif was confirmed to have low affinity binding with DEAF1. A DEAF1 binding consensus was identified in the EIF4G3 promoter and ChIP assay showed endogenous DEAF1 was bound to the region. We conclude that DEAF1 preferentially binds variably spaced and unmethylated CpG-containing half-sites when they occur within an appropriate consensus.
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Affiliation(s)
- Philip J. Jensik
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, Illinois, United States of America
- * E-mail:
| | - Jesse D. Vargas
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, Illinois, United States of America
| | - Sara N. Reardon
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, Illinois, United States of America
| | - Shivakumar Rajamanickam
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, Illinois, United States of America
| | - Jodi I. Huggenvik
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, Illinois, United States of America
| | - Michael W. Collard
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, Illinois, United States of America
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Abstract
Imbalanced cell death is a common phenomenon in many human diseases, including cancer. DAPK's essential function is in promoting apoptosis. DAPK interacts with stress-induced receptors through its death domain to initiate an apoptosis cascade. In addition, DAPK phosphorylates multiple cytosolic substrates and can mediate transfer of signaling pathways to the effector caspases. A series of studies demonstrated that, depending on stimuli, DAPK expression is regulated on both the transcriptional and posttranscriptional levels. Silencing of DAPK due to hypermethylation of its promoter was reported in many types of cancer. STAT3 and p52-NFkB transcription factors have been shown to down-regulate DAPK expression. In contrast, p53, C/EBP-β and Smad transcription factors bind to their specific response elements within the DAPK promoter and induce its transcription. Post-transcriptionally, DAPK undergoes alternative splicing, which results in the production of two functionally different isoforms. Moreover, miRNA 103 and miRNA 107 recently were shown to inhibit DAPK in colorectal cancer. Here we summarize our recent knowledge about transcriptional regulation of DAPK expression.
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Affiliation(s)
- Natalya Benderska
- Experimental Tumorpathology, Institute of Pathology, Friedrich-Alexander- University of Erlangen-Nuremberg, Universitätstrasse 22, 91054, Erlangen, Germany
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Zhou Y, Zhang T, Zhang QK, Jiang Y, Xu DG, Zhang M, Shen W, Pan QJ. Unstable expression of transgene is associated with the methylation of CAG promoter in the offspring from the same litter of homozygous transgenic mice. Mol Biol Rep 2014; 41:5177-86. [PMID: 24804614 DOI: 10.1007/s11033-014-3385-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Accepted: 04/22/2014] [Indexed: 01/17/2023]
Abstract
Transgenic animals have been established for studying gene function, improving animals' production traits, and providing organ models for the exploration of human diseases. However, the stability of inheritance and transgene expression in transgenic animals has gained extensive attention. The unstable expression of transgene through DNA methyltransferase (DNMT) targeting to the methylation of transgenic DNA such as CAG promoter and Egfp coding region in homozygous transgenic animals is still unknown. In the present study, the offspring from the same litter of homozygous transgenic mice carrying ubiquitously expressed enhanced green fluorescence protein driven by CMV early enhancer/chicken β-actin (CAG) promoter was observed to have unstable expression of transgene Egfp, quantitative PCR, western blot and bisulfite sequencing were conducted to quantify the expressional characteristics and methylation levels in various tissues. The correlation between transgene expression and methylation was analyzed. We have found that transgene expression is dependent on the methylation of CAG promoter, but not Egfp coding region. We have also characterized the correlation between the methylation of CAG promoter and DNMT, and found that only Dnmt3b expression is correlated with the methylation of CAG promoter. In conclusion, Dnmt3b-related methylation of CAG promoter can inhibit the transgene expression and may result in the unstable expression of transgene in the offspring from the same litter of homozygous transgenic mice.
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Affiliation(s)
- Yang Zhou
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, 266109, Shan Dong, China
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Abstract
The onset of chronic disease is often the prelude to the subsequent physiological and mental twilight in the aging population of modern society. While rates of obesity, specific types of cancer and cardiovascular disorders seem to be on the rise in this group, many new therapies have addressed diseases that have been largely untreatable in the past. Alzheimer's disease has also recently come to the forefront of ongoing maladies most typically associated with an aging population. Ironically, though, many people seem to be living longer than expected. Recent biochemical, nutritional and genomic approaches have been able to elucidate some of the complex mechanisms, which lead to chronic diseases associated with an aging population such as Alzheimer's, metabolic syndrome, tumor metastasis and cardiovascular disease. These diseases and their sequalae seem to be related in many respects, with the common culprit being the inflammatory environment created by the presence of excess fat - particularly within the vascular network. Although a substantial effort has been focused on the development of new-line therapeutics to address these issues, nutrition and overall fitness and their effects on stalling or potentially reversing the advent of these diseases has not been fully embraced in the research arena. This review discusses the role of the inflammatory environment in the development of chronic diseases in the aging population and also proposes a common pathology. The benefits that improvements and dedication in nutrition and fitness approaches may offer at the molecular level are also discussed.
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An J, Kim K, Rhee SM, Chae H, Nephew KP, Kim S. Genome-wide analysis and modeling of DNA methylation susceptibility in 30 breast cancer cell lines by using CpG flanking sequences. J Bioinform Comput Biol 2014; 11:1341003. [PMID: 23796180 DOI: 10.1142/s0219720013410035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
DNA methylation is an epigenetic modification of DNA that adds a methyl group to cytosine. Aberrant DNA methylation in the CpG context is frequently observed in cancer cells and it is known that aberrant DNA methylation silences tumor repressor genes. However, the mechanism of DNA methylation is not well understood. A widely accepted hypothesis is that DNA methylation does not randomly occur and may be controlled by some instructive mechanisms. In this paper, we conducted an extensive study on this important question by using proprietary sequencing data from methyl-binding domain protein (MBD)-Cap ChIP sequencing experiments for 30 breast cancer cell lines. The goal of our study is to investigate difference in nucleotide composition around CpG sites, where high levels of methylation are observed, and use the information for modeling DNA methylation susceptibility. First, we observed that DNA methylation is not uniform in the whole-genome region and also that the character composition of CpG flanking sequences are significantly different between hyper- and hypo-methylated groups. In an in-depth study, we used information theoretic approaches such as entropy and relative entropy to delineate character composition features and found enrichment of A (Adenine) and T (Thymine) in specific positions around hyper-methylated sites. As the methylation level is increased, A, T proportions in specific positions around hypermethylated sites are increased while A, T proportions in other positions around hypermethylated sites are decreased. Second, we built predictive models for methylation susceptibility by using characters flanking CpG sites as features and hyper-/hypo-methylation status as class. Third, we constructed predictive models using a log odds score of two profiles from DNA sequences surrounding CpG sites of hyper- and hypo-methylated groups. This analysis showed that distribution of profile scores of hyper-/hypo-methylated sites sequences is quite distinct. Our genome-wide CpG methylation study shows that nucleotides around CpG sites caries information for cytosine methylation. This is consistent with the seminal work on the instructive evidence of DNA methylation by Keshet et al. (Nature Genetics, 38(2), 149-153 2006). Our study is on the full genome scale and used the sequencing data, thus our study is significantly different in terms of resolution of data and analysis methods used for the study by Keshet et al.
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Affiliation(s)
- Jaehyun An
- Department of Computer Science and Engineering, Seoul National University, Seoul, Korea
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41
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Santos ES, Raez LE, DeCesare T, Singal R. DNA methylation: its role in lung carcinogenesis and therapeutic implications. Expert Rev Anticancer Ther 2014; 5:667-79. [PMID: 16111467 DOI: 10.1586/14737140.5.4.667] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A new era in the treatment of malignant diseases has been observed through the use of biologic agents targeting growth factor receptors, signaling pathways, gene mutations and others. The results have been impressive in some diseases and modest in others. The discovery of new targets has expanded our knowledge of different mechanisms in tumorigenesis. One of these mechanisms has been DNA methylation, which is an important gene transcription regulator. Although the role of methylation in lung carcinogenesis is not well understood, there is an enormous quantity of evolving data suggesting its critical role in lung cancer. In this review, the authors will discuss methylation in lung carcinogenesis and its possible clinical implications.
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Affiliation(s)
- Edgardo S Santos
- Division of Hematology-Oncology, Tulane University Health Sciences Center, 1430 Tulane Avenue, SL-78, New Orleans, LA 70112, USA.
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Frau M, Feo CF, Feo F, Pascale RM. New insights on the role of epigenetic alterations in hepatocellular carcinoma. J Hepatocell Carcinoma 2014; 1:65-83. [PMID: 27508177 PMCID: PMC4918272 DOI: 10.2147/jhc.s44506] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Emerging evidence assigns to epigenetic mechanisms heritable differences in gene function that come into being during cell development or via the effect of environmental factors. Epigenetic deregulation is strongly involved in the development of hepatocellular carcinoma (HCC). It includes changes in methionine metabolism, promoter hypermethylation, or increased proteasomal degradation of oncosuppressors, as well as posttranscriptional deregulation by microRNA or messenger RNA (mRNA) binding proteins. Alterations in the methylation of the promoter of methyl adenosyltransferase MAT1A and MAT2A genes in HCC result in decreased S-adenosylmethionine levels, global DNA hypomethylation, and deregulation of signal transduction pathways linked to methionine metabolism and methyl adenosyltransferases activity. Changes in S-adenosylmethionine levels may also depend on MAT1A mRNA destabilization associated with MAT2A mRNA stabilization by specific proteins. Decrease in MAT1A expression has also been attributed to miRNA upregulation in HCC. A complex deregulation of miRNAs is also strongly involved in hepatocarcinogenesis, with up-regulation of different miRNAs targeting oncosuppressor genes and down-regulation of miRNAs targeting genes involved in cell-cycle and signal transduction control. Oncosuppressor gene down-regulation in HCC is also induced by promoter hypermethylation or posttranslational deregulation, leading to proteasomal degradation. The role of epigenetic changes in hepatocarcinogenesis has recently suggested new promising therapeutic approaches for HCC on the basis of the administration of methylating agents, inhibition of methyl adenosyltransferases, and restoration of the expression of tumor-suppressor miRNAs.
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Affiliation(s)
- Maddalena Frau
- Department of Clinical and Experimental Medicine, Division of Experimental Pathology and Oncology, University of Sassari, Sassari, Italy
| | - Claudio F Feo
- Department of Clinical and Experimental Medicine, Division of Surgery, University of Sassari, Sassari, Italy
| | - Francesco Feo
- Department of Clinical and Experimental Medicine, Division of Experimental Pathology and Oncology, University of Sassari, Sassari, Italy
| | - Rosa M Pascale
- Department of Clinical and Experimental Medicine, Division of Experimental Pathology and Oncology, University of Sassari, Sassari, Italy
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Bina M, Wyss P, Novorolsky E, Zulkelfi N, Xue J, Price R, Fay M, Gutmann Z, Fogler B, Wang D. Discovery of MLL1 binding units, their localization to CpG Islands, and their potential function in mitotic chromatin. BMC Genomics 2013; 14:927. [PMID: 24373511 PMCID: PMC3890651 DOI: 10.1186/1471-2164-14-927] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 12/16/2013] [Indexed: 11/10/2022] Open
Abstract
Background Mixed Lineage Leukemia 1 (MLL1) is a mammalian ortholog of the Drosophila Trithorax. In Drosophila, Trithorax complexes transmit the memory of active genes to daughter cells through interactions with Trithorax Response Elements (TREs). However, despite their functional importance, nothing is known about sequence features that may act as TREs in mammalian genomic DNA. Results By analyzing results of reported DNA binding assays, we identified several CpG rich motifs as potential MLL1 binding units (defined as morphemes). We find that these morphemes are dispersed within a relatively large collection of human promoter sequences and appear densely packed near transcription start sites of protein-coding genes. Genome wide analyses localized frequent morpheme occurrences to CpG islands. In the human HOX loci, the morphemes are spread across CpG islands and in some cases tail into the surrounding shores and shelves of the islands. By analyzing results of chromatin immunoprecipitation assays, we found a connection between morpheme occurrences, CpG islands, and chromatin segments reported to be associated with MLL1. Furthermore, we found a correspondence of reported MLL1-driven “bookmarked” regions in chromatin to frequent occurrences of MLL1 morphemes in CpG islands. Conclusion Our results implicate the MLL1 morphemes in sequence-features that define the mammalian TREs and provide a novel function for CpG islands. Apparently, our findings offer the first evidence for existence of potential TREs in mammalian genomic DNA and the first evidence for a connection between CpG islands and gene-bookmarking by MLL1 to transmit the memory of highly active genes during mitosis. Our results further suggest a role for overlapping morphemes in producing closely packed and multiple MLL1 binding events in genomic DNA so that MLL1 molecules could interact and reside simultaneously on extended potential transcriptional maintenance elements in human chromosomes to transmit the memory of highly active genes during mitosis.
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Affiliation(s)
- Minou Bina
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA.
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Zhu G, Yang K, Zhang CY. Sensitive detection of methylated DNA using the short linear quencher–fluorophore probe and two-stage isothermal amplification assay. Biosens Bioelectron 2013; 49:170-5. [DOI: 10.1016/j.bios.2013.05.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2013] [Revised: 04/27/2013] [Accepted: 05/01/2013] [Indexed: 10/26/2022]
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Hedegaard C, Kjaer-Sorensen K, Madsen LB, Henriksen C, Momeni J, Bendixen C, Oxvig C, Larsen K. Porcine synapsin 1: SYN1 gene analysis and functional characterization of the promoter. FEBS Open Bio 2013; 3:411-20. [PMID: 24251104 PMCID: PMC3821028 DOI: 10.1016/j.fob.2013.10.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 10/01/2013] [Accepted: 10/01/2013] [Indexed: 11/22/2022] Open
Abstract
Synapsin 1 (SYN1) is a phosphoprotein involved in nerve signal transmission. The porcine SYN1 promoter orthologue was cloned and characterized to provide a means of expressing a transgene specifically in neurons. The nucleotide sequence of the promoter displayed a high degree of conservation of elements responsible for neuron-specific expression. Expression analysis of SYN1 demonstrated presence of transcript during embryonic development. Analysis of GFP expression in transgenic zebrafish embryos suggests that the pig SYN1 promoter directs expression in neuronal cells. Thus, the SYN1 promoter is a good candidate for use in the generation of pig models of human neurodegenerative disorders. The porcine synapsin1 (SYN1) promoter was cloned and characterized. SYN1 mRNA expression is detected in brain during embryo development. The SYN1 gene is mapped to pig chromosome X. Porcine SYN1 directs GFP expression in neuronal cells of transgenic zebrafish.
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Key Words
- Ab, antibody
- BSG, basal ganglia
- BST, brain stem
- CBE, cerebellum
- CMV, cytomegalovirus
- Chr, chromosome
- FB, forebrain
- FCO, frontal cortex
- GFP
- GFP, green fluorescent protein
- HB, hindbrain
- HIP, hippocampus
- LLG, lateral line ganglion
- MB, midbrain
- NRSE, neuron restrictive silencer element
- Neuron-specific promoter
- OC, optic chiasm
- ON, olfactory neuron
- Pig
- R, retina
- REST, RE1-silencing transcription factor
- TG, trigeminal ganglion
- TSS, transcription start site
- Transgenic
- WPRE, Woodchuck hepatitits virus Post-transcriptional Regulatory Element
- Zebrafish
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Affiliation(s)
- Claus Hedegaard
- Department of Molecular Biology and Genetics, Aarhus University, Blichers Alle 20, Tjele DK-8830, Denmark
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Segmenting the human genome based on states of neutral genetic divergence. Proc Natl Acad Sci U S A 2013; 110:14699-704. [PMID: 23959903 DOI: 10.1073/pnas.1221792110] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Many studies have demonstrated that divergence levels generated by different mutation types vary and covary across the human genome. To improve our still-incomplete understanding of the mechanistic basis of this phenomenon, we analyze several mutation types simultaneously, anchoring their variation to specific regions of the genome. Using hidden Markov models on insertion, deletion, nucleotide substitution, and microsatellite divergence estimates inferred from human-orangutan alignments of neutrally evolving genomic sequences, we segment the human genome into regions corresponding to different divergence states--each uniquely characterized by specific combinations of divergence levels. We then parsed the mutagenic contributions of various biochemical processes associating divergence states with a broad range of genomic landscape features. We find that high divergence states inhabit guanine- and cytosine (GC)-rich, highly recombining subtelomeric regions; low divergence states cover inner parts of autosomes; chromosome X forms its own state with lowest divergence; and a state of elevated microsatellite mutability is interspersed across the genome. These general trends are mirrored in human diversity data from the 1000 Genomes Project, and departures from them highlight the evolutionary history of primate chromosomes. We also find that genes and noncoding functional marks [annotations from the Encyclopedia of DNA Elements (ENCODE)] are concentrated in high divergence states. Our results provide a powerful tool for biomedical data analysis: segmentations can be used to screen personal genome variants--including those associated with cancer and other diseases--and to improve computational predictions of noncoding functional elements.
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Characterization of induced neural progenitors from skin fibroblasts by a novel combination of defined factors. Sci Rep 2013; 3:1345. [PMID: 23439431 PMCID: PMC3581826 DOI: 10.1038/srep01345] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 02/12/2013] [Indexed: 12/17/2022] Open
Abstract
Recent reports have demonstrated that somatic cells can be directly converted to other differentiated cell types through ectopic expression of sets of transcription factors, directly avoiding the transition through a pluripotent state. Our previous experiments generated induced neural progenitor-like cells (iNPCs) by a novel combination of five transcription factors (Sox2, Brn2, TLX, Bmi1 and c-Myc). Here we demonstrated that the iNPCs not only possess NPC-specific marker genes, but also have qualities of primary brain-derived NPCs (WT-NPCs), including tripotent differentiation potential, mature neuron differentiation capability and synapse formation. Importantly, the mature neurons derived from iNPCs exhibit significant physiological properties, such as potassium channel activity and generation of action potential-like spikes. These results suggest that directly reprogrammed iNPCs closely resemble WT-NPCs, which may suggest an alternative strategy to overcome the restricted proliferative and lineage potential of induced neurons (iNCs) and broaden applications of cell therapy in the treatment of neurodegenerative disorders.
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Leifer CA, Rose WA, Botelho F. Traditional biochemical assays for studying toll-like receptor 9. J Immunoassay Immunochem 2013; 34:1-15. [PMID: 23323977 DOI: 10.1080/15321819.2012.666222] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Understanding the mechanistic basis of receptor activation and regulation can offer therapeutic targets for disease treatment. Evidence is emerging for a role of the normally foreign responsive Toll-like receptors (TLRs) in the development of autoimmunity through response to self-patterns. Regulatory mechanisms governing this class of receptors are poorly understood, and failures within this system likely contribute to development of autoimmunity. In this article, we review biochemical assays used to study one of the self-pattern responsive TLRs, TLR9, and suggest that these studies are critical for development of new targets for autoimmune therapies.
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Affiliation(s)
- Cynthia A Leifer
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA.
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De Smet C, Loriot A. DNA hypomethylation and activation of germline-specific genes in cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 754:149-66. [PMID: 22956500 DOI: 10.1007/978-1-4419-9967-2_7] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
DNA methylation, occurring at cytosines in CpG dinucleotides, is a potent mechanism of transcriptional repression. Proper genomic methylation -patterns become profoundly altered in cancer cells: both gains (hypermethylation) and losses (hypomethylation) of methylated sites are observed. Although DNA hypomethylation is detected in a vast majority of human tumors and affects many genomic regions, its role in tumor biology remains elusive. Surprisingly, DNA hypomethylation in cancer was found to cause the aberrant activation of only a limited group of genes. Most of these are normally expressed exclusively in germline cells and were grouped under the term "cancer-germline" (CG) genes. CG genes represent unique examples of genes that rely primarily on DNA methylation for their tissue-specific expression. They are also being exploited to uncover the mechanisms that lead to DNA hypomethylation in tumors. Moreover, as CG genes encode tumor-specific antigens, their activation in cancer highlights a direct link between epigenetic alterations and tumor immunity. As a result, clinical trials combining epigenetic drugs with anti-CG antigen vaccines are being considered.
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Affiliation(s)
- Charles De Smet
- Laboratory of Genetics and Epigenetics, de Duve Institute, Catholic University of Louvain, Brussels, Belgium.
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