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Wu D, Huang K, Shi J, Liu S, Wang W, Jiang J, Ren H, Chen T, Ye S, Chen J, Wei W, Li X. Genome-Wide 5-Formylcytosine Redistribution in KCl-Stimulated Mouse Primary Cortical Neurons is Associated with Neuronal Activity. ACS Chem Neurosci 2023; 14:4352-4362. [PMID: 38019771 DOI: 10.1021/acschemneuro.3c00554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023] Open
Abstract
An abundant accumulation of DNA demethylation intermediates has been identified in mammalian neurons. While the roles of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) in neuronal function have been extensively studied, little is known about 5-formylcytosine (5fC) in neurons. Therefore, this study was to investigate the genome-wide distribution and potential functions of 5fC in neurons. In an in vitro culture model of mouse primary cortical neurons, we observed a dynamic increase in the total 5fC level in the neuronal genome after potassium chloride (KCl) stimulation. Subsequently, we employed chemical-labeling-enabled C-to-T conversion sequencing (CLEVER-seq) to examine the 5fC distribution at a single-base resolution. Bioinformatic analysis revealed that 5fC was enriched in promoter regions, and gene ontology (GO) analysis indicated that the differential formylation positions (DFP) were correlated with neuronal activities. Additionally, integration with previously published nascent RNA-seq data revealed a positive correlation between gene formylation and mRNA expression levels. As well, 6 neuro-activity-related genes with a positive correlation were validated. Furthermore, we observed higher chromatin accessibility and RNA pol II binding signals near the 5fC sites through multiomics analysis. Motif analysis identified potential reader proteins for 5fC. In conclusion, our work provides a valuable resource for studying the dynamic changes and functional roles of 5fC in activated mammalian neurons.
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Affiliation(s)
- Du Wu
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
- Brain Research Center, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
| | - Kaixin Huang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
- Brain Research Center, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
| | - Jichun Shi
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
- Brain Research Center, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
| | - Sha Liu
- Department of General Practice, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
| | - Wenjing Wang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
| | - Jiazhi Jiang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
| | - Haobin Ren
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane 4702, Australia
| | - Tongyu Chen
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
| | - Shengda Ye
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
| | - Jincao Chen
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
| | - Wei Wei
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
- Brain Research Center, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
| | - Xiang Li
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
- Brain Research Center, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, 430071 Wuhan, China
- Medical Research Institute, Wuhan University, 430071 Wuhan, China
- Sino-Italian Ascula Brain Science Joint Laboratory, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
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2
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Fukunaga Y, Harada M, Okada T. Surface-enhanced Raman scattering of DNA bases using frozen silver nanoparticle dispersion as a platform. Mikrochim Acta 2021; 188:406. [PMID: 34734344 DOI: 10.1007/s00604-021-05055-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 10/07/2021] [Indexed: 11/25/2022]
Abstract
Raman spectroscopy is a powerful method to characterize molecules in various media. Although surface-enhanced Raman scattering (SERS) is often employed to compensate for the intrinsically poor sensitivity of Raman spectroscopy, there remain serious tasks, such as simple preparations of SERS substrates, sensitivity control, and reproducible measurements. Here, we propose freezing as an efficient way to overcome these problems in SERS measurements using DNA bases as model targets. Solutes are expelled from ice crystals and concentrated in the liquid phase upon freezing. Silver nanoparticles (AgNPs) are also concentrated in the liquid phase to aggregate with Raman target analytes. The SERS signal intensity is maximized when the AgNP concentration exceeds the critical aggregation value. Freezing allows up to 5000 times enhancements of the SERS signal. Thus, an efficient SERS platform is prepared by simple freezing. The simultaneous detection of four DNA bases effectively eliminates variations of signal intensities and allows the reliable determination of concentration ratios.
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Affiliation(s)
- Yu Fukunaga
- Department of Chemistry, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8551, Japan
| | - Makoto Harada
- Department of Chemistry, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8551, Japan
| | - Tetsuo Okada
- Department of Chemistry, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8551, Japan.
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Simmonds P. Rampant C→U Hypermutation in the Genomes of SARS-CoV-2 and Other Coronaviruses: Causes and Consequences for Their Short- and Long-Term Evolutionary Trajectories. mSphere 2020; 5:e00408-20. [PMID: 32581081 PMCID: PMC7316492 DOI: 10.1128/msphere.00408-20] [Citation(s) in RCA: 156] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/11/2020] [Indexed: 12/14/2022] Open
Abstract
The pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has motivated an intensive analysis of its molecular epidemiology following its worldwide spread. To understand the early evolutionary events following its emergence, a data set of 985 complete SARS-CoV-2 sequences was assembled. Variants showed a mean of 5.5 to 9.5 nucleotide differences from each other, consistent with a midrange coronavirus substitution rate of 3 × 10-4 substitutions/site/year. Almost one-half of sequence changes were C→U transitions, with an 8-fold base frequency normalized directional asymmetry between C→U and U→C substitutions. Elevated ratios were observed in other recently emerged coronaviruses (SARS-CoV, Middle East respiratory syndrome [MERS]-CoV), and decreasing ratios were observed in other human coronaviruses (HCoV-NL63, -OC43, -229E, and -HKU1) proportionate to their increasing divergence. C→U transitions underpinned almost one-half of the amino acid differences between SARS-CoV-2 variants and occurred preferentially in both 5' U/A and 3' U/A flanking sequence contexts comparable to favored motifs of human APOBEC3 proteins. Marked base asymmetries observed in nonpandemic human coronaviruses (U ≫ A > G ≫ C) and low G+C contents may represent long-term effects of prolonged C→U hypermutation in their hosts. The evidence that much of sequence change in SARS-CoV-2 and other coronaviruses may be driven by a host APOBEC-like editing process has profound implications for understanding their short- and long-term evolution. Repeated cycles of mutation and reversion in favored mutational hot spots and the widespread occurrence of amino acid changes with no adaptive value for the virus represent a quite different paradigm of virus sequence change from neutral and Darwinian evolutionary frameworks and are not incorporated by standard models used in molecular epidemiology investigations.IMPORTANCE The wealth of accurately curated sequence data for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), its long genome, and its low substitution rate provides a relatively blank canvas with which to investigate effects of mutational and editing processes imposed by the host cell. The finding that a large proportion of sequence change in SARS-CoV-2 in the initial months of the pandemic comprised C→U mutations in a host APOBEC-like context provides evidence for a potent host-driven antiviral editing mechanism against coronaviruses more often associated with antiretroviral defense. In evolutionary terms, the contribution of biased, convergent, and context-dependent mutations to sequence change in SARS-CoV-2 is substantial, and these processes are not incorporated by standard models used in molecular epidemiology investigations.
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Affiliation(s)
- P Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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Bahado-Singh R, Vishweswaraiah S, Mishra NK, Guda C, Radhakrishna U. Placental DNA methylation changes in detection of tetralogy of Fallot. Ultrasound Obstet Gynecol 2020; 55:768-775. [PMID: 30977211 DOI: 10.1002/uog.20292] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 04/01/2019] [Accepted: 04/03/2019] [Indexed: 06/09/2023]
Abstract
OBJECTIVES To determine whether the methylation level of cytosine nucleotides in placental DNA can be used to predict tetralogy of Fallot (TOF) and provide insights into the developmental mechanism of this condition. METHODS Tissue sections were obtained from formalin-fixed paraffin-embedded specimens of placental tissue obtained at birth from eight cases with non-chromosomal, non-syndromic TOF and 10 unaffected newborns. The Illumina Infinium HumanMethylation450 BeadChip assay was used to measure cytosine ('CpG' or 'cg') methylation levels at loci throughout the placental genome. Differential methylation was assessed by comparing the β-values (a measure of the extent of cytosine methylation) for individual CpG loci in fetuses with TOF vs in controls. The most discriminating CpG sites were determined based on a preset cut-off of ≥ 2.0-fold change in the methylation level. The predictive accuracy of CpG loci with significant methylation changes for TOF was determined by the area under the receiver-operating-characteristics curve (AUC). A false-discovery-rate (FDR) P-value < 0.05 was used to define a statistically significant difference in the methylation level. Ingenuity Pathway Analysis (IPA) (Qiagen) was used to identify gene pathways that were significantly overexpressed, and thus altered, in TOF cases compared with controls. RESULTS We found a total of 165 significantly differentially methylated CpG loci in TOF cases compared with controls, in 165 separate genes. These biomarkers demonstrated from fair to excellent individual predictive accuracy for TOF detection, with AUCs ≥ 0.75 (FDR P-value < 0.001 for all). The following CpG loci (gene) had the highest predictive accuracy: cg05273049 (ARHGAP22; AUC = 1.00; 95% CI, 1.00-1.00), cg02540011 (CDK5; AUC = 0.96; 95% CI, 0.87-1.00), cg08404201 (TRIM27; AUC = 0.95; 95% CI, 0.84-1.00) and cg00687252 (IER3; AUC = 0.95; 95% CI, 0.84-1.00). IPA revealed over-representation (dysregulation) of 14 gene pathways involved in normal cardiac development, including cardiomyocyte differentiation via bone morphogenetic protein receptors, cardiac hypertrophy signaling and role of nuclear factor of activated T cells in cardiac hypertrophy. Cardiac hypertrophy is an important feature of TOF. CONCLUSIONS Analysis of placental DNA cytosine methylation changes yielded accurate markers for TOF detection and provided mechanistic information on TOF development. Our work appears to confirm the central role of epigenetic changes and of the placenta in the development of TOF. Copyright © 2019 ISUOG. Published by John Wiley & Sons Ltd.
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Affiliation(s)
- R Bahado-Singh
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, USA
| | - S Vishweswaraiah
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, USA
| | - N K Mishra
- Department of Genetics, Cell Biology & Anatomy College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - C Guda
- Department of Genetics, Cell Biology & Anatomy College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - U Radhakrishna
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, USA
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Liu J, Jiang J, Mo J, Liu D, Cao D, Wang H, He Y, Wang H. Global DNA 5-Hydroxymethylcytosine and 5-Formylcytosine Contents Are Decreased in the Early Stage of Hepatocellular Carcinoma. Hepatology 2019; 69:196-208. [PMID: 30070373 DOI: 10.1002/hep.30146] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 06/14/2018] [Indexed: 12/22/2022]
Abstract
Methylation of the fifth position of cytosine (5mC) is an important epigenetic modification of DNA. It has been shown that the oxidized derivatives of 5mC, namely 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC), are in dynamic existence and have distinct regulatory functions. In the current study, we investigated whether there are changes in the contents of all three 5mC-oxidized derivatives in the hepatocellular carcinoma (HCC) genome and further explored the underlying mechanisms. We showed that both global genomic 5hmC and 5fC contents were decreased significantly in the very early stage (stage 0, Barcelona Clinic Liver Cancer [BCLC] staging) of HCC compared with those of paratumor tissues. Noteworthily, 5fC content continued to decrease in the late stage (BCLC staging from 0 to A) of HCC. The 5caC content in HCC tissues was below the detection threshold. Hepatitis B virus (HBV) infection was associated with 5mC, 5hmC, or 5fC decrease in HCC; and measurements in cell lines integrated with or without HBV DNA showed consistent results. On the other hand, both the expression level of ten-eleven translocation enzyme 2 (TET2) and α-ketoglutarate content were decreased significantly in HCC. The significantly positive correlations among the expression levels of DNA methylation-related enzymes in paratumor tissues were generally attenuated or even disappeared in HCC tumor tissues. The decreases of both 5hmC and 5fC contents in genomic DNA were associated with poor prognosis of HCC patients. Conclusion: Global 5hmC and 5fC contents were decreased significantly in the very early stage of HCC; the decrease of 5hmC and 5fC was mainly due to the decrease of 5mC and associated with HBV infection, decreased TET enzyme activity, and uncoordinated expression of DNA methylation-related enzymes.
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Affiliation(s)
- Jiao Liu
- National Center for Liver Cancer, Eastern Hepatobiliary Surgery Hospital, Shanghai, People's Republic of China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Jinhua Jiang
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute/Hospital, Shanghai, People's Republic of China
| | - Jiezhen Mo
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Dan Liu
- National Center for Liver Cancer, Eastern Hepatobiliary Surgery Hospital, Shanghai, People's Republic of China
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center of Nanjing University, Nanjing, People's Republic of China
| | - Dan Cao
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute/Hospital, Shanghai, People's Republic of China
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yufei He
- National Center for Liver Cancer, Eastern Hepatobiliary Surgery Hospital, Shanghai, People's Republic of China
| | - Hongyang Wang
- National Center for Liver Cancer, Eastern Hepatobiliary Surgery Hospital, Shanghai, People's Republic of China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute/Hospital, Shanghai, People's Republic of China
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center of Nanjing University, Nanjing, People's Republic of China
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6
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Foksinski M, Zarakowska E, Gackowski D, Skonieczna M, Gajda K, Hudy D, Szpila A, Bialkowski K, Starczak M, Labejszo A, Czyz J, Rzeszowska-Wolny J, Olinski R. Profiles of a broad spectrum of epigenetic DNA modifications in normal and malignant human cell lines: Proliferation rate is not the major factor responsible for the 5-hydroxymethyl-2'-deoxycytidine level in cultured cancerous cell lines. PLoS One 2017; 12:e0188856. [PMID: 29190698 PMCID: PMC5708640 DOI: 10.1371/journal.pone.0188856] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 11/14/2017] [Indexed: 12/20/2022] Open
Abstract
Active demethylation of 5-methylcytosine moiety in DNA occurs by its sequential oxidation to 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxycytosine, catalysed by enzymes of the Ten-Eleven Translocation family proteins (TETs 1, 2 and 3). Here we analyzed for the first time all the intermediate products of DNA demethylation pathway in the form of deoxynucleosides (5-methyl-2′-deoxycytidine, 5-(hydroxymethyl)-2′-deoxycytidine, 5-formyl-2′-deoxycytidine and 5-carboxy-2′-deoxycytidine as well as 5-(hydroxymethyl)-2′-deoxyuridine) using automated isotope-dilution online two-dimensional ultra-performance liquid chromatography with tandem mass spectrometry. DNA was isolated from human malignant cell lines of colon adenocarcinoma (HCT 116), melanoma (Me45), myelogenous leukemia bone marrow blasts (K562), EBV-positive Burkitt’s lymphoma lymphoblasts (Raji), EBV-negative Burkitt’s lymphoma lymphoblasts (male-CA46 and female-ST486), as well as normal neonatal dermal fibroblasts (NHDF-Neo). The expression levels of TET1, TET2, TET3, SMUG1, and TDG genes were also assayed by RT-qPCR. Our results show a global erasure of 5-hydroxymethyl-2′-deoxycytidine and 5-carboxy-2′-deoxycytidine in DNA of cultured cells compared with DNA from primary malignant tissue. Moreover, malignant cells in culture have a quite different DNA epigenetic profile than cultured normal cells, and different types of malignant cells display different and characteristic profiles of DNA epigenetic marks. Similar analyses of a broader spectrum of epigenetic modifications, not restricted to 5-methyl-2′-deoxycytidine, could lead to better understanding of the mechanism(s) responsible for emergence of different types of cancer cells.
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Affiliation(s)
- Marek Foksinski
- Department of Clinical Biochemistry, Faculty of Pharmacy, L. Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Ewelina Zarakowska
- Department of Clinical Biochemistry, Faculty of Pharmacy, L. Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Daniel Gackowski
- Department of Clinical Biochemistry, Faculty of Pharmacy, L. Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Magdalena Skonieczna
- Biosystems Group, Institute of Automatic Control, Faculty of Automatics, Electronics, and Informatics, Silesian University of Technology, Gliwice, Poland
- Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Karolina Gajda
- Biosystems Group, Institute of Automatic Control, Faculty of Automatics, Electronics, and Informatics, Silesian University of Technology, Gliwice, Poland
- Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Dorota Hudy
- Biosystems Group, Institute of Automatic Control, Faculty of Automatics, Electronics, and Informatics, Silesian University of Technology, Gliwice, Poland
- Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Anna Szpila
- Department of Clinical Biochemistry, Faculty of Pharmacy, L. Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Karol Bialkowski
- Department of Clinical Biochemistry, Faculty of Pharmacy, L. Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Marta Starczak
- Department of Clinical Biochemistry, Faculty of Pharmacy, L. Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Anna Labejszo
- Department of Clinical Biochemistry, Faculty of Pharmacy, L. Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Jaroslaw Czyz
- Department of Hematology, Faculty of Medicine, L. Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Joanna Rzeszowska-Wolny
- Biosystems Group, Institute of Automatic Control, Faculty of Automatics, Electronics, and Informatics, Silesian University of Technology, Gliwice, Poland
- Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Ryszard Olinski
- Department of Clinical Biochemistry, Faculty of Pharmacy, L. Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
- * E-mail:
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Zhao MH, Liang S, Guo J, Choi JW, Kim NH, Lu WF, Cui XS. Analysis of Ferrous on Ten-Eleven Translocation Activity and Epigenetic Modifications of Early Mouse Embryos by Fluorescence Microscopy. Microsc Microanal 2016; 22:342-348. [PMID: 26947808 DOI: 10.1017/s1431927616000040] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Iron is an essential trace element that plays important roles in the cellular function of all organs and systems. However, the function of Fe(II) in mammalian embryo development is unknown. In this study, we investigated the role of Fe(II) during preimplantation embryo development. Depletion of Fe(II) using thiosemicarbazone-24 (TSC24), a specific Fe(II) chelator, rescued quenching of the Fe(II)-sensitive fluorophore phen green-SK. After in vitro fertilization, TSC24 significantly reduced the cleavage rate as well as blastocyst formation. The hatch rate of blastocysts was also reduced with 1 pM TSC24 treatment (20.25±1.86 versus 42.28±12.96%, p<0.05). Blastocysts were cultured in leukemia inhibitory factor-free mouse embryonic stem cell culture medium with or without TSC24, and those with depleted Fe(II) displayed delayed attachment and lost the ability to induce embryoid body formation. To further explore the mechanism of Fe(II) in embryo development, we assessed the expression of 5-hydroxymethylcytosine (5hmC) and OCT4 in the pronuclear and blastocyst stages, respectively. We observed that Fe(II) reduced 5hmC and OCT4 expression, which could be explained by low ten-eleven translocation (TET) enzyme activity induced by TSC24 treatment. These findings demonstrate that Fe(II) is required for mammalian embryo development and that it facilitates the process via regulation of TET activity.
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Affiliation(s)
- Ming-Hui Zhao
- 1Department of Animal Sciences,Chungbuk National University,Cheongju 361-763,Republic of Korea
| | - Shuang Liang
- 1Department of Animal Sciences,Chungbuk National University,Cheongju 361-763,Republic of Korea
| | - Jing Guo
- 1Department of Animal Sciences,Chungbuk National University,Cheongju 361-763,Republic of Korea
| | - Jeong-Woo Choi
- 1Department of Animal Sciences,Chungbuk National University,Cheongju 361-763,Republic of Korea
| | - Nam-Hyung Kim
- 1Department of Animal Sciences,Chungbuk National University,Cheongju 361-763,Republic of Korea
| | - Wen-Fa Lu
- 2College of Animal Science and Technology,Jilin Agricultural University,Changchun 130118,China
| | - Xiang-Shun Cui
- 1Department of Animal Sciences,Chungbuk National University,Cheongju 361-763,Republic of Korea
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8
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Bianchessi V, Vinci MC, Nigro P, Rizzi V, Farina F, Capogrossi MC, Pompilio G, Gualdi V, Lauri A. Methylation profiling by bisulfite sequencing analysis of the mtDNA Non-Coding Region in replicative and senescent Endothelial Cells. Mitochondrion 2016; 27:40-7. [PMID: 26910457 DOI: 10.1016/j.mito.2016.02.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 02/19/2016] [Accepted: 02/19/2016] [Indexed: 12/21/2022]
Abstract
The regulation and function of Mitochondrial DNA (mtDNA) cytosine methylation (5 mC) are largely unexplored. Mitochondria, Endothelial Cell (EC) senescence, and cardiovascular dysfunction are closely related. We extensively investigated the mtDNA Non-Coding Region (NCR) methylation pattern and its variations in EC replicative senescence. We observed previously undescribed 5 mC clusters and a biased distribution of 5 mC among DNA sites and throughout the NCR. The methylation pattern in senescent EC showed non-random variations, including the hypo-methylation of mtDNA replication regulatory sites. Additional experiments opened to a possible role for 5 mC in D-loop formation, rather than in mitochondrial gene expression.
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Affiliation(s)
- Valentina Bianchessi
- Unit of Vascular Biology and Regenerative Medicine, Centro Cardiologico Monzino (CCM), IRCCS, Milano, Italy
| | | | - Patrizia Nigro
- Unit of Vascular Biology and Regenerative Medicine, Centro Cardiologico Monzino (CCM), IRCCS, Milano, Italy
| | - Valeria Rizzi
- Genomics Core, Parco Tecnologico Padano, Lodi, Italy
| | - Floriana Farina
- Unit of Vascular Biology and Regenerative Medicine, Centro Cardiologico Monzino (CCM), IRCCS, Milano, Italy
| | - Maurizio C Capogrossi
- Laboratory of Vascular Pathology, Istituto Dermopatico dell'Immacolata (IDI), IRCCS, Roma, Italy
| | - Giulio Pompilio
- Unit of Vascular Biology and Regenerative Medicine, Centro Cardiologico Monzino (CCM), IRCCS, Milano, Italy
| | | | - Andrea Lauri
- Unit of Vascular Biology and Regenerative Medicine, Centro Cardiologico Monzino (CCM), IRCCS, Milano, Italy.
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9
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Bartošík M, Ondroušková E. [Novel Approaches in DNA Methylation Studies - MS-HRM Analysis and Electrochemistry]. Klin Onkol 2016; 29 Suppl 4:64-71. [PMID: 27846723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Cytosine methylation in DNA is an epigenetic mechanism regulating gene expression and plays a vital role in cell differentiation or proliferation. Tumor cells often exhibit aberrant DNA methylation, e.g. hypermethylation of tumor suppressor gene promoters. New methods, capable of determining methylation status of specific DNA sequences, are thus being developed. Among them, MS-HRM (methylation-specific high resolution melting) and electrochemistry offer relatively inexpensive instrumentation, fast assay times and possibility of screening multiple samples/DNA regions simultaneously. MS-HRM is due to its sensitivity and simplicity an interesting alternative to already established techniques, including methylation-specific PCR or bisulfite sequencing. Electrochemistry, when combined with suitable electroactive labels and electrode surfaces, has been applied in several unique strategies for discrimination of cytosines and methylcytosines. Both techniques were successfully tested in analysis of DNA methylation within promoters of important tumor suppressor genes and could thus help in achieving more precise diagnostics and prognostics of cancer. Aberrant methylation of promoters has already been described in hundreds of genes associated with tumorigenesis and could serve as important biomarker if new methods applicable into clinical practice are sufficiently advanced.Key words: DNA methylation - 5-methylcytosine - HRM analysis - melting temperature - DNA duplex - electrochemistry - nucleic acid hybridizationThis work was supported by MEYS - NPS I - LO1413.The authors declare they have no potential conflicts of interest concerning drugs, products, or services used in the study.The Editorial Board declares that the manuscript met the ICMJE recommendation for biomedical papers.Submitted: 6. 5. 2016Accepted: 16. 5. 2016.
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Abstract
Epigenetic modifications on DNA, especially on cytosine, play a critical role in regulating gene expression and genome stability. It is known that the levels of different cytosine derivatives are highly dynamic and are regulated by a variety of factors that act on the chromatin. Here we report an optical methodology based on hyperspectral dark-field imaging (HSDFI) using plasmonic nanoprobes to quantify the recently identified cytosine modifications on DNA in single cells. Gold (Au) and silver (Ag) nanoparticles (NPs) functionalized with specific antibodies were used as contrast-generating agents due to their strong local surface plasmon resonance (LSPR) properties. With this powerful platform we have revealed the spatial distribution and quantity of 5-carboxylcytosine (5caC) at the different stages in cell cycle and demonstrated that 5caC was a stably inherited epigenetic mark. We have also shown that the regional density of 5caC on a single chromosome can be mapped due to the spectral sensitivity of the nanoprobes in relation to the interparticle distance. Notably, HSDFI enables an efficient removal of the scattering noises from nonspecifically aggregated nanoprobes, to improve accuracy in the quantification of different cytosine modifications in single cells. Further, by separating the LSPR fingerprints of AuNPs and AgNPs, multiplex detection of two cytosine modifications was also performed. Our results demonstrate HSDFI as a versatile platform for spatial and spectroscopic characterization of plasmonic nanoprobe-labeled nuclear targets at the single-cell level for quantitative epigenetic screening.
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11
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Wagner M, Steinbacher J, Kraus TFJ, Michalakis S, Hackner B, Pfaffeneder T, Perera A, Müller M, Giese A, Kretzschmar HA, Carell T. Age-dependent levels of 5-methyl-, 5-hydroxymethyl-, and 5-formylcytosine in human and mouse brain tissues. Angew Chem Int Ed Engl 2015; 54:12511-4. [PMID: 26137924 PMCID: PMC4643189 DOI: 10.1002/anie.201502722] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 05/13/2015] [Indexed: 12/25/2022]
Abstract
The absolute levels of 5-hydroxymethylcytosine (hmC) and 5-methylcytosine (mC) in human brain tissues at various ages were determined. Additionally, absolute levels of 5-formylcytosine (fC) in adult individuals and cytosine modification levels in sorted neurons were quantified. These data were compared with age-related fC, hmC, and mC levels in mouse brain samples. For hmC, an initial steady increase is observed, which levels off with age to a final steady-state value of 1.2 % in human brain tissue. This level is nearly twice as high as in mouse cerebral cortex. In contrast, fC declines rapidly with age during early developmental stages, thus suggesting that while hmC is a stable epigenetic mark, fC is more likely an intermediate of active DNA demethylation during early brain development. The trends in global cytosine modification dynamics during the lifespan of an organism are conserved between humans and mice and show similar patterns in different organs.
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Affiliation(s)
- Mirko Wagner
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität MünchenButenandtstr. 5-13, 81377 Munich (Germany) E-mail:
| | - Jessica Steinbacher
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität MünchenButenandtstr. 5-13, 81377 Munich (Germany) E-mail:
| | - Theo F J Kraus
- Center for Neuropathology and Prion Research (ZNP), Ludwig-Maximilians-Universität MünchenFeodor-Lynen-Str. 28, 81377 Munich (Germany)
| | - Stylianos Michalakis
- Center for Integrated Protein Science at the Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität MünchenButenandtstr. 5-13, 81377 Munich (Germany)
| | - Benjamin Hackner
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität MünchenButenandtstr. 5-13, 81377 Munich (Germany) E-mail:
| | - Toni Pfaffeneder
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität MünchenButenandtstr. 5-13, 81377 Munich (Germany) E-mail:
| | - Arshan Perera
- Center for Integrated Protein Science at the Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität MünchenButenandtstr. 5-13, 81377 Munich (Germany)
| | - Markus Müller
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität MünchenButenandtstr. 5-13, 81377 Munich (Germany) E-mail:
| | - Armin Giese
- Center for Neuropathology and Prion Research (ZNP), Ludwig-Maximilians-Universität MünchenFeodor-Lynen-Str. 28, 81377 Munich (Germany)
| | - Hans A Kretzschmar
- Center for Neuropathology and Prion Research (ZNP), Ludwig-Maximilians-Universität MünchenFeodor-Lynen-Str. 28, 81377 Munich (Germany)
| | - Thomas Carell
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität MünchenButenandtstr. 5-13, 81377 Munich (Germany) E-mail:
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12
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Ganbold EO, Yoon J, Cho KH, Joo SW. Energetic stabilities of thiolated pyrimidines on gold nanoparticles investigated by Raman spectroscopy and density functional theory calculations. Spectrochim Acta A Mol Biomol Spectrosc 2015; 150:104-110. [PMID: 26037494 DOI: 10.1016/j.saa.2015.05.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 04/30/2015] [Accepted: 05/04/2015] [Indexed: 06/04/2023]
Abstract
The adsorption structures of 2-thiocytosine (2TC) on gold surfaces were examined by means of vibrational Raman spectroscopy and quantum mechanical density functional theory calculations. The 1H-thione-amino form was calculated to be most stable among the six examined tautomers. The three plausible binding geometries of sulfur, pyrimidine nitrogen, and amino group binding modes were calculated to estimate the binding energies of the 1H-thione-amino form with six gold cluster atoms. Thiouracils including 2-thiouracil (2TU), 4-thiouracil (4TU), and 6-methyl-2-thiouracil (6M2TU) were also studied to compare their relative binding energies on gold atoms. The intracellular localization of a DNA base analog of 2TC on gold nanoparticles (AuNPs) in HeLa cells was identified by means of surface-enhanced Raman scattering. AuNPs were modified with 2TC by self-assembly. Our dark-field microscopy and z-depth-dependent confocal Raman spectroscopy indicated that 2TC-assembled AuNPs could be found inside cancer cells. On the other hand, we did not observe noticeably strong Raman peaks in the cases of thiouracils including 2TU, 4TU, and 6M2TU. This may be due to the additional amino group of 2TC, which can lead to a stronger binding of adsorbates on AuNPs.
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Affiliation(s)
- Erdene-Ochir Ganbold
- Department of Chemistry, Soongsil University, Sangdo-dong, Dongjak-gu, Seoul 156-743, Republic of Korea
| | - Jinha Yoon
- Department of Chemistry, Soongsil University, Sangdo-dong, Dongjak-gu, Seoul 156-743, Republic of Korea
| | - Kwang-Hwi Cho
- School of Systems Biomedical Science, Soongsil University, Sangdo-dong, Dongjak-gu, Seoul, Republic of Korea
| | - Sang-Woo Joo
- Department of Chemistry, Soongsil University, Sangdo-dong, Dongjak-gu, Seoul 156-743, Republic of Korea.
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13
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Chowdhury B, McGovern A, Cui Y, Choudhury SR, Cho IH, Cooper B, Chevassut T, Lossie AC, Irudayaraj J. The hypomethylating agent Decitabine causes a paradoxical increase in 5-hydroxymethylcytosine in human leukemia cells. Sci Rep 2015; 5:9281. [PMID: 25901663 PMCID: PMC4894448 DOI: 10.1038/srep09281] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 02/19/2015] [Indexed: 12/20/2022] Open
Abstract
The USFDA approved "epigenetic drug", Decitabine, exerts its effect by hypomethylating DNA, demonstrating the pivotal role aberrant genome-wide DNA methylation patterns play in cancer ontology. Using sensitive technologies in a cellular model of Acute Myeloid Leukemia, we demonstrate that while Decitabine reduces the global levels of 5-methylcytosine (5mC), it results in paradoxical increase of 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) levels. Hitherto, the only biological mechanism known to generate 5hmC, 5fC and 5caC, involving oxidation of 5mC by members of Ten-Eleven-Translocation (TET) dioxygenase family, was not observed to undergo any alteration during DAC treatment. Using a multi-compartmental model of DNA methylation, we show that partial selectivity of TET enzymes for hemi-methylated CpG dinucleotides could lead to such alterations in 5hmC content. Furthermore, we investigated the binding of TET1-catalytic domain (CD)-GFP to DNA by Fluorescent Correlation Spectroscopy in live cells and detected the gradual increase of the DNA bound fraction of TET1-CD-GFP after treatment with Decitabine. Our study provides novel insights on the therapeutic activity of DAC in the backdrop of the newly discovered derivatives of 5mC and suggests that 5hmC has the potential to serve as a biomarker for monitoring the clinical success of patients receiving DAC.
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Affiliation(s)
- Basudev Chowdhury
- Department of Biological Sciences, Purdue University, West Lafayette 47907, IN
- Bindley Biosciences Center, Discovery Park, Purdue University, West Lafayette 47907, IN
| | - Andrew McGovern
- Department of Healthcare Management and Policy, University of Surrey, Guildford, GY2 7XH, UK
- Brighton and Sussex Medical School, Falmer, Brighton, East Sussex, BN1 9PS, UK
| | - Yi Cui
- Bindley Biosciences Center, Discovery Park, Purdue University, West Lafayette 47907, IN
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907
| | - Samrat Roy Choudhury
- Bindley Biosciences Center, Discovery Park, Purdue University, West Lafayette 47907, IN
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907
| | - Il-Hoon Cho
- Bindley Biosciences Center, Discovery Park, Purdue University, West Lafayette 47907, IN
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907
| | - Bruce Cooper
- Bindley Biosciences Center, Discovery Park, Purdue University, West Lafayette 47907, IN
| | - Timothy Chevassut
- Brighton and Sussex Medical School, Falmer, Brighton, East Sussex, BN1 9PS, UK
| | - Amy C. Lossie
- Bindley Biosciences Center, Discovery Park, Purdue University, West Lafayette 47907, IN
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - Joseph Irudayaraj
- Bindley Biosciences Center, Discovery Park, Purdue University, West Lafayette 47907, IN
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907
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14
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15
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Slifkin M, Merkow LP. The chicken embryo lethal orphan virus (CELO). Prog Exp Tumor Res 2015; 18:88-103. [PMID: 4632593 DOI: 10.1159/000393164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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16
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Grimme S, Bauer CA. Automated quantum chemistry based molecular dynamics simulations of electron ionization induced fragmentations of the nucleobases Uracil, Thymine, Cytosine, and Guanine. Eur J Mass Spectrom (Chichester) 2015; 21:125-140. [PMID: 26307693 DOI: 10.1255/ejms.1313] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The gas-phase decomposition pathways of electron ionization (EI)-induced radical cations of the nucleobases uracil, thymine, cytosine, and guanine are investigated by means of mixed quantum-classical molecular dynamics. No preconceived fragmentation channels are used in the calculations. The results compare well to a plethora of experimental and theoretical data for these important biomolecules. With our combined stochastic and dynamic approach, one can access in an unbiased way the energetically available decomposition mechanisms. Additionally, we are able to separate the EI mass spectra of different tautomers of cytosine and guanine. Our method (previously termed quantum chemistry electron ionization mass spectra) reproduces free nucleobase experimental mass spectra well and provides detailed mechanistic in-sight into high-energy unimolecular decomposition processes.
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Affiliation(s)
- Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Rheinischen Friedrich- Wilhelms-Universität Bonn, Beringstr. 4, D-53115, Bonn, Germany. - bonn.de
| | - Christopher Alexander Bauer
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Rheinischen Friedrich-Wilhelms-Universität Bonn, Beringstr. 4, D-53115, Bonn, Germany.
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17
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Lin Y, Cradick TJ, Brown MT, Deshmukh H, Ranjan P, Sarode N, Wile BM, Vertino PM, Stewart FJ, Bao G. CRISPR/Cas9 systems have off-target activity with insertions or deletions between target DNA and guide RNA sequences. Nucleic Acids Res 2014; 42:7473-85. [PMID: 24838573 PMCID: PMC4066799 DOI: 10.1093/nar/gku402] [Citation(s) in RCA: 446] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 04/17/2014] [Accepted: 04/24/2014] [Indexed: 12/11/2022] Open
Abstract
CRISPR/Cas9 systems are a versatile tool for genome editing due to the highly efficient targeting of DNA sequences complementary to their RNA guide strands. However, it has been shown that RNA-guided Cas9 nuclease cleaves genomic DNA sequences containing mismatches to the guide strand. A better understanding of the CRISPR/Cas9 specificity is needed to minimize off-target cleavage in large mammalian genomes. Here we show that genomic sites could be cleaved by CRISPR/Cas9 systems when DNA sequences contain insertions ('DNA bulge') or deletions ('RNA bulge') compared to the RNA guide strand, and Cas9 nickases used for paired nicking can also tolerate bulges in one of the guide strands. Variants of single-guide RNAs (sgRNAs) for four endogenous loci were used as model systems, and their cleavage activities were quantified at different positions with 1- to 5-bp bulges. We further investigated 114 putative genomic off-target loci of 27 different sgRNAs and confirmed 15 off-target sites, each harboring a single-base bulge and one to three mismatches to the guide strand. Our results strongly indicate the need to perform comprehensive off-target analysis related to DNA and sgRNA bulges in addition to base mismatches, and suggest specific guidelines for reducing potential off-target cleavage.
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Affiliation(s)
- Yanni Lin
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
| | - Thomas J Cradick
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
| | - Matthew T Brown
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
| | - Harshavardhan Deshmukh
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
| | - Piyush Ranjan
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Neha Sarode
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Brian M Wile
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
| | - Paula M Vertino
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Frank J Stewart
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Gang Bao
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
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18
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Calvo X, Nomdedeu M, Navarro A, Tejero R, Costa D, Muñoz C, Pereira A, Peña O, Risueño RM, Monzó M, Esteve J, Nomdedeu B. High levels of global DNA methylation are an independent adverse prognostic factor in a series of 90 patients with de novo myelodysplastic syndrome. Leuk Res 2014; 38:874-81. [PMID: 24880536 DOI: 10.1016/j.leukres.2014.04.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 04/23/2014] [Accepted: 04/27/2014] [Indexed: 12/31/2022]
Abstract
The prognostic impact of global DNA methylation and hydroxymethylation was assessed in 90 patients with de novo myelodysplastic syndrome (MDS). DNA was isolated from bone marrow samples obtained at diagnosis and global methylation and hydroxymethylation were determined by ELISA. Patients with a percentage of methylated DNA above 2.73% had a shorter overall survival than those with lower levels (P=0.018) and presented a negative trend in terms of leukemia-free survival (P=0.084), that was statistically significant after censoring 9 patients that received disease-modifying treatments both in univariate and multivariate analyses. Similarly, the low-risk MDS patients defined by the IPSS, WPSS and IPSS-R with 5-mC percentage in total DNA above 2.73% had a shorter overall survival (P=0.032; P=0.023; P=0.031). No cut-off value for the 5-hydroxymethylcytosine percentage with statistical significance for overall or leukemia-free survival was obtained. This study suggests that global DNA methylation predicts overall survival in myelodysplastic syndromes.
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Affiliation(s)
- Xavier Calvo
- Hematopathology Unit, Department of Pathology, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain.
| | - Meritxell Nomdedeu
- Hematology Department, Hospital Clínic, IDIBAPS, University of Barcelona, Barcelona, Spain; Josep Carreras Leukaemia Research Institute, Barcelona, Spain
| | - Alfons Navarro
- Molecular Oncology and Embryology Laboratory, Human Anatomy Unit, School of Medicine, University of Barcelona, IDIBAPS, Barcelona, Spain
| | - Rut Tejero
- Molecular Oncology and Embryology Laboratory, Human Anatomy Unit, School of Medicine, University of Barcelona, IDIBAPS, Barcelona, Spain
| | - Dolors Costa
- Hematopathology Unit, Department of Pathology, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Concha Muñoz
- Hematopathology Unit, Department of Pathology, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Arturo Pereira
- Department of Hemotherapy and Hemostasis, Hospital Clínic, IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Oscar Peña
- Hematology Department, Hospital Clínic, IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Ruth M Risueño
- Josep Carreras Leukaemia Research Institute, Barcelona, Spain
| | - Mariano Monzó
- Molecular Oncology and Embryology Laboratory, Human Anatomy Unit, School of Medicine, University of Barcelona, IDIBAPS, Barcelona, Spain
| | - Jordi Esteve
- Hematology Department, Hospital Clínic, IDIBAPS, University of Barcelona, Barcelona, Spain; Josep Carreras Leukaemia Research Institute, Barcelona, Spain
| | - Benet Nomdedeu
- Hematology Department, Hospital Clínic, IDIBAPS, University of Barcelona, Barcelona, Spain.
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19
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Madzo J, Liu H, Rodriguez A, Vasanthakumar A, Sundaravel S, Caces DBD, Looney TJ, Zhang L, Lepore JB, Macrae T, Duszynski R, Shih AH, Song CX, Yu M, Yu Y, Grossman R, Raumann B, Verma A, He C, Levine RL, Lavelle D, Lahn BT, Wickrema A, Godley LA. Hydroxymethylation at gene regulatory regions directs stem/early progenitor cell commitment during erythropoiesis. Cell Rep 2013; 6:231-244. [PMID: 24373966 DOI: 10.1016/j.celrep.2013.11.044] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 08/21/2013] [Accepted: 11/26/2013] [Indexed: 01/28/2023] Open
Abstract
Hematopoietic stem cell differentiation involves the silencing of self-renewal genes and induction of a specific transcriptional program. Identification of multiple covalent cytosine modifications raises the question of how these derivatized bases influence stem cell commitment. Using a replicative primary human hematopoietic stem/progenitor cell differentiation system, we demonstrate dynamic changes of 5-hydroxymethylcytosine (5-hmC) during stem cell commitment and differentiation to the erythroid lineage. Genomic loci that maintain or gain 5-hmC density throughout erythroid differentiation contain binding sites for erythroid transcription factors and several factors not previously recognized as erythroid-specific factors. The functional importance of 5-hmC was demonstrated by impaired erythroid differentiation, with augmentation of myeloid potential, and disrupted 5-hmC patterning in leukemia patient-derived CD34+ stem/early progenitor cells with TET methylcytosine dioxygenase 2 (TET2) mutations. Thus, chemical conjugation and affinity purification of 5-hmC-enriched sequences followed by sequencing serve as resources for deciphering functional implications for gene expression during stem cell commitment and differentiation along a particular lineage.
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Affiliation(s)
- Jozef Madzo
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Hui Liu
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Alexis Rodriguez
- Center for Research Informatics, The University of Chicago, Chicago, IL 60637, USA
| | - Aparna Vasanthakumar
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Sriram Sundaravel
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Donne Bennett D Caces
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Timothy J Looney
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789, USA
| | - Li Zhang
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789, USA
| | - Janet B Lepore
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Trisha Macrae
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Robert Duszynski
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Alan H Shih
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Chun-Xiao Song
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
| | - Miao Yu
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
| | - Yiting Yu
- Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Robert Grossman
- Center for Research Informatics, The University of Chicago, Chicago, IL 60637, USA
| | - Brigitte Raumann
- Center for Research Informatics, The University of Chicago, Chicago, IL 60637, USA
| | - Amit Verma
- Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
| | - Ross L Levine
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Don Lavelle
- Department of Medicine, University of Illinois, Chicago, Chicago, IL 60612, USA
- Jesse Brown VA Medical Center, Chicago, IL 60612, USA
| | - Bruce T Lahn
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789, USA
| | - Amittha Wickrema
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Lucy A Godley
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
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20
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Yan H, Fan WH, Zheng ZP, Liu J. [Terahertz spectroscopy of DNA nucleobases: cytosine and thymine]. Guang Pu Xue Yu Guang Pu Fen Xi 2013; 33:2612-2616. [PMID: 24409701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The absorption features of DNA nucleobases cytosine and thymine were measured by terahertz time-domain spectroscopy (THz-TDS) from 0.1 to 3.5 THz. Our experimental results clearly show that these important biomolecules exhibit distinctive absorption features in THz region. To the best of our knowledge, the subtle absorption peak of cytosine at 2.53 THz is reported for the first time. Moreover, geometry optimizations and lattice dynamic calculations on cytosine crystal were also performed with the pseudo-potential plane wave method of density functional theory by taking periodic boundary conditions into account. All measured terahertz absorption features of cytosine were assigned successfully and its absorption spectrum was reproduced according to our calculations. Furthermore, our results show that absorption features of cytosine below 3.5 THz arise from external modes in translation and rotation motions, which are dominated by the intermolecular hydrogen bonds.
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Affiliation(s)
- Hui Yan
- State Key Laboratory of Transient Optics and Photonics, Xi'an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi'an 710119, China.
| | - Wen-Hui Fan
- State Key Laboratory of Transient Optics and Photonics, Xi'an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi'an 710119, China
| | - Zhuan-Ping Zheng
- State Key Laboratory of Transient Optics and Photonics, Xi'an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi'an 710119, China
| | - Jia Liu
- State Key Laboratory of Transient Optics and Photonics, Xi'an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi'an 710119, China
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21
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Gabryelska MM, Barciszewski J. [The world of double helix--"it did not escape our notice"]. Postepy Biochem 2013; 59:246-256. [PMID: 24364207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
One of the key questions of biology is the nature and mechanisms of gene function. It has been 60 years since proposing the right-handed model of DNA double helix in 1953. This discovery was honored with Nobel Prize in 1962 and become a breakthrough in knowing and understanding mechanisms of heredity and genetic code. Since that time a great deal of data have been gathered considering functions, structure and DNA application. It became the basis of modern molecular biology, chemical biology and biotechnology. Today we know, that double helix is characterized by its dynamics and plasticity, which depend on its nucleotide sequence. Chromatin structure and DNA mediated charge transport have a crucial role in understanding mechanisms of its damage and repair. Progress in epigenetics allowed to identify new DNA bases, such as 5-methylcytosine, 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxycytosine. Design of new catalytic nucleic acids and the nanotechnology field of DNA origami reveal its application potential.
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Affiliation(s)
- Marta M Gabryelska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 12/14 Z. Noskowskiego St., 61-704 Poznań, Poland
| | - Jan Barciszewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 12/14 Z. Noskowskiego St., 61-704 Poznań, Poland
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Farcau C, Sangeetha NM, Decorde N, Astilean S, Ressier L. Microarrays of gold nanoparticle clusters fabricated by Stop&Go convective self-assembly for SERS-based sensor chips. Nanoscale 2012; 4:7870-7877. [PMID: 23149550 DOI: 10.1039/c2nr32781c] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
SERS substrates fabricated from chemically synthesized nanoparticles (NPs) offer a distinct advantage of localizing and enhancing the electromagnetic fields by facile tuning of NP size, shape and interparticle distances. In this report, two-dimensional arrays of micrometre-sized clusters of gold nanoparticles protected by (i) sodium citrate and (ii) tris(2,4-dimethyl-5-sulfonatophenyl)phosphine (TDSP) ligands were directly assembled from colloidal suspensions onto flat, non-patterned substrates by discontinuous ('Stop&Go') convective self-assembly. The micrometric spacing between the NP clusters makes it easy to address them individually by confocal Raman microscopy. The packing of the gold NPs within these clusters with interparticle spacings of the order of nanometres leads to an optical response dominated by coupled surface plasmon resonances, and favours a strong enhancement of electromagnetic fields useful for surface enhanced Raman scattering (SERS). These NP clusters make very uniform SERS substrates, with reproducible SERS responses from cluster to cluster. The potential of these NP clusters for optical biosensing is demonstrated by the SERS detection of a biologically relevant molecule, cytosine, adsorbed onto the NP clusters. The presented results are promising for designing an original class of nanoparticle-based SERS microarrays. The new paradigm of convective self-assembly could be exploited generally for the patterning of various other types of colloidal micro- and nano-objects, such as semiconducting NPs, magnetic NPs, bacteria or proteins.
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Affiliation(s)
- Cosmin Farcau
- Babes-Bolyai University, Faculty of Physics, Institute for Interdisciplinary Research in Bio-Nano-Sciences, 1 M. Kogalniceanu, 400084 Cluj-Napoca, Romania
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Yu M, Hon GC, Szulwach KE, Song CX, Zhang L, Kim A, Li X, Dai Q, Park B, Min JH, Jin P, Ren B, He C. Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome. Cell 2012; 149:1368-80. [PMID: 22608086 PMCID: PMC3589129 DOI: 10.1016/j.cell.2012.04.027] [Citation(s) in RCA: 760] [Impact Index Per Article: 63.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 04/02/2012] [Accepted: 04/19/2012] [Indexed: 10/28/2022]
Abstract
The study of 5-hydroxylmethylcytosines (5hmC) has been hampered by the lack of a method to map it at single-base resolution on a genome-wide scale. Affinity purification-based methods cannot precisely locate 5hmC nor accurately determine its relative abundance at each modified site. We here present a genome-wide approach, Tet-assisted bisulfite sequencing (TAB-Seq), that when combined with traditional bisulfite sequencing can be used for mapping 5hmC at base resolution and quantifying the relative abundance of 5hmC as well as 5mC. Application of this method to embryonic stem cells not only confirms widespread distribution of 5hmC in the mammalian genome but also reveals sequence bias and strand asymmetry at 5hmC sites. We observe high levels of 5hmC and reciprocally low levels of 5mC near but not on transcription factor-binding sites. Additionally, the relative abundance of 5hmC varies significantly among distinct functional sequence elements, suggesting different mechanisms for 5hmC deposition and maintenance.
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Affiliation(s)
- Miao Yu
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 E. 57th Street, Chicago, Illinois 60637, USA
| | - Gary C. Hon
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093-0653, USA
| | - Keith E. Szulwach
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Atlanta, Georgia 30322, USA
| | - Chun-Xiao Song
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 E. 57th Street, Chicago, Illinois 60637, USA
| | - Liang Zhang
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 E. 57th Street, Chicago, Illinois 60637, USA
| | - Audrey Kim
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093-0653, USA
| | - Xuekun Li
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Atlanta, Georgia 30322, USA
| | - Qing Dai
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 E. 57th Street, Chicago, Illinois 60637, USA
| | - Beomseok Park
- Department of Chemistry, The University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60606, USA
| | - Jung-Hyun Min
- Department of Chemistry, The University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60606, USA
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Atlanta, Georgia 30322, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093-0653, USA
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 E. 57th Street, Chicago, Illinois 60637, USA
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Wilkinson J. New sequencing technique produces high-resolution map of 5-hydroxymethylcytosine. Epigenomics 2012; 4:249. [PMID: 22872914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023] Open
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25
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Abstract
Artificial induction of active DNA demethylation appears to be a possible and useful strategy in molecular biology research and therapy development. Dimethyl sulfoxide (DMSO) was shown to cause phenotypic changes in embryonic stem cells altering the genome-wide DNA methylation profiles. Here we report that DMSO increases global and gene-specific DNA hydroxymethylation levels in pre-osteoblastic MC3T3-E1 cells. After 1 day, DMSO increased the expression of genes involved in DNA hydroxymethylation (TET) and nucleotide excision repair (GADD45) and decreased the expression of genes related to DNA methylation (Dnmt1, Dnmt3b, Hells). Already 12 hours after seeding, before first replication, DMSO increased the expression of the pro-apoptotic gene Fas and of the early osteoblastic factor Dlx5, which proved to be Tet1 dependent. At this time an increase of 5-methyl-cytosine hydroxylation (5-hmC) with a concomitant loss of methyl-cytosines on Fas and Dlx5 promoters as well as an increase in global 5-hmC and loss in global DNA methylation was observed. Time course-staining of nuclei suggested euchromatic localization of DMSO induced 5-hmC. As consequence of induced Fas expression, caspase 3/7 and 8 activities were increased indicating apoptosis. After 5 days, the effect of DMSO on promoter- and global methylation as well as on gene expression of Fas and Dlx5 and on caspases activities was reduced or reversed indicating down-regulation of apoptosis. At this time, up regulation of genes important for matrix synthesis suggests that DMSO via hydroxymethylation of the Fas promoter initially stimulates apoptosis in a subpopulation of the heterogeneous MC3T3-E1 cell line, leaving a cell population of extra-cellular matrix producing osteoblasts.
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Affiliation(s)
- Roman Thaler
- Ludwig Boltzmann Institute of Osteology at the Hanusch Hospital of WGKK and AUVA Trauma Center Meidling; First Medical Department; Hanusch Hospital; Vienna, Austria
| | - Silvia Spitzer
- Ludwig Boltzmann Institute of Osteology at the Hanusch Hospital of WGKK and AUVA Trauma Center Meidling; First Medical Department; Hanusch Hospital; Vienna, Austria
| | - Heidrun Karlic
- Ludwig Boltzmann Institute for Leukemia Research and Hematology; Hanusch Hospital; Ludwig Boltzmann Cluster Oncology; Vienna, Austria
| | - Klaus Klaushofer
- Ludwig Boltzmann Institute of Osteology at the Hanusch Hospital of WGKK and AUVA Trauma Center Meidling; First Medical Department; Hanusch Hospital; Vienna, Austria
| | - Franz Varga
- Ludwig Boltzmann Institute of Osteology at the Hanusch Hospital of WGKK and AUVA Trauma Center Meidling; First Medical Department; Hanusch Hospital; Vienna, Austria
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26
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Zhang YX, Gao KR, Yu SY. [Progress of research on 5-hydroxymethylcytosine]. Yi Chuan 2012; 34:509-518. [PMID: 22659422 DOI: 10.3724/sp.j.1005.2012.00509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
5-methylcytosine (5mC) in cytosine-guanine dinucleotide (CpG) is a usual epigenetic modification in mammals. It plays crucial roles in gene regulation, development, genomic imprinting and so on. In the last three years, it was discovered that in addition to 5mC, another modified cytosine base-5-hydroxymethylcytosine (5hmC) was abundant in many mammalian tissues, which may have different biological function from 5mC. This paper reviews the recent progresses in the studies of 5hmC.
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Affiliation(s)
- Yan-Xia Zhang
- Shanghai Mental Health Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China.
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27
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Abstract
The minimal essential section of DNA helices, the dinucleoside phosphate deoxyguanylyl-3',5'-deoxycytidine dimer octahydrate, [dGpdC](2), has been constructed, fully optimized, and analyzed by using quantum chemical methods at the B3LYP/6-31+G(d,p) level of theory. Study of the electrons attached to [dGpdC](2) reveals that DNA double strands are capable of capturing low-energy electrons and forming electronically stable radical anions. The relatively large vertical electron affinity (VEA) predicted for [dGpdC](2) (0.38 eV) indicates that the cytosine bases are good electron captors in DNA double strands. The structure, charge distribution, and molecular orbital analysis for the fully optimized radical anion [dGpdC](2)(·-) suggest that the extra electron tends to be redistributed to one of the cytosine base moieties, in an electronically stable structure (with adiabatic electron affinity (AEA) 1.14 eV and vertical detachment energy (VDE) 2.20 eV). The structural features of the optimized radical anion [dGpdC](2)(·-) also suggest the probability of interstrand proton transfer. The interstrand proton transfer leads to a distonic radical anion [d(G-H)pdC:d(C+H)pdG](·-), which contains one deprotonated guanine anion and one protonated cytosine radical. This distonic radical anion is predicted to be more stable than [dGpdC](2)(·-). Therefore, experimental evidence for electron attachment to the DNA double helices should be related to [d(G-H)pdC:d(C+H)pdG](·-) complexes, for which the VDE might be as high as 2.7 eV (in dry conditions) to 3.3 eV (in fully hydrated conditions). Effects of the polarizable medium have been found to be important for increasing the electron capture ability of the dGpdC dimer. The ultimate AEA value for cytosine in DNA duplexes is predicted to be 2.03 eV in aqueous solution.
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Affiliation(s)
- Jiande Gu
- Drug Design & Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, CAS, Shanghai 201203, P. R. China.
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28
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Di Ventra M. Nanobiotechnology: sequencing at the end of the tunnel. Nat Nanotechnol 2010; 5:828-829. [PMID: 21076403 DOI: 10.1038/nnano.2010.238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Affiliation(s)
- Massimiliano Di Ventra
- Physics Department, University of California, San Diego, La Jolla, California 92093, USA.
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Huang CY, Ho CH, Lin CJ, Lo CC. Exposure effect of fungicide kasugamycin on bacterial community in natural river sediment. J Environ Sci Health B 2010; 45:485-491. [PMID: 20512740 DOI: 10.1080/03601231003800412] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The degradation of kasugamycin in water and the effects of kasugamycin on the bacterial communities in sediment and overlying water were analyzed over a 30-day period. Kasugamycin is generally regarded as nontoxic to microorganisms, but in this study we demonstrated that kasugamycin inhibited the growth of some aquatic bacteria but also stimulated the growth of other resistant bacteria. Microcosms were contaminated with kasugamycin at the 168.4 mg/L (700 times field application rate), and 1462.9 mg/L (6000 times field application rate). The percentages of kasugamycin degraded after 30 days of exposure were 34.1%, and 12.1% in the overlying water treated with 168.4 mg/L and 1462.9 mg/L, respectively. The degradation rates of kanamycin after 30 days of exposure were 1.92 mg/L/day for 164.8 mg/L treated water and 5.88 mg/L/day for 1462.9 mg/L treated water. Degradation rate of kasugamycin in overlying water was associated with an increase in the concentration of kasugamycin. Comparison of DGGE (denaturing gradient gel electrophoresis) profiles showed that the bacterial communities in treated microcosms were varied. Certain species were eliminated whereas some species were stimulated by the application of kasugamycin. The DGGE profiles and UPGMA (unweighted pair-group method using arithmetic averages) dendrograms revealed that the bacterial communities were more complex in treated sediment than in treated overlying water.
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Affiliation(s)
- Chi-Yu Huang
- Department of Environmental Science and Engineering, Tunghai University, Taichung, Taiwan, ROC
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30
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Reyn A, Birch-Andersen A, Berger U. Fine structure and taxonomic position of Neisseria haemolysans (Thjotta and Boe 1938) or Gemella haemolysans (Berger 1960). Acta Pathol Microbiol Scand B Microbiol Immunol 2009; 78:375-89. [PMID: 4097691 DOI: 10.1111/j.1699-0463.1970.tb04317.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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31
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Zhang XC, Hu YH, Wang XJ. [Characteristic vibration analysis of M-RNA nucleic acid bases complexes (M = Ca+ and Mg+) by DFT]. Guang Pu Xue Yu Guang Pu Fen Xi 2009; 29:146-150. [PMID: 19385226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A density functional investigation of the interaction between calcium and magnesium univalent cations and RNA pyrimidine base (cytosine, thymine and uracil) was performed to determine geometric coordinates and free energies for all possible stable isomers at B3LYP/6-311 + G (2df, 2p) level. The most stable isomers C1M, T1M and U1M (M = Ca+ and Mg+) with the lowest free energy among the same pyrimidine base tautomers were calculated to determine the characters of infrared vibrations. According to the results, two characteristic infrared vibrations at wave numbers 1,684 and 1,765 cm(-1) were found for single pyrimidine base C1, at 1,747 and 1,792 cm(-1) for T1, 1,763 and at 1,796 cm(-1) for U1. In addition, spectrum shifts were found when the cations interact with the pyrimidine base tautomers. For deeper analysis, we found that when the stable complexes are formed, the cations are prone to act on the oxygen atoms, and cause the vibrational frequencies to change, the spectral lines belonging to the vibration of C--O--M turn out to redshift and the others turn out to blueshift. When the stable complex C1M is formed, the characteristic infrared vibration at 1,684 cm(-1) mainly caused by the ring's vibration turns out to blueshift about 10 cm(-1), and the another characteristic vibration of 1,765 cm(-1) caused by vibration of bond C--O with oxygen atom acting on cations directly turns out to redshift by 112 cm(-1) for complex C1Ca+ and by 110 cm(-1) for C1Mg+. When the stable complexes T1M are formed, the characteristic vibration of bond C--O--M turns out to redshift about 130 cm(-1) and the vibration of bond C--O turns out to blueshift about 55 cm(-1). When the stable complexes U1M are formed, the vibration of bond C--O--M turns out to redshift about 90 cm(-1) and about 50 cm(-1) for another C--O. The characteristic infrared vibration frequencies are changed obviously when tautomers act on the cations, which is mainly because cations take part in molecule's vibrations and change the force constants and reduced masses.
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Affiliation(s)
- Xing-Chu Zhang
- Department of Electromechanical Engineering, Guangzhou Polytechnic of Science and Trade, Guangzhou 511442, China.
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32
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Yang I, Kim SK, Burke DG, Griffiths K, Kassir Z, Emslie KR, Gao Y, Wang J, Foy CA, Pardos-Pardos AC, Ellison S, Domann PJ, Fujii SI, Park SR. An international comparability study on quantification of total methyl cytosine content. Anal Biochem 2008; 384:288-95. [PMID: 18929528 DOI: 10.1016/j.ab.2008.09.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2008] [Revised: 09/19/2008] [Accepted: 09/25/2008] [Indexed: 12/31/2022]
Abstract
Various methods have been developed for quantitative analysis of DNA methylation. However, there is currently no reference analysis system regarding DNA methylation with which other analytical approaches can be compared and evaluated. A standard measurement system that includes reference methods and reference materials may improve comparability and credibility of data obtained from different analytical environments. In an effort to establish a standard system for measurement of DNA methylation, the Korea Research Institute of Standards and Science (KRISS) coordinated an international comparison study among different national metrology institutes. An initial stage of the study involved an intercomparison regarding quantitative measurement of total methyl cytosine contents in artificially constructed DNA samples. The measurement principle involved measurement of dNMP contents following enzymatic hydrolysis of DNA samples. Results of the study showed good comparability among four of five participants and close agreement with reference values assigned by the coordinating laboratory. Conflicting data from one participant may have resulted from incomplete hydrolysis of samples due to use of insufficient amounts of enzymes. These results indicate that comparable and accurate results can be obtained from different measurement environments if digestion conditions are controlled appropriately and valid calibration systems are employed.
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Affiliation(s)
- Inchul Yang
- Health Metrology Group, Korea Research Institute of Standards and Science, 1 Doryong-dong, Yusung-gu, Daejon 305-340, Republic of Korea
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Thust R, Rønne M. Localization of SCEs and their possible relationship to dA . dT- or dG . dC-clusters, respectively, in Chinese hamster V79-E chromosomes. Hereditas 2008; 96:295-8. [PMID: 6286538 DOI: 10.1111/j.1601-5223.1982.tb00862.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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34
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Cui FL, Wang JL, Cui YR, Qu GR, Lu Y, Fan J. [Determination of the proteins in serum albumins by synchronous fluorescence technique with 3-(2-cyanoethyl) cytosine as a probe]. Guang Pu Xue Yu Guang Pu Fen Xi 2008; 28:384-388. [PMID: 18479028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Under simulative biological conditions and upon the interactions between 3-(2-cyanoethyl) cytosine (CECT) and human serum albumin (HSA) or bovine serum albumin (BSA), the authors studied the characteristics of synchronous fluorescence spectra of CECT-protein system with CECT as a molecular spectral probe. The spectral characteristics and intensity of synchronous fluorescence were related to the value of deltalambda, reaction medium, reaction temperature and so on. On the basis of these, the new method for the determination of proteins in serum albumin was developed with CECT as a molecular spectral probe. Under the optimum experimental conditions, the synchronous fluorescence intensities of CECT-HSA and CECT-BSA systems were in good proportion to the concentrations of HSA and BSA in the ranges of 0-441.4 and 0-351.0 microg x mL(-1), respectively. The detection limits were 0.023 and 0.035 microg x mL(-1), respectively. Relative standard deviations located between 12% and 3.3%, and the addition standard recovery was 97.2%-100.4% for all elements. The results suggested that the method features easy of implementation, rapidity, high sensitivity, broad linear range, and better RSD and recovery etc., and was employed directly to determine the total proteins in serum albumin samples with satisfactory results.
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Affiliation(s)
- Feng-Ling Cui
- College of Chemistry and Environmental Science, Henan Normal University, Xinxiang 453007, China.
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35
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Abstract
We designed a detection system of 5-methylcytosine ((m)C) in DNA by a combination of photooxidative DNA cleavage reaction of 2-methyl-1,4-naphthoquinone chromophore with invader technology. Enzymatic treatment of a mixture of photochemically fragmented target oligodeoxynucleotides (ODNs) at (m)C and probe oligomer possessing a fluorophore and a quencher resulted in a dramatic enhancement of fluorescence. In contrast, fluorescence emission for the ODN containing C but not (m)C at the target sequence was extremely weak. We could detect (m)C in sub-femtomol DNA by monitoring the fluorescence change.
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Affiliation(s)
- Hisatsugu Yamada
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Katsura Campus, Kyoto 615-8510, Japan
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Kalyanaraman S, Krishnakumar V, Ganesan K. Vibrational spectroscopic analysis of cytosine monohydrate and its copper(II) complex. Spectrochim Acta A Mol Biomol Spectrosc 2007; 66:1340-6. [PMID: 16920005 DOI: 10.1016/j.saa.2006.04.046] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2006] [Accepted: 04/15/2006] [Indexed: 05/11/2023]
Abstract
Single crystals of cytosine monohydrate and its copper(II) complex were grown by slow evaporation in an aqueous solution at room temperature. The solubility studies were carried out at different temperatures in deionized water. Cytosine monohydrate and the copper(II) complex of cytosine were characterized by recording IR, Raman and UV spectra. The various vibrational modes of the crystals have been classified using factor group and site group analysis. Vibrational assignments were proposed for both the systems based on the spectral investigations.
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Affiliation(s)
- S Kalyanaraman
- Department of Physics, Sri Paramakalyani College, Alwarkurichi, India
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Peuranen S, Tiihonen K, Apajalahti J, Kettunen A, Saarinen M, Rautonen N. Combination of polydextrose and lactitol affects microbial ecosystem and immune responses in rat gastrointestinal tract. Br J Nutr 2007; 91:905-14. [PMID: 15182394 DOI: 10.1079/bjn20041114] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The effects of various dietary fibres on gut health have been studied extensively but their combined effects are scarcely documented. In the present study the effects of 2 % (w/w) polydextrose (PDX), 2 % (w/w) disaccharide lactitol, or 2 % (w/w) PDX+2 % (w/w) lactitol on gut microflora, microbial metabolism and gut immune responses were investigated in rats. Both PDX and lactitol alone had an effect on many of the studied parameters, but their combination had stronger than additive effects in some parameters. The PDX+lactitol combination altered the microbial community structure as seen by a culture-independent method, percentage guanine+cytosine (%G+C) profiling, increasing the areas of %G+C 35–39 (P<0·0001) and %G+C 45–49 (P=0·0002), and decreasing %G+C 65–74 (P<0·0003). These changes were also reflected in the microbial metabolism so that the production of biogenic amines and branched volatile fatty acids was significantly reduced, by 12 (P=0·03) and 50 % (P=0·002), respectively, indicating a shift from putrefactive towards saccharolytic metabolism. PDX increased the secretion of IgA in the caecum (P=0·007). Secretion of IgA increased even more, almost ten-fold, with the combination of PDX+lactitol (P<0·0001) when compared with the control group. Lactitol increased the production of butyrate by caecal microbes by two- to three-fold when compared with the PDX or control group (P<0·0001). Butyrate is a preferred energy source for mucosal cells; thus a boost in the availability of energy for immune cells may have still added to the synergistic effects of PDX and lactitol on immune cells. It is noteworthy that improvement in the IgA secretion occurred without signs of mucosal inflammation.
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Affiliation(s)
- Seppo Peuranen
- Danisco Innovation, Enteromix Research, Sokeritehtaantie 20, FIN-02460 Kantvik, Finland.
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Hu J, Zhao X, Zhang Z, Yu J. Compositional dynamics of guanine and cytosine content in prokaryotic genomes. Res Microbiol 2007; 158:363-70. [PMID: 17449227 DOI: 10.1016/j.resmic.2007.02.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2006] [Revised: 02/07/2007] [Accepted: 02/15/2007] [Indexed: 11/20/2022]
Abstract
Nucleotide compositional analyses of disparities in genomic guanine and cytosine (gGC) content directly relate to the amino acid composition, through the union of the genetic code. Here we analyzed 229 prokaryotic genomes to address the intricate relationships between gGC, amino acids and their codons in the context of genes. First, we not only confirmed the universal rule that the average GC content at codon position 1 (GC1) is always higher than that at codon position 2 (GC2), but also extended the rule to show that it holds true even when codon-position-related GC contents are calculated on a per gene basis. The "GC1>GC2 rule" is attributable essentially to a few dominant amino acids that have GC at one of these two codon positions or the intermediate-GC group of amino acids. Second, we found that gGC fluctuations were largely compensated for at the codon level, when codons belonging to high-GC and low-GC amino acid groups varied accordingly. Finally, we found that prokaryotic genes also have a GC content gradient (Gd) distributed along their transcripts. The gradients at three codon positions (Gd1, Gd2 and Gd3) all correlated with gGC in two different directions: Gd3 was positive, whereas the other two were negative.
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Affiliation(s)
- Jianfei Hu
- College of Life Sciences, Peking University, Beijing 100871, China
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39
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Abstract
DNA base composition expressed as mol% of guanine plus cytosine (% GC) or GC content is a key parameter of bacterial taxonomy and genomic analyses. Direct chemical determination methods such as HPLC as well as indirect methods based on physical properties of deoxyribonucleic acid (DNA), melting point (T(m)), and buoyant density (B(d)) have been conventionally applied to determine the GC content. However, these methods require relatively large amounts of sample DNA, time, and labor. We have developed a protocol to determine the GC content by fine separation of nucleosides with CZE. Genomic DNAs with known GC content from 23 bacterial strains were determined by CE at the optimized conditions of 27 degrees C, 20 kV in 50 mM of NaHCO(3) (pH 9.0) and 70 mM SDS added. Nucleosides from <1 microg of DNA hydrolyzed with nuclease-P1 and bacterial alkaline phosphatase were separated in a 75 microm wide and 80 cm long silica capillary. The nucleoside peak areas were determined at 254 nm in less than 12 min. The CE-based determination of GC content requires only small amounts of DNA, and thus should be applicable to environmental genomics (metagenomics), as >90% of environmental micro-organisms are nonculturable and produce only small amounts of genomic DNA.
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Affiliation(s)
- Ngoc-Phuc Hua
- Graduate School of Biosphere Science, Hiroshima University, Kagamiyama, Higashi-Hiroshima, Japan
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Tanaka K, Tainaka K, Okamoto A. Methylcytosine-selective fluorescence quenching by osmium complexation. Bioorg Med Chem 2006; 15:1615-21. [PMID: 17194597 DOI: 10.1016/j.bmc.2006.12.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2006] [Revised: 12/12/2006] [Accepted: 12/13/2006] [Indexed: 10/23/2022]
Abstract
We report on the control of the emission from a fluorophore fixed on DNA using the methylcytosine-selective addition of an osmium-bipyridine complex. We have synthesized DNA modified by a microenvironment-sensitive fluorophore, 2-dimethylamino-6-acyl-naphthalene. The emission from the fluorophore tethered to a probe DNA was effectively quenched by a methylcytosine glycol-osmium-bipyridine triad, which was located in the immediate neighborhood of the fluorophore. The discrimination of the cytosine methylation status at a methylation hot spot in the p53 gene was also executed using a well-designed fluorescent DNA probe.
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Affiliation(s)
- Kazuo Tanaka
- Frontier Research System, RIKEN (The Institute of Physical and Chemical Research), Wako, Saitama 351-0198, Japan
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41
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Abstract
Methylation of DNA is an epigenetic modification that can play an important role in the control of gene expression in mammalian cells. The development of a simple and convenient method for site-specific discrimination of cytosine methylation is imperative for genomic studies. Here we report a facile method for distinguishing between cytosine and 5-methylcytosine. Osmium tetroxide caused the dihydroxylation of the C5-C6 double bond of 5-methylcytosine under an appropriate reaction conditions. The oxidation of 5-methylcytosine-containing target DNA was controlled by hybridization with a guide DNA. This technique facilitates the typing of cytosine methylation at a specific site of the target DNA.
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Affiliation(s)
- Akimitsu Okamoto
- Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering, Kyoto University, Kyoto 615-8510, Japan
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42
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Abstract
The Ubiquitin Specific Protease 26 gene is a testis-specific gene that is located on the X chromosome. Sequence variants of this gene were previously reported in men with azoospermia caused by defects at the level of spermatogenesis. Especially a cluster of three changes (c.370_371insACA, c.494T>C and c.1423C>T) was frequently observed. To further define the role of this cluster of sequence variants in the USP26 gene, we have now analysed 202 control samples and 146 patients of Caucasian origin with cryptozoospermia or oligozoospermia. The detection method was based on a restriction reaction, by which the change c.494T>C can be detected. In none of the patients, the change c.494T>C was observed. Only in one man with normal spermatogenesis this sequence variant was detected. Sequencing can confirm the presence of the three changes of the USP26 gene. These data indicate that the cluster of changes is not restricted to men with severe testicular dysfunction.
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Affiliation(s)
- Katrien Stouffs
- Research Centre Reproduction and Genetics, Vrije Universiteit Brussel, Brussels, Belgium.
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43
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Skelley AM, Cleaves HJ, Jayarajah CN, Bada JL, Mathies RA. Application of the Mars Organic Analyzer to nucleobase and amine biomarker detection. Astrobiology 2006; 6:824-37. [PMID: 17155883 DOI: 10.1089/ast.2006.6.824] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The Mars Organic Analyzer (MOA), a portable microfabricated capillary electrophoresis instrument being developed for planetary exploration, is used to analyze a wide variety of fluorescamine-labeled amine-containing biomarker compounds, including amino acids, mono and diaminoalkanes, amino sugars, nucleobases, and nucleobase degradation products. The nucleobases cytosine and adenine, which contain an exocyclic primary amine, were effectively labeled, separated, and detected at concentrations <500 nM. To test the general applicability of the MOA for biomarker detection, amino acids and mono- and diamines were extracted from bacterial cells using both hydrolysis and sublimation followed by analysis. The extrapolated limit of detection provided by the valine biomarker was approximately 4 x 10(3) cells per sample. Products of an NH(4)CN polymerization that simulate a prebiotic synthesis were also successfully isolated via sublimation and analyzed. Adenine and alanine/serine were detected with no additional sample cleanup at 120 +/- 13 microM and 4.1 +/- 1 microM, respectively, corresponding to a reaction yield of 0.04% and 0.0003%, respectively. This study demonstrates that the MOA provides sensitive detection and analysis of low levels of a wide variety of amine-containing organic compounds from both biological and abiotic sources.
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Affiliation(s)
- Alison M Skelley
- Department of Chemistry, University of California at Berkeley, 94720, USA
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44
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Horvath C. High-performance ion-exchange chromatography with narrow-bore columns: rapid analysis of nucleic acid constituents at the subnanomole level. Methods Biochem Anal 2006; 21:79-154. [PMID: 4594522 DOI: 10.1002/9780470110416.ch3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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45
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Bag SS, Saito Y, Hanawa K, Kodate S, Suzuka I, Saito I. Intelligent fluorescent nucleoside in sensing cytosine base: importance of hydrophobic nature of perylene fluorophore. Bioorg Med Chem Lett 2006; 16:6338-41. [PMID: 17035014 DOI: 10.1016/j.bmcl.2006.09.039] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2006] [Revised: 09/01/2006] [Accepted: 09/05/2006] [Indexed: 10/24/2022]
Abstract
Fluorescence response upon hybridization of perylene labeled oligonucleotide probes depends on the microenvironment experienced by the perylene fluorophore. In mismatched duplex ((Per)U-C), enhanced fluorescence was observed while in matched duplex ((Per)U-A) fluorescence intensity decreased considerably. This observation will be a promising research effort in giving rise to a new powerful tool in detection of SNP.
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Affiliation(s)
- Subhendu Sekhar Bag
- NEWCAT Institute, School of Engineering, Nihon University, Koriyama, Fukushima 963-8642, Japan
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46
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Li W, Liu XH, Tung CH, Hao ZP. The observation of abnormal signals in laser flash photolysis: a type of probable synchronized nuclear spin signals. Spectrochim Acta A Mol Biomol Spectrosc 2006; 65:345-50. [PMID: 16503189 DOI: 10.1016/j.saa.2005.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2005] [Revised: 10/22/2005] [Accepted: 11/07/2005] [Indexed: 05/06/2023]
Abstract
In laser flash photolysis (LFP) work, noise-like signals were observed together with transient absorption decay spectra in time domain. Analyzed results show that it is a valuable resonance spectrum of excited state molecules, in which four molecular cases are given here. We proposed that this kind signal might originate from nuclear or nuclear and electron spin resonance features in the excited molecules based on radio wave frequency spectrum levels and the significant interaction with static magnetic field.
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Affiliation(s)
- Wen Li
- Technical Institute of Physics & Chemistry, The Chinese Academy of Sciences, Datun Road,Chaoyang District, Beijing 100101, PR China
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47
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Charles H, Calevro F, Vinuelas J, Fayard JM, Rahbe Y. Codon usage bias and tRNA over-expression in Buchnera aphidicola after aromatic amino acid nutritional stress on its host Acyrthosiphon pisum. Nucleic Acids Res 2006; 34:4583-92. [PMID: 16963497 PMCID: PMC1636365 DOI: 10.1093/nar/gkl597] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Codon usage bias and relative abundances of tRNA isoacceptors were analysed in the obligate intracellular symbiotic bacterium, Buchnera aphidicola from the aphid Acyrthosiphon pisum, using a dedicated 35mer oligonucleotide microarray. Buchnera is archetypal of organisms living with minimal metabolic requirements and presents a reduced genome with high-evolutionary rate. Codonusage in Buchnera has been overcome by the high mutational bias towards AT bases. However, several lines of evidence for codon usage selection are given here. A significant correlation was found between tRNA relative abundances and codon composition of Buchnera genes. A significant codon usage bias was found for the choice of rare codons in Buchnera: C-ending codons are preferred in highly expressed genes, whereas G-ending codons are avoided. This bias is not explained by GC skew in the bacteria and might correspond to a selection for perfect matching between codon-anticodon pairs for some essential amino acids in Buchnera proteins. Nutritional stress applied to the aphid host induced a significant overexpression of most of the tRNA isoacceptors in bacteria. Although, molecular regulation of the tRNA operons in Buchnera was not investigated, a correlation between relative expression levels and organization in transcription unit was found in the genome of Buchnera.
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Affiliation(s)
- Hubert Charles
- Laboratoire de Biologie Fonctionnelle Insectes et Interactions, UMR INRA/INSA de Lyon, 203 Bâtiment Louis Pasteur, 69621 Villeurbanne Cedex, France.
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48
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Abstract
In order to understand the evolution, structure and function of genomes, it is important to know the general compositional features of DNA sequences. Based on the quadratic divergence, a new segmentation algorithm to partition a given genome or DNA sequence into compositionally distinct domains has been put forward. With the aid of the technique of cumulative GC profile, the distribution of segmentation points can be displayed intuitively. We have therefore developed them into GC-Profile, an interactive web-based software system, which can be used to segment prokaryotic and eukaryotic genomes. GC-Profile provides a quantitative and qualitative view of genome organization. Based on the obtained results, the relationships between the G+C content and other genomic features, such as distributions of genes and CpG islands, can be analyzed in a perceivable manner. It shows that GC-Profile would be an appropriate starting point for analyzing the isochore structure of higher eukaryotic genomes, and an intuitive tool for identifying genomic islands in prokaryotic genomes. GC-Profile is freely available at the website . In addition, precompiled binaries, together with examples and documentation, can also be freely downloaded for a local execution.
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Affiliation(s)
| | - Chun-Ting Zhang
- To whom correspondence should be addressed. Tel: +86 22 2740 2987; Fax: +86 22 2740 2697;
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49
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Abstract
CorGen is a web server that measures long-range correlations in the base composition of DNA and generates random sequences with the same correlation parameters. Long-range correlations are characterized by a power-law decay of the auto correlation function of the GC-content. The widespread presence of such correlations in eukaryotic genomes calls for their incorporation into accurate null models of eukaryotic DNA in computational biology. For example, the score statistics of sequence alignment and the performance of motif finding algorithms are significantly affected by the presence of genomic long-range correlations. We use an expansion-randomization dynamics to efficiently generate the correlated random sequences. The server is available at http://corgen.molgen.mpg.de.
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Affiliation(s)
- Philipp W Messer
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany.
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50
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Abstract
We present the results of a simple, statistical assay that measures the G+C content sensitivity bias of gene expression experiments without the requirement of a duplicate experiment. We analyse five gene expression profiling methods: Affymetrix GeneChip, Long Serial Analysis of Gene Expression (LongSAGE), LongSAGELite, 'Classic' Massively Parallel Signature Sequencing (MPSS) and 'Signature' MPSS. We demonstrate the methods have systematic and random errors leading to a different G+C content sensitivity. The relationship between this experimental error and the G+C content of the probe set or tag that identifies each gene influences whether the gene is detected and, if detected, the level of gene expression measured. LongSAGE has the least bias, while Signature MPSS shows a strong bias to G+C rich tags and Affymetrix data show different bias depending on the data processing method (MAS 5.0, RMA or GC-RMA). The bias in the Affymetrix data primarily impacts genes expressed at lower levels. Despite the larger sampling of the MPSS library, SAGE identifies significantly more genes (60% more RefSeq genes in a single comparison).
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Affiliation(s)
| | | | | | | | | | - Marco A. Marra
- To whom correspondence should be addressed at Genome Sciences Centre, Suite 100, 570 West 7th Avenue, Vancouver BC, Canada V5Z 4S6. Tel: 604 877 6082; Fax: 604 877 6085;
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