1
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Biswas A, Basu A. The impact of the sequence-dependent physical properties of DNA on chromatin dynamics. Curr Opin Struct Biol 2023; 83:102698. [PMID: 37696706 DOI: 10.1016/j.sbi.2023.102698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 07/07/2023] [Accepted: 08/14/2023] [Indexed: 09/13/2023]
Abstract
The local mechanical properties of DNA depend on local sequence. Here we review recent genomic, structural, and computational efforts at deciphering the "mechanical code", i.e., the mapping between sequence and mechanics. We then discuss works that suggest how evolution has exploited the mechanical code to control the energetics of DNA-deforming biological processes such as nucleosome organization, transcription factor binding, DNA supercoiling, gene regulation, and 3D chromatin organization. As a whole, these recent works suggest that DNA sequence in diverse organisms can encode regulatory information governing diverse processes via the mechanical code.
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Affiliation(s)
- Aditi Biswas
- Department of Biosciences, Durham University, Durham, UK
| | - Aakash Basu
- Department of Biosciences, Durham University, Durham, UK.
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2
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Das SK, Huynh MT, Lee TH. Spontaneous histone exchange between nucleosomes. J Biol Chem 2023; 299:105037. [PMID: 37442235 PMCID: PMC10406861 DOI: 10.1016/j.jbc.2023.105037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/26/2023] [Accepted: 07/07/2023] [Indexed: 07/15/2023] Open
Abstract
The nucleosome is the fundamental gene-packing unit in eukaryotes. Nucleosomes comprise ∼147 bp DNA wrapped around an octameric histone protein core composed of two H2A-H2B dimers and one (H3-H4)2 tetramer. The strong yet flexible DNA-histone interactions are the physical basis of the dynamic regulation of genes packaged in chromatin. The dynamic nature of DNA-histone interactions also implies that nucleosomes dissociate DNA-histone contacts both transiently and repeatedly. This kinetic instability may lead to spontaneous nucleosome disassembly or histone exchange between nucleosomes. At high nucleosome concentrations, nucleosome-nucleosome collisions and subsequent histone exchange would be a more likely event, where nucleosomes could act as their own histone chaperone. This spontaneous histone exchange could serve as a mechanism for maintaining overall chromatin stability, although it has never been reported. Here we employed three-color single-molecule FRET (smFRET) to demonstrate that histone H2A-H2B dimers are exchanged spontaneously between nucleosomes on a time scale of a few tens of seconds at a physiological nucleosome concentration. We show that the rate of histone exchange increases at a higher monovalent salt concentration, with histone-acetylated nucleosomes, and in the presence of histone chaperone Nap1, while it remains unchanged at a higher temperature, and decreases upon DNA methylation. These results support the notion of histone exchange via transient and repetitive partial disassembly of the nucleosome and corroborate spontaneous histone diffusion in a compact chromatin context, modulating the local concentrations of histone modifications and variants.
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Affiliation(s)
- Subhra Kanti Das
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Mai Thao Huynh
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Tae-Hee Lee
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA.
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3
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Das SK, Huynh MT, Gao J, Sengupta B, Yadav SP, Lee TH. Methods to investigate nucleosome structure and dynamics with single-molecule FRET. Methods 2023; 215:17-27. [PMID: 37236433 PMCID: PMC10330475 DOI: 10.1016/j.ymeth.2023.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 04/13/2023] [Accepted: 05/21/2023] [Indexed: 05/28/2023] Open
Abstract
The nucleosome is the fundamental building block of chromatin. Changes taking place at the nucleosome level are the molecular basis of chromatin transactions with various enzymes and factors. These changes are directly and indirectly regulated by chromatin modifications such as DNA methylation and histone post-translational modifications including acetylation, methylation, and ubiquitylation. Nucleosomal changes are often stochastic, unsynchronized, and heterogeneous, making it very difficult to monitor with traditional ensemble averaging methods. Diverse single-molecule fluorescence approaches have been employed to investigate the structure and structural changes of the nucleosome in the context of its interactions with various enzymes such as RNA Polymerase II, histone chaperones, transcription factors, and chromatin remodelers. We utilize diverse single-molecule fluorescence methods to study the nucleosomal changes accompanying these processes, elucidate the kinetics of these processes, and eventually learn the implications of various chromatin modifications in directly regulating these processes. The methods include two- and three-color single-molecule fluorescence resonance energy transfer (FRET), single-molecule fluorescence correlation spectroscopy, and fluorescence (co-)localization. Here we report the details of the two- and three-color single-molecule FRET methods we currently use. This report will help researchers design their single-molecule FRET approaches to investigating chromatin regulation at the nucleosome level.
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Affiliation(s)
- Subhra K Das
- Department of Chemistry, the Pennsylvania State University, University Park, PA 16802, USA
| | - Mai T Huynh
- Department of Chemistry, the Pennsylvania State University, University Park, PA 16802, USA
| | - Jia Gao
- Department of Chemistry, the Pennsylvania State University, University Park, PA 16802, USA
| | - Bhaswati Sengupta
- Department of Chemistry, the Pennsylvania State University, University Park, PA 16802, USA
| | - Satya P Yadav
- Department of Chemistry, the Pennsylvania State University, University Park, PA 16802, USA
| | - Tae-Hee Lee
- Department of Chemistry, the Pennsylvania State University, University Park, PA 16802, USA.
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4
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Das SK, Huynh MT, Lee TH. Spontaneous Histone Exchange Between Nucleosomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.540004. [PMID: 37215040 PMCID: PMC10197660 DOI: 10.1101/2023.05.09.540004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The nucleosome is the fundamental gene-packing unit in eukaryotes. Nucleosomes comprise ∼147 bp DNA wrapped around an octameric histone protein core composed of two H2A-H2B dimers and one (H3-H4) 2 tetramer. The strong yet flexible DNA-histone interactions are a physical basis of the dynamic regulation of genes packaged in chromatin. The dynamic nature of DNA-histone interactions implies that nucleosomes dissociate DNA-histone contacts transiently and repeatedly. This kinetic instability may lead to spontaneous nucleosome disassembly or histone exchange between nucleosomes. At a high nucleosome concentration, nucleosome-nucleosome collisions and subsequent histone exchange would be a more likely pathway, where nucleosomes act as their own histone chaperone. The spontaneous histone exchange would serve as a mechanism for maintaining the overall chromatin stability although it has never been reported. We employed three-color single-molecule FRET (smFRET) to demonstrate that histone H2A-H2B dimers are exchanged spontaneously between nucleosomes and that the time scale is on a few tens of seconds at a physiological nucleosome concentration. The rate of histone exchange increases at a higher monovalent salt concentration, with histone acetylated nucleosomes, and in the presence of histone chaperone Nap1, while it remains unchanged at a higher temperature, and decreases upon DNA methylation. These results support histone exchange via transient and repetitive partial disassembly of the nucleosome and corroborate spontaneous histone diffusion in a compact chromatin context, modulating the local concentrations of histone modifications and variants.
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5
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Shi D, Huang Y, Bai C. Studies of the Mechanism of Nucleosome Dynamics: A Review on Multifactorial Regulation from Computational and Experimental Cases. Polymers (Basel) 2023; 15:polym15071763. [PMID: 37050377 PMCID: PMC10096840 DOI: 10.3390/polym15071763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/28/2023] [Accepted: 03/31/2023] [Indexed: 04/05/2023] Open
Abstract
The nucleosome, which organizes the long coil of genomic DNA in a highly condensed, polymeric way, is thought to be the basic unit of chromosomal structure. As the most important protein–DNA complex, its structural and dynamic features have been successively revealed in recent years. However, its regulatory mechanism, which is modulated by multiple factors, still requires systemic discussion. This study summarizes the regulatory factors of the nucleosome’s dynamic features from the perspective of histone modification, DNA methylation, and the nucleosome-interacting factors (transcription factors and nucleosome-remodeling proteins and cations) and focuses on the research exploring the molecular mechanism through both computational and experimental approaches. The regulatory factors that affect the dynamic features of nucleosomes are also discussed in detail, such as unwrapping, wrapping, sliding, and stacking. Due to the complexity of the high-order topological structures of nucleosomes and the comprehensive effects of regulatory factors, the research on the functional modulation mechanism of nucleosomes has encountered great challenges. The integration of computational and experimental approaches, the construction of physical modes for nucleosomes, and the application of deep learning techniques will provide promising opportunities for further exploration.
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Affiliation(s)
- Danfeng Shi
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
| | - Yuxin Huang
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China
| | - Chen Bai
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China
- Chenzhu (MoMeD) Biotechnology Co., Ltd., Hangzhou 310005, China
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6
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Toniyan KA, Gorbacheva EY, Boyarintsev VV, Ogneva IV. Endometriosis of the Cervix: A Rare Clinical Case with the Possibility of Comparing the Eutopic and Ectopic Endometrium at the Cellular Level. Int J Mol Sci 2023; 24:ijms24032184. [PMID: 36768508 PMCID: PMC9916952 DOI: 10.3390/ijms24032184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/19/2023] [Accepted: 01/21/2023] [Indexed: 01/24/2023] Open
Abstract
Endometriosis of the cervix is a rare form of genital endometriosis, which is characterized by the appearance of tissue on the vaginal part of the cervix, similar to the tissue of the mucous membrane of the uterine cavity. We describe a clinical case in which we compared the content of cytoskeletal proteins, H3 histone modifications and DNA methylation (total and 5-hydroxymethylcytosine content) in the eutopic endometrium and in tissue from endometriosis foci on the cervix. The patient had elevated levels of estradiol, interleukin-1β and interleukin-8. At the cellular level, the content of tubulin and the marker of stable microtubules were reduced in the ectopic endometrium (by 45% and 37%, p < 0.05, respectively), but the alpha-actinin-1 content was increased (by 75%, p < 0.05) with an increase in the expression of its gene. At the same time, the total level of DNA methylation in the endometriotic focus was reduced by more than 2 times with the accumulation of the intermediate product 5-hydroxymethylcytosine (the content increased by more than 3 times), probably due to an increase in the content of tet methylcytosine dioxygenase 1 (more than 4 times).
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Affiliation(s)
- Konstantin A. Toniyan
- Gynecology Department, FGBU KB1 (Volynskaya) UDP RF, 121352 Moscow, Russia
- Cell Biophysics Lab., State Scientific Center of the Russian Federation Institute of Biomedical Problems of the Russian Academy of Sciences, 123007 Moscow, Russia
| | - Elena Yu. Gorbacheva
- Gynecology Department, FGBU KB1 (Volynskaya) UDP RF, 121352 Moscow, Russia
- Cell Biophysics Lab., State Scientific Center of the Russian Federation Institute of Biomedical Problems of the Russian Academy of Sciences, 123007 Moscow, Russia
| | - Valery V. Boyarintsev
- Emergency and Extreme Medicine Department, FGBU DPO CGMA UDP RF, 121359 Moscow, Russia
| | - Irina V. Ogneva
- Cell Biophysics Lab., State Scientific Center of the Russian Federation Institute of Biomedical Problems of the Russian Academy of Sciences, 123007 Moscow, Russia
- Correspondence: ; Tel.: +7-499-195-6398
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7
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An Y, Zhao X, Zhang Z, Xia Z, Yang M, Ma L, Zhao Y, Xu G, Du S, Wu X, Zhang S, Hong X, Jin X, Sun K. DNA methylation analysis explores the molecular basis of plasma cell-free DNA fragmentation. Nat Commun 2023; 14:287. [PMID: 36653380 PMCID: PMC9849216 DOI: 10.1038/s41467-023-35959-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 01/10/2023] [Indexed: 01/19/2023] Open
Abstract
Plasma cell-free DNA (cfDNA) are small molecules generated through a non-random fragmentation procedure. Despite commendable translational values in cancer liquid biopsy, however, the biology of cfDNA, especially the principles of cfDNA fragmentation, remains largely elusive. Through orientation-aware analyses of cfDNA fragmentation patterns against the nucleosome structure and integration with multidimensional functional genomics data, here we report a DNA methylation - nuclease preference - cutting end - size distribution axis, demonstrating the role of DNA methylation as a functional molecular regulator of cfDNA fragmentation. Hence, low-level DNA methylation could increase nucleosome accessibility and alter the cutting activities of nucleases during DNA fragmentation, which further leads to variation in cutting sites and size distribution of cfDNA. We further develop a cfDNA ending preference-based metric for cancer diagnosis, whose performance has been validated by multiple pan-cancer datasets. Our work sheds light on the molecular basis of cfDNA fragmentation towards broader applications in cancer liquid biopsy.
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Affiliation(s)
- Yunyun An
- Institute of Cancer Research, Shenzhen Bay Laboratory, 518132, Shenzhen, China
| | - Xin Zhao
- Hepato-Biliary Surgery Division, Shenzhen Third People's Hospital, The Second Affiliated Hospital, Southern University of Science and Technology, 518100, Shenzhen, China
| | - Ziteng Zhang
- Hepato-Biliary Surgery Division, Shenzhen Third People's Hospital, The Second Affiliated Hospital, Southern University of Science and Technology, 518100, Shenzhen, China
| | - Zhaohua Xia
- Thoracic Surgical Department, Shenzhen Third People's Hospital, The Second Affiliated Hospital, Southern University of Science and Technology, 518100, Shenzhen, China
| | - Mengqi Yang
- Institute of Cancer Research, Shenzhen Bay Laboratory, 518132, Shenzhen, China
| | - Li Ma
- Institute of Cancer Research, Shenzhen Bay Laboratory, 518132, Shenzhen, China
| | - Yu Zhao
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, 518107, Shenzhen, China
| | - Gang Xu
- Department of Liver Surgery and Liver Transplant Center, West China Hospital of Sichuan University, 610041, Chengdu, China
| | - Shunda Du
- Department of Liver Surgery, Peking Union Medical College Hospital, PUMC and Chinese Academy of Medical Sciences, 100730, Beijing, Dongcheng, China
| | - Xiang'an Wu
- Department of Liver Surgery, Peking Union Medical College Hospital, PUMC and Chinese Academy of Medical Sciences, 100730, Beijing, Dongcheng, China
| | - Shuowen Zhang
- Department of Liver Surgery, Peking Union Medical College Hospital, PUMC and Chinese Academy of Medical Sciences, 100730, Beijing, Dongcheng, China
| | - Xin Hong
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Xin Jin
- BGI-Shenzhen, 518083, Shenzhen, China. .,School of Medicine, South China University of Technology, 510006, Guangzhou, Guangdong, China.
| | - Kun Sun
- Institute of Cancer Research, Shenzhen Bay Laboratory, 518132, Shenzhen, China.
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8
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Zhao XC, Dong HL, Li XL, Yang HY, Chen XF, Dai L, Wu WQ, Tan ZJ, Zhang XH. 5-Methyl-cytosine stabilizes DNA but hinders DNA hybridization revealed by magnetic tweezers and simulations. Nucleic Acids Res 2022; 50:12344-12354. [PMID: 36477372 PMCID: PMC9757033 DOI: 10.1093/nar/gkac1122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/31/2022] [Accepted: 11/07/2022] [Indexed: 12/12/2022] Open
Abstract
5-Methyl-cytosine (5mC) is one of the most important DNA modifications and plays versatile biological roles. It is well known that 5mC stabilizes DNA duplexes. However, it remains unclear how 5mC affects the kinetics of DNA melting and hybridization. Here, we studied the kinetics of unzipping and rezipping using a 502-bp DNA hairpin by single-molecule magnetic tweezers. Under constant loading rates, 5mC increases the unzipping force but counterintuitively decreases the rezipping force at various salt and temperature conditions. Under constant forces, the non-methylated DNA hops between metastable states during unzipping and rezipping, which implies low energy barriers. Surprisingly, the 5mC DNA can't rezip after fully unzipping unless much lower forces are applied, where it rezips stochastically in a one-step manner, which implies 5mC kinetically hinders DNA hybridization and high energy barriers in DNA hybridization. All-atom molecular dynamics simulations reveal that the 5mC kinetically hinders DNA hybridization due to steric effects rather than electrostatic effects caused by the additional methyl groups of cytosines. Considering the possible high speed of DNA unzipping and zipping during replication and transcription, our findings provide new insights into the biological roles of 5mC.
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Affiliation(s)
| | | | - Xiao-Lu Li
- The Institute for Advanced Studies, College of Life Sciences, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Hong-Yu Yang
- The Institute for Advanced Studies, College of Life Sciences, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Xue-Feng Chen
- The Institute for Advanced Studies, College of Life Sciences, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Liang Dai
- Department of Physics, City University of Hong Kong, Hong Kong 999077, China
| | - Wen-Qiang Wu
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, Henan University, Kaifeng 475001, China
| | - Zhi-Jie Tan
- Correspondence may also be addressed to Zhi-Jie Tan. Tel: +86 15827627809; Fax: +86 02768752569;
| | - Xing-Hua Zhang
- To whom correspondence should be addressed. Tel: +86 15827632615; Fax: +86 02768753780;
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9
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Basu A, Bobrovnikov DG, Cieza B, Arcon JP, Qureshi Z, Orozco M, Ha T. Deciphering the mechanical code of the genome and epigenome. Nat Struct Mol Biol 2022; 29:1178-1187. [PMID: 36471057 PMCID: PMC10142808 DOI: 10.1038/s41594-022-00877-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 10/18/2022] [Indexed: 12/12/2022]
Abstract
Diverse DNA-deforming processes are impacted by the local mechanical and structural properties of DNA, which in turn depend on local sequence and epigenetic modifications. Deciphering this mechanical code (that is, this dependence) has been challenging due to the lack of high-throughput experimental methods. Here we present a comprehensive characterization of the mechanical code. Utilizing high-throughput measurements of DNA bendability via loop-seq, we quantitatively established how the occurrence and spatial distribution of dinucleotides, tetranucleotides and methylated CpG impact DNA bendability. We used our measurements to develop a physical model for the sequence and methylation dependence of DNA bendability. We validated the model by performing loop-seq on mouse genomic sequences around transcription start sites and CTCF-binding sites. We applied our model to test the predictions of all-atom molecular dynamics simulations and to demonstrate that sequence and epigenetic modifications can mechanically encode regulatory information in diverse contexts.
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Affiliation(s)
- Aakash Basu
- Department of Biosciences, Durham University, Durham, UK. .,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Dmitriy G Bobrovnikov
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Basilio Cieza
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Juan Pablo Arcon
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Zan Qureshi
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain.,Department of Biochemistry and Biomedicine, Universitat de Barcelona, Barcelona, Spain
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA. .,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA. .,Howard Hughes Medical Institute, Baltimore, MD, USA.
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10
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Zhang Z, Lin J, Liu Z, Tian G, Li XM, Jing Y, Li X, Li XD. Photo-Cross-Linking To Delineate Epigenetic Interactome. J Am Chem Soc 2022; 144:20979-20997. [DOI: 10.1021/jacs.2c06135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Zhuoyuan Zhang
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Jianwei Lin
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Zheng Liu
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Gaofei Tian
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Xiao-Meng Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yihang Jing
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Xin Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Xiang David Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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11
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Abstract
Cell-free DNA (cfDNA) is nonrandomly fragmented and contains a wealth of molecular information useful for noninvasive prenatal testing and cancer detection. cfDNA fragmentomics contains information beyond genetics, such as gene expression inference. However, the feasibility of using cfDNA fragmentomics for deducing cfDNA methylomics remains unexplored. This study demonstrated the possibility of using cfDNA fragmentation patterns to deduce the methylation patterns of cfDNA molecules, breaking free from the limitation of bisulfite sequencing. By using cfDNA cleavage profiles surrounding a cytosine-phosphate-guanine (CpG) site, we determined the methylation status ranging from a particular region down to a single CpG assisted by a deep learning algorithm. Both genetic and epigenetic information of cfDNA can therefore be obtained in a single nondestructive assay. Cell-free DNA (cfDNA) fragmentation patterns contain important molecular information linked to tissues of origin. We explored the possibility of using fragmentation patterns to predict cytosine-phosphate-guanine (CpG) methylation of cfDNA, obviating the use of bisulfite treatment and associated risks of DNA degradation. This study investigated the cfDNA cleavage profile surrounding a CpG (i.e., within an 11-nucleotide [nt] window) to analyze cfDNA methylation. The cfDNA cleavage proportion across positions within the window appeared nonrandom and exhibited correlation with methylation status. The mean cleavage proportion was ∼twofold higher at the cytosine of methylated CpGs than unmethylated ones in healthy controls. In contrast, the mean cleavage proportion rapidly decreased at the 1-nt position immediately preceding methylated CpGs. Such differential cleavages resulted in a characteristic change in relative presentations of CGN and NCG motifs at 5′ ends, where N represented any nucleotide. CGN/NCG motif ratios were correlated with methylation levels at tissue-specific methylated CpGs (e.g., placenta or liver) (Pearson’s absolute r > 0.86). cfDNA cleavage profiles were thus informative for cfDNA methylation and tissue-of-origin analyses. Using CG-containing end motifs, we achieved an area under a receiver operating characteristic curve (AUC) of 0.98 in differentiating patients with and without hepatocellular carcinoma and enhanced the positive predictive value of nasopharyngeal carcinoma screening (from 19.6 to 26.8%). Furthermore, we elucidated the feasibility of using cfDNA cleavage patterns to deduce CpG methylation at single CpG resolution using a deep learning algorithm and achieved an AUC of 0.93. FRAGmentomics-based Methylation Analysis (FRAGMA) presents many possibilities for noninvasive prenatal, cancer, and organ transplantation assessment.
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12
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Li S, Peng Y, Panchenko AR. DNA methylation: Precise modulation of chromatin structure and dynamics. Curr Opin Struct Biol 2022; 75:102430. [PMID: 35914496 DOI: 10.1016/j.sbi.2022.102430] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/06/2022] [Accepted: 06/16/2022] [Indexed: 11/19/2022]
Abstract
DNA methylation plays a vital role in epigenetic regulation in both plants and animals, and typically occurs at the 5-carbon position of the cytosine pyrimidine ring within the CpG dinucleotide steps. Cytosine methylation can alter DNA's geometry, mechanical and physico-chemical properties - thus influencing the molecular signaling events vital for transcription, replication and chromatin remodeling. Despite the profound effect cytosine methylation can have on DNA, the underlying atomistic mechanisms remain enigmatic. Many studies so far have produced controversial findings on how cytosine methylation dictates DNA flexibility and accessibility, nucleosome stability and dynamics. Here, we review the most recent experimental and computational studies that provide precise characterization of structure and function of cytosine methylation and its versatile roles in modulating DNA mechanics, nucleosome and chromatin structure, stability and dynamics. Moreover, the review briefly discusses the relationship between DNA methylation and nucleosome positioning, and the crosstalk between DNA methylation and histone tail modifications.
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Affiliation(s)
- Shuxiang Li
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, ON, Canada
| | - Yunhui Peng
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Anna R Panchenko
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, ON, Canada.
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13
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Meghani K, Folgosa Cooley L, Piunti A, Meeks JJ. Role of Chromatin Modifying Complexes and Therapeutic Opportunities in Bladder Cancer. Bladder Cancer 2022; 8:101-112. [PMID: 35898580 PMCID: PMC9278011 DOI: 10.3233/blc-211609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 02/14/2022] [Indexed: 11/15/2022]
Abstract
BACKGROUND Chromatin modifying enzymes, mainly through post translational modifications, regulate chromatin architecture and by extension the underlying transcriptional kinetics in normal and malignant cells. Muscle invasive bladder cancer (MIBC) has a high frequency of alterations in chromatin modifiers, with 76% of tumors exhibiting mutation in at least one chromatin modifying enzyme [1]. Additionally, clonal expansion of cells with inactivating mutations in chromatin modifiers has been identified in the normal urothelium, pointing to a currently unknown role of these proteins in normal bladder homeostasis. OBJECTIVE To review current knowledge of chromatin modifications and enzymes regulating these processes in Bladder cancer (BCa). METHODS By reviewing current literature, we summarize our present knowledge of external stimuli that trigger loss of equilibrium in the chromatin accessibility landscape and emerging therapeutic interventions for targeting these processes. RESULTS Genetic lesions in BCa lead to altered function of chromatin modifying enzymes, resulting in coordinated dysregulation of epigenetic processes with disease progression. CONCLUSION Mutations in chromatin modifying enzymes are wide-spread in BCa and several promising therapeutic targets for modulating activity of these genes are currently in clinical trials. Further research into understanding how the epigenetic landscape evolves as the disease progresses, could help identify patients who might benefit the most from these targeted therapies.
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Affiliation(s)
- Khyati Meghani
- Department of Urology, Feinberg School of Medicine, Chicago, IL, USA,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Chicago, IL, USA
| | - Lauren Folgosa Cooley
- Department of Urology, Feinberg School of Medicine, Chicago, IL, USA,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Chicago, IL, USA
| | - Andrea Piunti
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Chicago, IL, USA
| | - Joshua J. Meeks
- Department of Urology, Feinberg School of Medicine, Chicago, IL, USA,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Chicago, IL, USA,Jesse Brown VA Medical Center, Chicago IL, USA,Correspondence to: Joshua J. Meeks, Chicago, IL, USA. E-mail:
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14
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Yeou S, Hwang J, Yi J, Kim C, Kim SK, Lee NK. Cytosine methylation regulates DNA bendability depending on the curvature. Chem Sci 2022; 13:7516-7525. [PMID: 35872822 PMCID: PMC9242020 DOI: 10.1039/d1sc07115g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 06/01/2022] [Indexed: 11/21/2022] Open
Abstract
Cytosine methylation plays an essential role in many biological processes, such as nucleosome inactivation and regulation of gene expression. The modulation of DNA mechanics may be one of the regulatory mechanisms influenced by cytosine methylation. However, it remains unclear how methylation influences DNA mechanics. Here, we show that methylation has contrasting effects on the bending property of dsDNA depending on DNA curvature. We directly applied bending force on 30 base pairs of dsDNA using a D-shaped DNA nanostructure and measured the degree of bending using single-molecule fluorescence resonance energy transfer without surface immobilization. When dsDNA is weakly bent, methylation increases the stiffness of dsDNA. The stiffness of dsDNA increased by approximately 8% with a single methylation site for 30 bp dsDNA. When dsDNA is highly bent by a strong force, it forms a kink, i.e., a sharp bending of dsDNA. Under strong bending, methylation destabilizes the non-kink form compared with the kink form, which makes dsDNA near the kink region apparently more bendable. However, if the kink region is methylated, the kink form is destabilized, and dsDNA becomes stiffer. As a result, methylation increases the stiffness of weakly bent dsDNA and concurrently can promote kink formation, which may stabilize the nucleosome structure. Our results provide new insight into the effect of methylation, showing that cytosine methylation has opposite effects on DNA mechanics depending on its curvature and methylation location.
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Affiliation(s)
- Sanghun Yeou
- Department of Chemistry, Seoul National University 08832 Seoul Republic of Korea
| | - Jihee Hwang
- Department of Chemistry, Seoul National University 08832 Seoul Republic of Korea
| | - Jaehun Yi
- Department of Chemistry, Seoul National University 08832 Seoul Republic of Korea
| | - Cheolhee Kim
- National Science Museum Daejeon 34143 Republic of Korea
| | - Seong Keun Kim
- Department of Chemistry, Seoul National University 08832 Seoul Republic of Korea
| | - Nam Ki Lee
- Department of Chemistry, Seoul National University 08832 Seoul Republic of Korea
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15
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Li S, Peng Y, Landsman D, Panchenko AR. DNA methylation cues in nucleosome geometry, stability and unwrapping. Nucleic Acids Res 2022; 50:1864-1874. [PMID: 35166834 DOI: 10.1093/nar/gkac097] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 01/29/2022] [Accepted: 02/01/2022] [Indexed: 01/04/2023] Open
Abstract
Cytosine methylation at the 5-carbon position is an essential DNA epigenetic mark in many eukaryotic organisms. Although countless structural and functional studies of cytosine methylation have been reported, our understanding of how it influences the nucleosome assembly, structure, and dynamics remains obscure. Here, we investigate the effects of cytosine methylation at CpG sites on nucleosome dynamics and stability. By applying long molecular dynamics simulations on several microsecond time scale, we generate extensive atomistic conformational ensembles of full nucleosomes. Our results reveal that methylation induces pronounced changes in geometry for both linker and nucleosomal DNA, leading to a more curved, under-twisted DNA, narrowing the adjacent minor grooves, and shifting the population equilibrium of sugar-phosphate backbone geometry. These DNA conformational changes are associated with a considerable enhancement of interactions between methylated DNA and the histone octamer, doubling the number of contacts at some key arginines. H2A and H3 tails play important roles in these interactions, especially for DNA methylated nucleosomes. This, in turn, prevents a spontaneous DNA unwrapping of 3-4 helical turns for the methylated nucleosome with truncated histone tails, otherwise observed in the unmethylated system on several microseconds time scale.
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Affiliation(s)
- Shuxiang Li
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, ON, Canada
| | - Yunhui Peng
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
| | - David Landsman
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
| | - Anna R Panchenko
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, ON, Canada
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16
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Ho L, Hossen N, Nguyen T, Vo A, Ahsan F. Epigenetic Mechanisms as Emerging Therapeutic Targets and Microfluidic Chips Application in Pulmonary Arterial Hypertension. Biomedicines 2022; 10:biomedicines10010170. [PMID: 35052850 PMCID: PMC8773438 DOI: 10.3390/biomedicines10010170] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/09/2022] [Accepted: 01/11/2022] [Indexed: 12/15/2022] Open
Abstract
Pulmonary arterial hypertension (PAH) is a disease that progress over time and is defined as an increase in pulmonary arterial pressure and pulmonary vascular resistance that frequently leads to right-ventricular (RV) failure and death. Epigenetic modifications comprising DNA methylation, histone remodeling, and noncoding RNAs (ncRNAs) have been established to govern chromatin structure and transcriptional responses in various cell types during disease development. However, dysregulation of these epigenetic mechanisms has not yet been explored in detail in the pathology of pulmonary arterial hypertension and its progression with vascular remodeling and right-heart failure (RHF). Targeting epigenetic regulators including histone methylation, acetylation, or miRNAs offers many possible candidates for drug discovery and will no doubt be a tempting area to explore for PAH therapies. This review focuses on studies in epigenetic mechanisms including the writers, the readers, and the erasers of epigenetic marks and targeting epigenetic regulators or modifiers for treatment of PAH and its complications described as RHF. Data analyses from experimental cell models and animal induced PAH models have demonstrated that significant changes in the expression levels of multiple epigenetics modifiers such as HDMs, HDACs, sirtuins (Sirt1 and Sirt3), and BRD4 correlate strongly with proliferation, apoptosis, inflammation, and fibrosis linked to the pathological vascular remodeling during PAH development. The reversible characteristics of protein methylation and acetylation can be applied for exploring small-molecule modulators such as valproic acid (HDAC inhibitor) or resveratrol (Sirt1 activator) in different preclinical models for treatment of diseases including PAH and RHF. This review also presents to the readers the application of microfluidic devices to study sex differences in PAH pathophysiology, as well as for epigenetic analysis.
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Affiliation(s)
- Linh Ho
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, California Northstate University, Elk Grove, CA 95757, USA; (N.H.); (T.N.)
- Correspondence: (L.H.); (F.A.); Tel.: +1-916-686-7370 (L.H.); +1-916-686-3529 (F.A.)
| | - Nazir Hossen
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, California Northstate University, Elk Grove, CA 95757, USA; (N.H.); (T.N.)
| | - Trieu Nguyen
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, California Northstate University, Elk Grove, CA 95757, USA; (N.H.); (T.N.)
- East Bay Institute for Research & Education (EBIRE), Mather, CA 95655, USA
| | - Au Vo
- Department of Life Sciences, University of California Los Angeles, Los Angeles, CA 90095, USA;
| | - Fakhrul Ahsan
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, California Northstate University, Elk Grove, CA 95757, USA; (N.H.); (T.N.)
- Correspondence: (L.H.); (F.A.); Tel.: +1-916-686-7370 (L.H.); +1-916-686-3529 (F.A.)
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17
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Abhange K, Makler A, Wen Y, Ramnauth N, Mao W, Asghar W, Wan Y. Small extracellular vesicles in cancer. Bioact Mater 2021; 6:3705-3743. [PMID: 33898874 PMCID: PMC8056276 DOI: 10.1016/j.bioactmat.2021.03.015] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 02/07/2023] Open
Abstract
Extracellular vesicles (EV) are lipid-bilayer enclosed vesicles in submicron size that are released from cells. A variety of molecules, including proteins, DNA fragments, RNAs, lipids, and metabolites can be selectively encapsulated into EVs and delivered to nearby and distant recipient cells. In tumors, through such intercellular communication, EVs can regulate initiation, growth, metastasis and invasion of tumors. Recent studies have found that EVs exhibit specific expression patterns which mimic the parental cell, providing a fingerprint for early cancer diagnosis and prognosis as well as monitoring responses to treatment. Accordingly, various EV isolation and detection technologies have been developed for research and diagnostic purposes. Moreover, natural and engineered EVs have also been used as drug delivery nanocarriers, cancer vaccines, cell surface modulators, therapeutic agents and therapeutic targets. Overall, EVs are under intense investigation as they hold promise for pathophysiological and translational discoveries. This comprehensive review examines the latest EV research trends over the last five years, encompassing their roles in cancer pathophysiology, diagnostics and therapeutics. This review aims to examine the full spectrum of tumor-EV studies and provide a comprehensive foundation to enhance the field. The topics which are discussed and scrutinized in this review encompass isolation techniques and how these issues need to be overcome for EV-based diagnostics, EVs and their roles in cancer biology, biomarkers for diagnosis and monitoring, EVs as vaccines, therapeutic targets, and EVs as drug delivery systems. We will also examine the challenges involved in EV research and promote a framework for catalyzing scientific discovery and innovation for tumor-EV-focused research.
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Affiliation(s)
- Komal Abhange
- The Pq Laboratory of Micro/Nano BiomeDx, Department of Biomedical Engineering, Binghamton University-SUNY, Binghamton, NY 13902, USA
| | - Amy Makler
- Micro and Nanotechnology in Medicine, Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Yi Wen
- The Pq Laboratory of Micro/Nano BiomeDx, Department of Biomedical Engineering, Binghamton University-SUNY, Binghamton, NY 13902, USA
| | - Natasha Ramnauth
- Micro and Nanotechnology in Medicine, Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Wenjun Mao
- Department of Cardiothoracic Surgery, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
| | - Waseem Asghar
- Micro and Nanotechnology in Medicine, Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Yuan Wan
- The Pq Laboratory of Micro/Nano BiomeDx, Department of Biomedical Engineering, Binghamton University-SUNY, Binghamton, NY 13902, USA
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18
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Toniyan KA, Povorova VV, Gorbacheva EY, Boyarintsev VV, Ogneva IV. Organization of the Cytoskeleton in Ectopic Foci of the Endometrium with Rare Localization. Biomedicines 2021; 9:biomedicines9080998. [PMID: 34440202 PMCID: PMC8394853 DOI: 10.3390/biomedicines9080998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 08/10/2021] [Indexed: 11/16/2022] Open
Abstract
(1) Background: Endometriosis is a common pathology of the female reproductive system, often accompanied by pain and decreased fertility. However, its pathogenesis has not been sufficiently studied regarding the role of the cytoskeleton. In this study, we describe two clinical cases involving rare localization of extragenital endometriosis (umbilicus) and compare them with genital endometriosis of different localization (ovaries and uterus), as well as eutopic endometrium obtained with separate diagnostic curettage without confirmed pathology. (2) Methods: The relative content of actin and tubulin cytoskeleton proteins was determined by Western blotting, and the expression of genes encoding these proteins was determined by RT-PCR in the obtained intraoperative biopsies. The content of 5hmC was estimated by dot blot experiments, and the methylase/demethylase and acetylase/deacetylase contents were determined. (3) Results: The obtained results indicate that the content of the actin-binding protein alpha-actinin1 significantly increased (p < 0.05) in the groups with endometriosis, and this increase was most pronounced in patients with umbilical endometriosis. In addition, both the mRNA content of the ACTN1 gene and 5hmC content increased. It can be assumed that the increase in 5hmC is associated with a decrease in the TET3 demethylase content. Moreover, in the groups with extragenital endometriosis, alpha- and beta-tubulin content was decreased (p < 0.05) compared to the control levels. (4) Conclusions: In analyzing the results, further distance of ectopic endometrial foci from the eutopic localization may be associated with an increase in the content of alpha-actinin1, probably due to an increase in the expression of its gene and an increase in migration potential. In this case, a favorable prognosis can be explained by a decrease in tubulin content and, consequently, a decrease in the rate of cell division.
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Affiliation(s)
- Konstantin A. Toniyan
- Gynecology Department, FGBU KB1 (Volynskaya) UDP RF, 121352 Moscow, Russia; (K.A.T.); (V.V.P.); (E.Y.G.)
- Cell Biophysics Laboratory, SSC RF-IBMP RAS, 123007 Moscow, Russia
| | - Victoria V. Povorova
- Gynecology Department, FGBU KB1 (Volynskaya) UDP RF, 121352 Moscow, Russia; (K.A.T.); (V.V.P.); (E.Y.G.)
| | - Elena Yu. Gorbacheva
- Gynecology Department, FGBU KB1 (Volynskaya) UDP RF, 121352 Moscow, Russia; (K.A.T.); (V.V.P.); (E.Y.G.)
| | - Valery V. Boyarintsev
- Emergency and Extreme Medicine Department, FGBU DPO CGMA UDP RF, 121359 Moscow, Russia;
| | - Irina V. Ogneva
- Cell Biophysics Laboratory, SSC RF-IBMP RAS, 123007 Moscow, Russia
- Medical and Biological Physics Department, I. M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
- Correspondence:
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19
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Pappalardo XG, Barra V. Losing DNA methylation at repetitive elements and breaking bad. Epigenetics Chromatin 2021; 14:25. [PMID: 34082816 PMCID: PMC8173753 DOI: 10.1186/s13072-021-00400-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 05/21/2021] [Indexed: 02/08/2023] Open
Abstract
Background DNA methylation is an epigenetic chromatin mark that allows heterochromatin formation and gene silencing. It has a fundamental role in preserving genome stability (including chromosome stability) by controlling both gene expression and chromatin structure. Therefore, the onset of an incorrect pattern of DNA methylation is potentially dangerous for the cells. This is particularly important with respect to repetitive elements, which constitute the third of the human genome. Main body Repetitive sequences are involved in several cell processes, however, due to their intrinsic nature, they can be a source of genome instability. Thus, most repetitive elements are usually methylated to maintain a heterochromatic, repressed state. Notably, there is increasing evidence showing that repetitive elements (satellites, long interspersed nuclear elements (LINEs), Alus) are frequently hypomethylated in various of human pathologies, from cancer to psychiatric disorders. Repetitive sequences’ hypomethylation correlates with chromatin relaxation and unscheduled transcription. If these alterations are directly involved in human diseases aetiology and how, is still under investigation. Conclusions Hypomethylation of different families of repetitive sequences is recurrent in many different human diseases, suggesting that the methylation status of these elements can be involved in preservation of human health. This provides a promising point of view towards the research of therapeutic strategies focused on specifically tuning DNA methylation of DNA repeats.
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Affiliation(s)
- Xena Giada Pappalardo
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, 95125, Catania, Italy.,National Council of Research, Institute for Biomedical Research and Innovation (IRIB), Unit of Catania, 95125, Catania, Italy
| | - Viviana Barra
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128, Palermo, Italy.
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20
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Wang B, Chen Y, Zhang X, Jiang Z, Wang Y, Chen K, Wang F, Weng X, Zhou X. A far-red emissive two-photon fluorescent probe for quantification of uracil in genomic DNA. Chem Commun (Camb) 2021; 57:2784-2787. [PMID: 33599665 DOI: 10.1039/d1cc00016k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a new method for dU detection in genomic DNA combined with UNG excision and fluorescent probe labeling. UNG can remove uracil bases to introduce abasic sites, which can react with NRNO to produce intense fluorescence because of the inhibition of the PET effect. It can also cause the polymerase extension to stop to provide details of dU site information.
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Affiliation(s)
- Bingyao Wang
- The Institute of Advanced Studies, College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, China.
| | - Yi Chen
- The Institute of Advanced Studies, College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, China.
| | - Xiong Zhang
- The Institute of Advanced Studies, College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, China.
| | - Zhuoran Jiang
- The Institute of Advanced Studies, College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, China.
| | - Yafen Wang
- The Institute of Advanced Studies, College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, China.
| | - Kun Chen
- The Institute of Advanced Studies, College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, China.
| | - Fang Wang
- Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China
| | - Xiaocheng Weng
- The Institute of Advanced Studies, College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, China.
| | - Xiang Zhou
- The Institute of Advanced Studies, College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei 430072, China.
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21
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Proctor NK, Ertan-Bolelli T, Bolelli K, Taylor EW, Chiu NHL, Bowen JP. Towards a Better Understanding of Computational Models for Predicting DNA Methylation Effects at the Molecular Level. Curr Top Med Chem 2021; 20:901-909. [PMID: 32101127 DOI: 10.2174/1568026620666200226110019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 12/24/2019] [Accepted: 12/24/2019] [Indexed: 11/22/2022]
Abstract
Human DNA is a very sensitive macromolecule and slight changes in the structure of DNA can have disastrous effects on the organism. When nucleotides are modified, or changed, the resulting DNA sequence can lose its information, if it is part of a gene, or it can become a problem for replication and repair. Human cells can regulate themselves by using a process known as DNA methylation. This methylation is vitally important in cell differentiation and expression of genes. When the methylation is uncontrolled, however, or does not occur in the right place, serious pathophysiological consequences may result. Excess methylation causes changes in the conformation of the DNA double helix. The secondary structure of DNA is highly dependent upon the sequence. Therefore, if the sequence changes slightly the secondary structure can change as well. These slight changes will then cause the doublestranded DNA to be more open and available in some places where large adductions can come in and react with the DNA base pairs. Computer models have been used to simulate a variety of biological processes including protein function and binding, and there is a growing body of evidence that in silico methods can shed light on DNA methylation. Understanding the anomeric effect that contributes to the structural and conformational flexibility of furanose rings through a combination of quantum mechanical and experimental studies is critical for successful molecular dynamic simulations.
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Affiliation(s)
- Nathanael K Proctor
- Department of Chemistry & Biochemistry, University of North Carolina Greensboro, Greensboro, NC 27402, United States
| | - Tugba Ertan-Bolelli
- Department of Pharmaceutical Sciences, College of Pharmacy, Mercer University, Atlanta, GA 30341, United States.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ankara University, Ankara, TR 06560, Turkey
| | - Kayhan Bolelli
- Department of Pharmaceutical Sciences, College of Pharmacy, Mercer University, Atlanta, GA 30341, United States.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ankara University, Ankara, TR 06560, Turkey.,LumiLabs LLC, Ulus, Ankara, TR 06050, Turkey
| | - Ethan W Taylor
- Department of Chemistry & Biochemistry, University of North Carolina Greensboro, Greensboro, NC 27402, United States
| | - Norman H L Chiu
- Department of Chemistry & Biochemistry, University of North Carolina Greensboro, Greensboro, NC 27402, United States
| | - J Phillip Bowen
- Department of Pharmaceutical Sciences, College of Pharmacy, Mercer University, Atlanta, GA 30341, United States
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22
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Han Y, Li X, Zhang M, Yang Y, Ge G, Wang K, Gong Y, Liang Y, Niu H, Ci W. Enhanced Detection of Genitourinary Cancers Using Fragmentation and Copy Number Profiles Obtained from Urinary Cell-Free DNA. Clin Chem 2020; 67:394-403. [PMID: 33523215 DOI: 10.1093/clinchem/hvaa283] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/23/2020] [Indexed: 12/30/2022]
Abstract
BACKGROUND Recent studies have reported that examining the fragmentation profiles (FP) of plasma cell-free DNA (cfDNA) further improves the clinical sensitivity of tumor detection. We hypothesized that considering the differences of the FP of urinary cfDNA would increase the clinical sensitivity of genitourinary (GU) cancer detection. METHODS 177 patients with GU cancer and 94 individuals without tumors were enrolled in the discovery cohort. An independent validation dataset comprising 30 patients without tumors and 66 patients with GU cancer was also collected. We constructed an ensemble classifier, GUIDER, to detect and localize GU cancers using fragmentation and copy number profiles obtained from shallow whole-genome sequencing of urinary cfDNA. RESULTS Urinary cfDNA of patients with GU cancer had a higher proportion of long fragments (209-280 bp) and a lower proportion of short fragments (140-208 bp) compared to controls. The overall mean classification accuracy of the FP was 74.62%-85.39% for different algorithms, and integration of the FP and copy number alteration (CNA) features further enhanced the classification of samples from patients with GU cancer. The mean diagnostic accuracy was further improved by the ensemble classifier GUIDER, which integrated the FP and CNA profiles and resulted in a higher mean accuracy (87.52%) compared to the analysis performed without FP features (74.62%). GUIDER performed well in an independent validation dataset. CONCLUSIONS The lengthening and shortening of urinary cfDNA within specific size ranges were identified in patients with GU cancer. Integration of the FP should further enhance the ability to use urinary cfDNA as a molecular diagnostic tool.
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Affiliation(s)
- Yang Han
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing China.,China National Center for Bioinformation, Beijing China.,University of the Chinese Academy of Sciences, Beijing China
| | - Xinxin Li
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing China.,China National Center for Bioinformation, Beijing China
| | - Mingxin Zhang
- Department of Urology, the Affiliated Hospital of Qingdao University, Qingdao China
| | - Yang Yang
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing China.,China National Center for Bioinformation, Beijing China.,University of the Chinese Academy of Sciences, Beijing China
| | - Guangzhe Ge
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing China.,China National Center for Bioinformation, Beijing China
| | - Kunxiang Wang
- Department of Urology, the Affiliated Hospital of Qingdao University, Qingdao China
| | - Yanqing Gong
- Department of Urology, Peking University First Hospital, Beijing China.,Institute of Urology, Peking University, Beijing China.,National Urological Cancer Center, Beijing China
| | - Yuan Liang
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing China.,China National Center for Bioinformation, Beijing China
| | - Haitao Niu
- Department of Urology, the Affiliated Hospital of Qingdao University, Qingdao China
| | - Weimin Ci
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing China.,China National Center for Bioinformation, Beijing China.,University of the Chinese Academy of Sciences, Beijing China.,Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing China
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23
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Sina AAI, Lin TY, Vaidyanathan R, Wang Z, Dey S, Wang J, Behren A, Wuethrich A, Carrascosa LG, Trau M. Methylation dependent gold adsorption behaviour identifies cancer derived extracellular vesicular DNA. NANOSCALE HORIZONS 2020; 5:1317-1323. [PMID: 32530449 DOI: 10.1039/d0nh00258e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Extracellular vesicles (EV) play a major role in intercellular communication by transmitting cellular materials (e.g. protein, RNA) among distant cells. Recent evidence suggests that they could also contribute to carrying DNA which could inform on the mutational status of the parent tumour DNA. Thus, the fundamental analysis of evDNA could open a better understanding of tumour metastasis and provide new pathways for noninvasive detection and monitoring of cancer. To explore the potential of evDNA for diagnostics, the isolation of pure evDNA from body fluids free of cfDNA contamination is crucial. Herein, we use a liposome based model system to develop an improved evDNA isolation protocol free from cfDNA contamination and evaluate the methylation dependent physicochemical properties of evDNA to develop a simple test for detecting cancer evDNA. Using a highly sensitive multiplex microelectrode device, we demonstrate that serum-evDNA derived from cancer patients show different solution and surface based properties than normal evDNA due to their different methylation landscape (i.e. methylscape). This microdevice allows simultaneous analysis of multiple samples in a single platform from as low as 500 pg μL-1 of evDNA.
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Affiliation(s)
- Abu Ali Ibn Sina
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia.
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24
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Khezri A, Narud B, Stenseth EB, Zeremichael TT, Myromslien FD, Wilson RC, Ahmad R, Kommisrud E. Sperm DNA Hypomethylation Proximal to Reproduction Pathway Genes in Maturing Elite Norwegian Red Bulls. Front Genet 2020; 11:922. [PMID: 32849856 PMCID: PMC7431628 DOI: 10.3389/fgene.2020.00922] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/24/2020] [Indexed: 01/08/2023] Open
Abstract
Genomic selection in modern farming demands sufficient semen production in young bulls. Factors affecting semen quality and production capacity in young bulls are not well understood; DNA methylation, a complicated phenomenon in sperm cells, is one such factors. In this study, fresh and frozen-thawed semen samples from the same Norwegian Red (NR) bulls at both 14 and 17 months of age were examined for sperm chromatin integrity parameters, ATP content, viability, and motility. Furthermore, reduced representation bisulfite libraries constructed according to two protocols, the Ovation® RRBS Methyl-Seq System (Ovation method) and a previously optimized gel-free method and were sequenced to study the sperm DNA methylome in frozen-thawed semen samples. Sperm quality analyses indicated that sperm concentration, total motility and progressivity in fresh semen from 17 months old NR bulls were significantly higher compared to individuals at 14 months of age. The percentage of DNA fragmented sperm cells significantly decreased in both fresh and frozen-thawed semen samples in bulls with increasing age. Libraries from the Ovation method exhibited a greater percentage of read loss and shorter read size following trimming. Downstream analyses for reads obtained from the gel-free method revealed similar global sperm DNA methylation but differentially methylated regions (DMRs) between 14- and 17 months old NR bulls. The majority of identified DMRs were hypomethylated in 14 months old bulls. Most of the identified DMRs (69%) exhibited a less than 10% methylation difference while only 1.5% of DMRs exceeded a 25% methylation difference. Pathway analysis showed that genes annotated with DMRs having low methylation differences (less than 10%) and DMRs having between 10 and 25% methylation differences, could be associated with important hormonal signaling and sperm function relevant pathways, respectively. The current research shows that RRBS in parallel with routine sperm quality analyses could be informative in reproductive capacity of young NR bulls. Although global sperm DNA methylation levels in 14 and 17 months old NR bulls were similar, regions with low and varying levels of DNA methylation differences can be identified and linked with important sperm function and hormonal pathways.
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Affiliation(s)
- Abdolrahman Khezri
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Birgitte Narud
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Else-Berit Stenseth
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | | | | | - Robert C Wilson
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Rafi Ahmad
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Elisabeth Kommisrud
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
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25
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Shinjo K, Hara K, Nagae G, Umeda T, Katsushima K, Suzuki M, Murofushi Y, Umezu Y, Takeuchi I, Takahashi S, Okuno Y, Matsuo K, Ito H, Tajima S, Aburatani H, Yamao K, Kondo Y. A novel sensitive detection method for DNA methylation in circulating free DNA of pancreatic cancer. PLoS One 2020; 15:e0233782. [PMID: 32520974 PMCID: PMC7286528 DOI: 10.1371/journal.pone.0233782] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/12/2020] [Indexed: 12/26/2022] Open
Abstract
Despite recent advances in clinical treatment, pancreatic cancer remains a highly lethal malignancy. In order to improve the survival rate of patients with pancreatic cancer, the development of non-invasive diagnostic methods using effective biomarkers is urgently needed. Here, we developed a highly sensitive method to detect DNA methylation in cell-free (cf)DNA samples based on the enrichment of methyl-CpG binding (MBD) protein coupled with a digital PCR method (MBD–ddPCR). Five DNA methylation markers for the diagnosis of pancreatic cancer were identified through DNA methylation microarray analysis in 37 pancreatic cancers. The sensitivity and specificity of the five markers were validated in another independent cohort of pancreatic cancers (100% and 100%, respectively; n = 46) as well as in The Cancer Genome Atlas data set (96% and 90%, respectively; n = 137). MBD–ddPCR analysis revealed that DNA methylation in at least one of the five markers was detected in 23 (49%) samples of cfDNA from 47 patients with pancreatic cancer. Further, a combination of DNA methylation markers and the KRAS mutation status improved the diagnostic capability of this method (sensitivity and specificity, 68% and 86%, respectively). Genome-wide MBD-sequencing analysis in cancer tissues and corresponding cfDNA revealed that more than 80% of methylated regions were overlapping; DNA methylation profiles of cancerous tissues and cfDNA significantly correlated with each other (R = 0.97). Our data indicate that newly developed MBD–ddPCR is a sensitive method to detect cfDNA methylation and that using five marker genes plus KRAS mutations may be useful for the detection of pancreatic cancers.
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Affiliation(s)
- Keiko Shinjo
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazuo Hara
- Department of Gastroenterology, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Genta Nagae
- Genome Science Laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Takayoshi Umeda
- Genome Science Laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Keisuke Katsushima
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Miho Suzuki
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshiteru Murofushi
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuta Umezu
- Department of Computer Science, Nagoya Institute of Technology, Nagoya, Japan.,School of Information and Data Sciences, Nagasaki University, Nagasaki, Japan
| | - Ichiro Takeuchi
- Department of Computer Science, Nagoya Institute of Technology, Nagoya, Japan.,RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | - Satoru Takahashi
- Department of Experimental Pathology and Tumor Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Yusuke Okuno
- Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya, Japan
| | - Keitaro Matsuo
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan.,Department of Cancer Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hidemi Ito
- Division of Cancer Information and Control, Aichi Cancer Center Research Institute, Nagoya, Japan.,Department of Descriptive Cancer Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shoji Tajima
- Laboratory of Epigenetics, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Hiroyuki Aburatani
- Genome Science Laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Kenji Yamao
- Department of Gastroenterology, Aichi Cancer Center Hospital, Nagoya, Japan.,Department of Gastroenterology, Narita Memorial Hospital, Toyohashi, Japan
| | - Yutaka Kondo
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
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26
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Abramov G, Velyvis A, Rennella E, Wong LE, Kay LE. A methyl-TROSY approach for NMR studies of high-molecular-weight DNA with application to the nucleosome core particle. Proc Natl Acad Sci U S A 2020; 117:12836-12846. [PMID: 32457157 PMCID: PMC7293644 DOI: 10.1073/pnas.2004317117] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The development of methyl-transverse relaxation-optimized spectroscopy (methyl-TROSY)-based NMR methods, in concert with robust strategies for incorporation of methyl-group probes of structure and dynamics into the protein of interest, has facilitated quantitative studies of high-molecular-weight protein complexes. Here we develop a one-pot in vitro reaction for producing NMR quantities of methyl-labeled DNA at the C5 and N6 positions of cytosine (5mC) and adenine (6mA) nucleobases, respectively, enabling the study of high-molecular-weight DNA molecules using TROSY approaches originally developed for protein applications. Our biosynthetic strategy exploits the large number of naturally available methyltransferases to specifically methylate DNA at a desired number of sites that serve as probes of structure and dynamics. We illustrate the methodology with studies of the 153-base pair Widom DNA molecule that is simultaneously methyl-labeled at five sites, showing that high-quality 13C-1H spectra can be recorded on 100 μM samples in a few minutes. NMR spin relaxation studies of labeled methyl groups in both DNA and the H2B histone protein component of the 200-kDa nucleosome core particle (NCP) establish that methyl groups at 5mC and 6mA positions are, in general, more rigid than Ile, Leu, and Val methyl probes in protein side chains. Studies focusing on histone H2B of NCPs wrapped with either wild-type DNA or DNA methylated at all 26 CpG sites highlight the utility of NMR in investigating the structural dynamics of the NCP and how its histone core is affected through DNA methylation, an important regulator of transcription.
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Affiliation(s)
- Gili Abramov
- Department of Molecular Genetics, The University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Biochemistry, The University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Chemistry, The University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Algirdas Velyvis
- Department of Molecular Genetics, The University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Biochemistry, The University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Chemistry, The University of Toronto, Toronto, ON M5S 1A8, Canada
- Bioscience Department, Syngenta, Jealott's Hill Research Centre, Bracknell RG42 6EY, United Kingdom
| | - Enrico Rennella
- Department of Molecular Genetics, The University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Biochemistry, The University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Chemistry, The University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Leo E Wong
- Department of Molecular Genetics, The University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Biochemistry, The University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Chemistry, The University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Lewis E Kay
- Department of Molecular Genetics, The University of Toronto, Toronto, ON M5S 1A8, Canada;
- Department of Biochemistry, The University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Chemistry, The University of Toronto, Toronto, ON M5S 1A8, Canada
- Program in Molecular Medicine, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
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27
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Yang YJ, Dong HL, Qiang XW, Fu H, Zhou EC, Zhang C, Yin L, Chen XF, Jia FC, Dai L, Tan ZJ, Zhang XH. Cytosine Methylation Enhances DNA Condensation Revealed by Equilibrium Measurements Using Magnetic Tweezers. J Am Chem Soc 2020; 142:9203-9209. [DOI: 10.1021/jacs.9b11957] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Ya-Jun Yang
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Hai-Long Dong
- Department of Physics and Key Laboratory of Artificial Micro & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Xiao-Wei Qiang
- Department of Physics and Key Laboratory of Artificial Micro & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Hang Fu
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Er-Chi Zhou
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Chen Zhang
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Lei Yin
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Xue-Feng Chen
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Fu-Chao Jia
- Laboratory of Functional Molecules and Materials, School of Physics and Optoelectronic Engineering, Shandong University of Technology, Zibo 255000, China
| | - Liang Dai
- Department of Physics, City University of Hong Kong, Hong Kong 999077, China
| | - Zhi-Jie Tan
- Department of Physics and Key Laboratory of Artificial Micro & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Xing-Hua Zhang
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
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28
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Bassiri F, Tavalaee M, Dattilio M, Nasr-Esfahani MH. Micronutrients in Support to The Carbon Cycle Activate Antioxidant Defences and Reduce Sperm DNA Damage in Infertile Men Attending Assisted Reproductive Technology Programs: Clinical Trial Study. INTERNATIONAL JOURNAL OF FERTILITY & STERILITY 2020; 14:57-62. [PMID: 32112637 PMCID: PMC7139231 DOI: 10.22074/ijfs.2020.6084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 07/01/2019] [Indexed: 11/04/2022]
Abstract
Background Micronutrients in support to the carbon cycle were shown to reduce sperm DNA damage both in animal
models and infertile men. Besides supporting DNA methylation, their positive effect may be mediated by an improved
performance of the endogenous antioxidant system but this has not yet been proven in clinical settings. The present
study aimed at evaluating the effects of micronutrient supplementation in infertile male partners of assisted reproductive technology (ART) resistant couples. Materials and Methods In this experimental clinical trial study, infertile male partners of couples resistant to at least
one ART cycle, with a sperm fragmentation rate >20% (TUNEL), underwent a 4-month oral supplementation with
micronutrients in support to the carbon cycle including folates, B vitamins, zinc and cysteines. Semen, sperm DNA
fragmentation (TUNEL), nuclear maturation (CMA3 and blue aniline staining) and lipid peroxidation (BODIPY) were
assessed before and after treatment. The couples were followed-up to record clinical outcomes. Results Forty-three patients completed the program but full data of pre- and post-treatment were available only
for 25 patients. The treatment did not modify sperm concentration or motility but improved morphology. Nuclear
maturation, DNA fragmentation and lipid peroxidation significantly improved after the treatment. Overall, 10 clinical
pregnancies (23.3%) and 4 live births (9.3%) were recorded during the follow-up following expectant management
(25 couples) or a new intracytoplasmic sperm injection (ICSI) cycle (18 couples). Conclusion The micronutrients appeared to induce both DNA methylation, resulting in improved sperm nuclear matu-
ration, and antioxidant defences, resulting in less DNA fragmentation and lipid peroxidation. The clinical outcomes
were aligned with a possible positive effect on reproductive function. Micronutrients could be regarded as an alternative to antioxidants in correcting oxidative damage in infertile men; however, to confirm such findings, further clinical
investigations are warranted (Registration number: IRCT201510207223N6).
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Affiliation(s)
- Farzaneh Bassiri
- Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Marziyeh Tavalaee
- Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Maurizio Dattilio
- R and D Department, Parthenogen, Piazza Indipendenza 11, Lugano 6900, Switzerland. Electronic Address:
| | - Mohammad Hossein Nasr-Esfahani
- Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran. Electronic Address: .,Isfahan Fertility and Infertility Center, Isfahan, Iran
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29
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Bisserier M, Janostiak R, Lezoualc'h F, Hadri L. Targeting epigenetic mechanisms as an emerging therapeutic strategy in pulmonary hypertension disease. VASCULAR BIOLOGY 2020; 2:R17-R34. [PMID: 32161845 PMCID: PMC7065685 DOI: 10.1530/vb-19-0030] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Pulmonary arterial hypertension (PAH) is a multifactorial cardiopulmonary disease characterized by an elevation of pulmonary artery pressure (PAP) and pulmonary vascular resistance (PVR), which can lead to right ventricular (RV) failure, multi-organ dysfunction, and ultimately to premature death. Despite the advances in molecular biology, the mechanisms underlying pulmonary hypertension (PH) remain unclear. Nowadays, there is no curative treatment for treating PH. Therefore, it is crucial to identify novel, specific therapeutic targets and to offer more effective treatments against the progression of PH. Increasing amounts of evidence suggest that epigenetic modification may play a critical role in the pathogenesis of PAH. In the presented paper, we provide an overview of the epigenetic mechanisms specifically, DNA methylation, histone acetylation, histone methylation, and ncRNAs. As the recent identification of new pharmacological drugs targeting these epigenetic mechanisms has opened new therapeutic avenues, we also discuss the importance of epigenetic-based therapies in the context of PH.
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Affiliation(s)
- Malik Bisserier
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Radoslav Janostiak
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Frank Lezoualc'h
- Inserm, UMR-1048, Institut des Maladies Metaboliques et Cardiovasculaires, University of Toulouse, Toulouse Cedex 4, France
| | - Lahouaria Hadri
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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30
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Lee TH. Physical Chemistry of Epigenetics: Single-Molecule Investigations. J Phys Chem B 2019; 123:8351-8362. [PMID: 31404497 PMCID: PMC6790939 DOI: 10.1021/acs.jpcb.9b06214] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 08/03/2019] [Indexed: 02/06/2023]
Abstract
The nucleosome is the fundamental building block of the eukaryotic genome, composed of an ∼147 base-pair DNA fragment wrapping around an octameric histone protein core. DNA and histone proteins are targets of enzymatic chemical modifications that serve as signals for gene regulation. These modifications are often referred to as epigenetic modifications that govern gene activities without altering the DNA sequence. Although the term epigenetics initially required inheritability, it now frequently includes noninherited histone modifications associated with gene regulation. Important epigenetic modifications for healthy cell growth and proliferation include DNA methylation, histone acetylation, methylation, phosphorylation, ubiquitination, and SUMOylation (SUMO = Small Ubiquitin-like Modifier). Our research focuses on the biophysical roles of these modifications in altering the structure and structural dynamics of the nucleosome and their implications in gene regulation mechanisms. As the changes are subtle and complex, we employ various single-molecule fluorescence approaches for their investigations. Our investigations revealed that these modifications induce changes in the structure and structural dynamics of the nucleosome and their thermodynamic and kinetic stabilities. We also suggested the implications of these changes in gene regulation mechanisms that are the foci of our current and future research.
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Affiliation(s)
- Tae-Hee Lee
- Department of Chemistry, The
Pennsylvania State University, University Park 16803, Pennsylvania, United States
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31
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Laporte M, Le Luyer J, Rougeux C, Dion-Côté AM, Krick M, Bernatchez L. DNA methylation reprogramming, TE derepression, and postzygotic isolation of nascent animal species. SCIENCE ADVANCES 2019; 5:eaaw1644. [PMID: 31663013 PMCID: PMC6795504 DOI: 10.1126/sciadv.aaw1644] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 09/19/2019] [Indexed: 05/05/2023]
Abstract
The genomic shock hypothesis stipulates that the stress associated with divergent genome admixture can cause transposable element (TE) derepression, which could act as a postzygotic isolation mechanism. TEs affect gene structure, expression patterns, and chromosome organization and may have deleterious consequences when released. For these reasons, they are silenced by heterochromatin formation, which includes DNA methylation. Here, we show that a significant proportion of TEs are differentially methylated between the "dwarf" (limnetic) and the "normal" (benthic) whitefish, two nascent species that diverged some 15,000 generations ago within the Coregonus clupeaformis species complex. Moreover, TEs are overrepresented among loci that were demethylated in hybrids, indicative of their transcriptional derepression. These results are consistent with earlier studies in this system that revealed TE transcriptional derepression causes abnormal embryonic development and death of hybrids. Hence, this supports a role of DNA methylation reprogramming and TE derepression in postzygotic isolation of nascent animal species.
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32
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Teng X, Hwang W. Effect of Methylation on Local Mechanics and Hydration Structure of DNA. Biophys J 2019; 114:1791-1803. [PMID: 29694859 DOI: 10.1016/j.bpj.2018.03.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 03/03/2018] [Accepted: 03/14/2018] [Indexed: 12/31/2022] Open
Abstract
Cytosine methylation affects mechanical properties of DNA and potentially alters the hydration fingerprint for recognition by proteins. The atomistic origin for these effects is not well understood, and we address this via all-atom molecular dynamics simulations. We find that the stiffness of the methylated dinucleotide step changes marginally, whereas the neighboring steps become stiffer. Stiffening is further enhanced for consecutively methylated steps, providing a mechanistic origin for the effect of hypermethylation. Steric interactions between the added methyl groups and the nonpolar groups of the neighboring nucleotides are responsible for the stiffening in most cases. By constructing hydration maps, we found that methylation also alters the surface hydration structure in distinct ways. Its resistance to deformation may contribute to the stiffening of DNA for deformational modes lacking steric interactions. These results highlight the sequence- and deformational-mode-dependent effects of cytosine methylation.
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Affiliation(s)
- Xiaojing Teng
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas
| | - Wonmuk Hwang
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas; Department of Materials Science & Engineering, Texas A&M University, College Station, Texas; School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Korea.
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33
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Lee J, Lee TH. How Protein Binding Sensitizes the Nucleosome to Histone H3K56 Acetylation. ACS Chem Biol 2019; 14:506-515. [PMID: 30768236 DOI: 10.1021/acschembio.9b00018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The nucleosome, the fundamental gene-packing unit comprising an octameric histone protein core wrapped with DNA, has a flexible structure that enables dynamic gene regulation mechanisms. Histone lysine acetylation at H3K56 removes a positive charge from the histone core where it interacts with the termini of the nucleosomal DNA and acts as a critical gene regulatory signal that is implicated in transcription initiation and elongation. The predominant proposal for the biophysical role of H3K56 acetylation (H3K56ac) is that weakened electrostatic interaction between DNA termini and the histone core results in facilitated opening and subsequent disassembly of the nucleosome. However, this effect alone is too weak to account for the strong coupling between H3K56ac and its regulatory outcomes. Here we utilized a semisynthetically modified nucleosome with H3K56ac in order to address this discrepancy. Based on the results, we propose an innovative mechanism by which the charge neutralization effect of H3K56ac is significantly amplified via protein binding. We employed three-color single-molecule fluorescence resonance energy transfer (smFRET) to monitor the opening rate of nucleosomal DNA termini induced by binding of histone chaperone Nap1. We observed an elevated opening rate upon H3K56ac by 5.9-fold, which is far larger than the 1.5-fold previously reported for the spontaneous opening dynamics in the absence of Nap1. Our proposed mechanism successfully reconciles this discrepancy because DNA opening for Nap1 binding must be larger than the average spontaneous opening. This is a novel mechanism that can explain how a small biophysical effect of histone acetylation results in a significant change in protein binding rate.
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Affiliation(s)
- Jaehyoun Lee
- Department of Chemistry, the Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Tae-Hee Lee
- Department of Chemistry, the Pennsylvania State University, University Park, Pennsylvania 16802, United States
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34
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Single-molecule FRET method to investigate the dynamics of transcription elongation through the nucleosome by RNA polymerase II. Methods 2019; 159-160:51-58. [PMID: 30660864 DOI: 10.1016/j.ymeth.2019.01.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 01/07/2019] [Accepted: 01/14/2019] [Indexed: 12/27/2022] Open
Abstract
Transcription elongation through the nucleosome is a precisely coordinated activity to ensure timely production of RNA and accurate regulation of co-transcriptional histone modifications. Nucleosomes actively participate in transcription regulation at various levels and impose physical barriers to RNA polymerase II (RNAPII) during transcription elongation. Despite its high significance, the detailed dynamics of how RNAPII translocates along nucleosomal DNA during transcription elongation and how the nucleosome structure dynamically conforms to the changes necessary for RNAPII progression remain poorly understood. Transcription elongation through the nucleosome is a complex process and investigating the changes of the nucleosome structure during this process by ensemble measurements is daunting. This is because it is nearly impossible to synchronize elongation complexes within a nucleosome or a sub-nucleosome to a designated location at a high enough efficiency for desired sample homogeneity. Here we review our recently developed single-molecule FRET experimental system and method that has fulfilled this deficiency. With our method, one can follow the changes in the structure of individual nucleosomes during transcription elongation. We demonstrated that this method enables the detailed measurements of the kinetics of transcription elongation through the nucleosome and its regulation by a transcription factor, which can be easily extended to investigations of the roles of environmental variables and histone post-translational modifications in regulating transcription elongation.
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35
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Karimi MA, Dadmehr M, Hosseini M, Korouzhdehi B, Oroojalian F. Sensitive detection of methylated DNA and methyltransferase activity based on the lighting up of FAM-labeled DNA quenched fluorescence by gold nanoparticles. RSC Adv 2019; 9:12063-12069. [PMID: 35516994 PMCID: PMC9063544 DOI: 10.1039/c9ra01564g] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 04/04/2019] [Indexed: 12/27/2022] Open
Abstract
DNA methylation of cytosine bases, which is catalyzed by methyltransferase enzymes, involve biochemical processes that contribute to gene expression and gene regulation in cells. Detection of abnormal patterns of both methylated DNA and methyltransferase enzyme activity at early stages could be considered as promising targets for early cancer diagnosis. In the present study, a novel and facile method is introduced for the sensitive detection of the M.SssI methyltransferase (M.SssI MTase) enzyme and methylated DNA based on the fluorescence recovery of FAM-labeled DNA coupled with gold nanoparticles (AuNPs). Thiol-modified probes were functionalized with AuNPs, which brought the FAM fluorophore into the close proximity of the AuNPs. This led to the overlap between the FAM fluorescence emission and AuNPs absorption spectra, introducing a FRET occurrence and causing fluorescence quenching. The hybridization of the probe and its complementary target provided specific CpG sites for M.SssI MTase enzyme activity. The methylation process gradually converted the quenched FAM fluorophore into an emissive fluorophore upon the addition of the MTase enzyme, and the observed fluorescence recovery proved the efficiency of the assay for the detection of MTase enzyme. The fluorescence intensity showed an increasing trend with M.SssI MTase enzyme activity in the range of 1–8 U mL−1 with a detection limit of 0.14 U mL−1. The addition of methylated ssDNA targets to a ssDNA FAM-labeled probe resulted in a DNA duplex formation, leading to a strong fluorescence signal emission due to the recovery of the fluorophore signal. Conversely, the unmethylated ssDNA target caused no changes in the fluorescence signal. In the presence of methylated DNA targets, the biosensor could specifically recognize it and accordingly trigger the methylated targets through a fluorescence enhancement in the range of 5–100 pM by monitoring the increase in the fluorescence intensity with a detection limit of 2.2 pM. The obtained results showed that the assay could realize the detection of M.SssI MTase and methylated DNA effectively in diluted human serum samples. Human serum conditions showed no significant interference with the assay performance, indicating that the present method has great potential for further application in real samples. A novel method for detection of DNA methylation based on fluorescence recovery of FAM labeled DNA/Au NPs was introduced.![]()
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Affiliation(s)
| | - Mehdi Dadmehr
- Department of Biology
- Payame Noor University
- Tehran
- Iran
| | - Morteza Hosseini
- Department of Life Science Engineering
- Faculty of New Sciences & Technologies
- University of Tehran
- Tehran
- Iran
| | | | - Fatemeh Oroojalian
- Department of Advanced Sciences and Technologies
- School of Medicine
- North Khorasan University of Medical Sciences
- Bojnurd
- Iran
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36
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Lai W, Mo J, Yin J, Lyu C, Wang H. Profiling of epigenetic DNA modifications by advanced liquid chromatography-mass spectrometry technologies. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2018.10.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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37
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Epigenetically reprogrammed methylation landscape drives the DNA self-assembly and serves as a universal cancer biomarker. Nat Commun 2018; 9:4915. [PMID: 30514834 PMCID: PMC6279781 DOI: 10.1038/s41467-018-07214-w] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 10/21/2018] [Indexed: 02/02/2023] Open
Abstract
Epigenetic reprogramming in cancer genomes creates a distinct methylation landscape encompassing clustered methylation at regulatory regions separated by large intergenic tracks of hypomethylated regions. This methylation landscape that we referred to as Methylscape is displayed by most cancer types, thus may serve as a universal cancer biomarker. To-date most research has focused on the biological consequences of DNA Methylscape changes whereas its impact on DNA physicochemical properties remains unexplored. Herein, we examine the effect of levels and genomic distribution of methylcytosines on the physicochemical properties of DNA to detect the Methylscape biomarker. We find that DNA polymeric behaviour is strongly affected by differential patterning of methylcytosine, leading to fundamental differences in DNA solvation and DNA-gold affinity between cancerous and normal genomes. We exploit these Methylscape differences to develop simple, highly sensitive and selective electrochemical or colorimetric one-step assays for the detection of cancer. These assays are quick, i.e., analysis time ≤10 minutes, and require minimal sample preparation and small DNA input. DNA methylation is an epigenetic modification that control genetic programs. Here, the authors found that the methylation landscape influences the physicochemical properties of DNA and that it can serve as a universal cancer biomarker, and developed a one-step assay for the detection of cancer DNA.
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38
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Han JH, Park S, Hashiya F, Sugiyama H. Approach to the Investigation of Nucleosome Structure by Using the Highly Emissive Nucleobase
th
dG–tC FRET Pair. Chemistry 2018; 24:17091-17095. [DOI: 10.1002/chem.201803382] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/07/2018] [Indexed: 01/27/2023]
Affiliation(s)
- Ji Hoon Han
- Department of ChemistryGraduate School of ScienceKyoto University Kitashirakawa-Oiwakecho Sakyo-ku Kyoto 606–8502 Japan
| | - Soyoung Park
- Department of ChemistryGraduate School of ScienceKyoto University Kitashirakawa-Oiwakecho Sakyo-ku Kyoto 606–8502 Japan
| | - Fumitaka Hashiya
- Department of ChemistryGraduate School of ScienceKyoto University Kitashirakawa-Oiwakecho Sakyo-ku Kyoto 606–8502 Japan
| | - Hiroshi Sugiyama
- Department of ChemistryGraduate School of ScienceKyoto University Kitashirakawa-Oiwakecho Sakyo-ku Kyoto 606–8502 Japan
- Institute for Integrated Cell-Material Sciences (iCeMS)Kyoto University Yoshida-ushinomiyacho Sakyo-ku Kyoto 606–8501 Japan
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39
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Raiber EA, Portella G, Martínez Cuesta S, Hardisty R, Murat P, Li Z, Iurlaro M, Dean W, Spindel J, Beraldi D, Liu Z, Dawson MA, Reik W, Balasubramanian S. 5-Formylcytosine organizes nucleosomes and forms Schiff base interactions with histones in mouse embryonic stem cells. Nat Chem 2018; 10:1258-1266. [PMID: 30349137 DOI: 10.1038/s41557-018-0149-x] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/29/2018] [Indexed: 12/27/2022]
Abstract
Nucleosomes are the basic unit of chromatin that help the packaging of genetic material while controlling access to the genetic information. The underlying DNA sequence, together with transcription-associated proteins and chromatin remodelling complexes, are important factors that influence the organization of nucleosomes. Here, we show that the naturally occurring DNA modification, 5-formylcytosine (5fC) is linked to tissue-specific nucleosome organization. Our study reveals that 5fC is associated with increased nucleosome occupancy in vitro and in vivo. We demonstrate that 5fC-associated nucleosomes at enhancers in the mammalian hindbrain and heart are linked to elevated gene expression. Our study also reveals the formation of a reversible-covalent Schiff base linkage between lysines of histone proteins and 5fC within nucleosomes in a cellular environment. We define their specific genomic loci in mouse embryonic stem cells and look into the biological consequences of these DNA-histone Schiff base sites. Collectively, our findings show that 5fC is a determinant of nucleosome organization and plays a role in establishing distinct regulatory regions that control transcription.
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Affiliation(s)
- Eun-Ang Raiber
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | | | - Sergio Martínez Cuesta
- Department of Chemistry, University of Cambridge, Cambridge, UK.,Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Robyn Hardisty
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Pierre Murat
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Zhe Li
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Mario Iurlaro
- Epigenetics Programme, The Babraham Institute, Cambridge, UK.,Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Wendy Dean
- Epigenetics Programme, The Babraham Institute, Cambridge, UK
| | - Julia Spindel
- Epigenetics Programme, The Babraham Institute, Cambridge, UK
| | - Dario Beraldi
- Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Zheng Liu
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | | | - Wolf Reik
- Epigenetics Programme, The Babraham Institute, Cambridge, UK.,The Wellcome Trust Sanger Institute, Cambridge, UK
| | - Shankar Balasubramanian
- Department of Chemistry, University of Cambridge, Cambridge, UK. .,Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK. .,School of Clinical Medicine, University of Cambridge, Cambridge, UK.
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40
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Sueoka T, Koyama K, Hayashi G, Okamoto A. Chemistry-Driven Epigenetic Investigation of Histone and DNA Modifications. CHEM REC 2018; 18:1727-1744. [PMID: 30070422 DOI: 10.1002/tcr.201800040] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/22/2018] [Indexed: 12/26/2022]
Abstract
In the regulation processes of gene expression, genomic DNA and nuclear proteins, including histone proteins, cooperate with each other, leading to the distinctive functions of eukaryotic cells such as pluripotency and differentiation. Chemical modification of histone proteins and DNA has been revealed as one of the major driving forces in the complicated epigenetic regulation system. However, understanding of the precise molecular mechanisms is still limited. To address this issue, researchers have proposed both biological and chemical strategies for the preparation and detection of modified proteins and nucleic acids. In this review, we focus on chemical methods around the field of epigenetics. Chemical protein synthesis has enabled the preparation of site-specifically modified histones and their successful application to various in vitro assays, which have emphasized the significance of posttranslational modifications of interest. We also review the modification-specific chemical reactions against synthetic and genomic DNA, which enabled discrimination of several modified bases at single-base resolution.
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Affiliation(s)
- Takuma Sueoka
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Kenta Koyama
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Gosuke Hayashi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Akimitsu Okamoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan
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41
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Cheng X, Hou Y, Nie Y, Zhang Y, Huang H, Liu H, Sun X. Nucleosome Positioning of Intronless Genes in the Human Genome. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 15:1111-1121. [PMID: 26415210 DOI: 10.1109/tcbb.2015.2476811] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Nucleosomes, the basic units of chromatin, are involved in transcription regulation and DNA replication. Intronless genes, which constitute 3 percent of the human genome, differ from intron-containing genes in evolution and function. Our analysis reveals that nucleosome positioning shows a distinct pattern in intronless and intron-containing genes. The nucleosome occupancy upstream of transcription start sites of intronless genes is lower than that of intron-containing genes. In contrast, high occupancy and well positioned nucleosomes are observed along the gene body of intronless genes, which is perfectly consistent with the barrier nucleosome model. Intronless genes have a significantly lower expression level than intron-containing genes and most of them are not expressed in CD4+ T cell lines and GM12878 cell lines, which results from their tissue specificity. However, the highly expressed genes are at the same expression level between the two types of genes. The highly expressed intronless genes require a higher density of RNA Pol II in an elongating state to compensate for the lack of introns. Additionally, 5' and 3' nucleosome depleted regions of highly expressed intronless genes are deeper than those of highly expressed intron-containing genes.
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42
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Size-tagged preferred ends in maternal plasma DNA shed light on the production mechanism and show utility in noninvasive prenatal testing. Proc Natl Acad Sci U S A 2018; 115:E5106-E5114. [PMID: 29760053 PMCID: PMC5984542 DOI: 10.1073/pnas.1804134115] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Cell-free DNA molecules in the plasma of pregnant women exhibit nonrandom fragmentation with preferred end sites. We studied if such preferred end sites might bear any relationship with fragment lengths of plasma DNA. Short and long plasma DNA molecules were associated with different preferred DNA end sites. Analysis of size-tagged preferred ends could be used for measuring fetal DNA fraction and for facilitating fetal trisomy 21 detection. Fetal preferred end sites were generally located in the nucleosome cores, while the maternal ones were located in the linker regions. This conceptual framework provides an explanation of the relative shortness of fetal DNA in maternal plasma and brings us closer to understanding the biological mechanisms that influence plasma DNA fragmentation. Cell-free DNA in human plasma is nonrandomly fragmented and reflects genomewide nucleosomal organization. Previous studies had demonstrated tissue-specific preferred end sites in plasma DNA of pregnant women. In this study, we performed integrative analysis of preferred end sites with the size characteristics of plasma DNA fragments. We mined the preferred end sites in short and long plasma DNA molecules separately and found that these “size-tagged” ends showed improved accuracy in fetal DNA fraction estimation and enhanced noninvasive fetal trisomy 21 testing. Further analysis revealed that the fetal and maternal preferred ends were generated from different locations within the nucleosomal structure. Hence, fetal DNA was frequently cut within the nucleosome core while maternal DNA was mostly cut within the linker region. We further demonstrated that the nucleosome accessibility in placental cells was higher than that for white blood cells, which might explain the difference in the cutting positions and the shortness of fetal DNA in maternal plasma. Interestingly, short and long size-tagged ends were also observable in the plasma of nonpregnant healthy subjects and demonstrated size differences similar to those in the pregnant samples. Because the nonpregnant samples did not contain fetal DNA, the data suggested that the interrelationship of preferred DNA ends, chromatin accessibility, and plasma DNA size profile is likely a general one, extending beyond the context of pregnancy. Plasma DNA fragment end patterns have thus shed light on production mechanisms and show utility in future developments in plasma DNA-based noninvasive molecular diagnostics.
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43
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Lövkvist C, Sneppen K, Haerter JO. Exploring the Link between Nucleosome Occupancy and DNA Methylation. Front Genet 2018; 8:232. [PMID: 29379519 PMCID: PMC5771128 DOI: 10.3389/fgene.2017.00232] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/22/2017] [Indexed: 12/21/2022] Open
Abstract
Near promoters, both nucleosomes and CpG sites form characteristic spatial patterns. Previously, nucleosome depleted regions were observed upstream of transcription start sites and nucleosome occupancy was reported to correlate both with CpG density and the level of CpG methylation. Several studies imply a causal link where CpG methylation might induce nucleosome formation, whereas others argue the opposite, i.e., that nucleosome occupancy might influence CpG methylation. Correlations are indeed evident between nucleosomes, CpG density and CpG methylation—at least near promoter sites. It is however less established whether there is an immediate causal relation between nucleosome occupancy and the presence of CpG sites—or if nucleosome occupancy could be influenced by other factors. In this work, we test for such causality in human genomes by analyzing the three quantities both near and away from promoter sites. For data from the human genome we compare promoter regions with given CpG densities with genomic regions without promoters but of similar CpG densities. We find the observed correlation between nucleosome occupancy and CpG density, respectively CpG methylation, to be specific to promoter regions. In other regions along the genome nucleosome occupancy is statistically independent of the positioning of CpGs or their methylation levels. Anti-correlation between CpG density and methylation level is however similarly strong in both regions. On promoters, nucleosome occupancy is more strongly affected by the level of gene expression than CpG density or CpG methylation—calling into question any direct causal relation between nucleosome occupancy and CpG organization. Rather, our results suggest that for organisms with cytosine methylation nucleosome occupancy might be primarily linked to gene expression, with no strong impact on methylation.
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Affiliation(s)
- Cecilia Lövkvist
- Center for Models of Life, Niels Bohr Institue, University of Copenhagen, Copenhagen, Denmark
| | - Kim Sneppen
- Center for Models of Life, Niels Bohr Institue, University of Copenhagen, Copenhagen, Denmark
| | - Jan O Haerter
- Center for Models of Life, Niels Bohr Institue, University of Copenhagen, Copenhagen, Denmark
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44
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Raiber EA, Hardisty R, van Delft P, Balasubramanian S. Mapping and elucidating the function of modified bases in DNA. Nat Rev Chem 2017. [DOI: 10.1038/s41570-017-0069] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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45
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Gibson MD, Brehove M, Luo Y, North J, Poirier MG. Methods for Investigating DNA Accessibility with Single Nucleosomes. Methods Enzymol 2017; 581:379-415. [PMID: 27793287 DOI: 10.1016/bs.mie.2016.08.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Nucleosomes are the fundamental organizing unit of all eukaryotic genomes. Understanding how proteins gain access to DNA-binding sites located within nucleosomes is important for understanding DNA processing including transcription, replication, and repair. Single-molecule total internal reflection fluorescence (smTIRF) microscopy measurements can provide key insight into how proteins gain and maintain access to DNA sites within nucleosomes. Here, we describe methods for smTIRF experiments including the preparation of fluorophore-labeled nucleosomes, the smTIRF system, data acquisition, analysis, and controls. These methods are presented for investigating transcription factor binding within nucleosomes. However, they are applicable for investigating the binding of any site-specific DNA-binding protein within nucleosomes.
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Affiliation(s)
- M D Gibson
- The Ohio State University, Columbus, OH, United States
| | - M Brehove
- The Ohio State University, Columbus, OH, United States
| | - Y Luo
- The Ohio State University, Columbus, OH, United States
| | - J North
- The Ohio State University, Columbus, OH, United States
| | - M G Poirier
- The Ohio State University, Columbus, OH, United States.
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46
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Lee J, Lee TH. Single-Molecule Investigations on Histone H2A-H2B Dynamics in the Nucleosome. Biochemistry 2017; 56:977-985. [PMID: 28128545 DOI: 10.1021/acs.biochem.6b01252] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Nucleosomes impose physical barriers to DNA-templated processes, playing important roles in eukaryotic gene regulation. DNA is packaged into nucleosomes by histone proteins mainly through strong electrostatic interactions that can be modulated by various post-translational histone modifications. Investigating the dynamics of histone dissociation from the nucleosome and how it is altered upon histone modifications is important for understanding eukaryotic gene regulation mechanisms. In particular, histone H2A-H2B dimer displacement in the nucleosome is one of the most important and earliest steps of histone dissociation. Two conflicting hypotheses on the requirement for dimer displacement are that nucleosomal DNA needs to be unwrapped before a dimer can displace and that a dimer can displace without DNA unwrapping. In order to test the hypotheses, we employed three-color single-molecule FRET and monitored in a time-resolved manner the early kinetics of H2A-H2B dimer dissociation triggered by high salt concentration and by histone chaperone Nap1. The results reveal that dimer displacement requires DNA unwrapping in the vast majority of the nucleosomes in the salt-induced case, while dimer displacement precedes DNA unwrapping in >60% of the nucleosomes in the Nap1-mediated case. We also found that acetylation at histone H4K16 or H3K56 affects the kinetics of Nap1-mediated dimer dissociation and facilitates the process both kinetically and thermodynamically. On the basis of these results, we suggest a mechanism by which histone chaperone facilitates H2A-H2B dimer displacement from the histone core without requiring another factor to unwrap the nucleosomal DNA.
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Affiliation(s)
- Jaehyoun Lee
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Tae-Hee Lee
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
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47
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Sultanov DC, Gerasimova NS, Kudryashova KS, Maluchenko NV, Kotova EY, Langelier MF, Pascal JM, Kirpichnikov MP, Feofanov AV, Studitsky VM. Unfolding of core nucleosomes by PARP-1 revealed by spFRET microscopy. AIMS GENETICS 2017; 4:21-31. [PMID: 28804761 PMCID: PMC5552189 DOI: 10.3934/genet.2017.1.21] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DNA accessibility to various protein complexes is essential for various processes in the cell and is affected by nucleosome structure and dynamics. Protein factor PARP-1 (poly(ADP-ribose) polymerase 1) increases the accessibility of DNA in chromatin to repair proteins and transcriptional machinery, but the mechanism and extent of this chromatin reorganization are unknown. Here we report on the effects of PARP-1 on single nucleosomes revealed by spFRET (single-particle Förster Resonance Energy Transfer) microscopy. PARP-1 binding to a double-strand break in the vicinity of a nucleosome results in a significant increase of the distance between the adjacent gyres of nucleosomal DNA. This partial uncoiling of the entire nucleosomal DNA occurs without apparent loss of histones and is reversed after poly(ADP)-ribosylation of PARP-1. Thus PARP-1-nucleosome interactions result in reversible, partial uncoiling of the entire nucleosomal DNA.
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Affiliation(s)
- Daniel C Sultanov
- Biology Faculty, Lomonosov Moscow State University, Moscow, 119992, Russia.,Fox Chase Cancer Center, Philadelphia, PA, 19111-2497, USA
| | | | - Kseniya S Kudryashova
- Biology Faculty, Lomonosov Moscow State University, Moscow, 119992, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of Russian Academy of Sciences, 117997 Moscow, Russia
| | | | - Elena Y Kotova
- Fox Chase Cancer Center, Philadelphia, PA, 19111-2497, USA
| | - Marie-France Langelier
- Department of Biochemistry and Molecular Medicine, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC H3T 1J4, Canada
| | - John M Pascal
- Department of Biochemistry and Molecular Medicine, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC H3T 1J4, Canada
| | | | - Alexey V Feofanov
- Biology Faculty, Lomonosov Moscow State University, Moscow, 119992, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of Russian Academy of Sciences, 117997 Moscow, Russia
| | - Vasily M Studitsky
- Biology Faculty, Lomonosov Moscow State University, Moscow, 119992, Russia.,Fox Chase Cancer Center, Philadelphia, PA, 19111-2497, USA
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48
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Osakabe A, Adachi F, Arimura Y, Maehara K, Ohkawa Y, Kurumizaka H. Influence of DNA methylation on positioning and DNA flexibility of nucleosomes with pericentric satellite DNA. Open Biol 2016; 5:rsob.150128. [PMID: 26446621 PMCID: PMC4632512 DOI: 10.1098/rsob.150128] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
DNA methylation occurs on CpG sites and is important to form pericentric heterochromatin domains. The satellite 2 sequence, containing seven CpG sites, is located in the pericentric region of human chromosome 1 and is highly methylated in normal cells. In contrast, the satellite 2 region is reportedly hypomethylated in cancer cells, suggesting that the methylation status may affect the chromatin structure around the pericentric regions in tumours. In this study, we mapped the nucleosome positioning on the satellite 2 sequence in vitro and found that DNA methylation modestly affects the distribution of the nucleosome positioning. The micrococcal nuclease assay revealed that the DNA end flexibility of the nucleosomes changes, depending on the DNA methylation status. However, the structures and thermal stabilities of the nucleosomes are unaffected by DNA methylation. These findings provide new information to understand how DNA methylation functions in regulating pericentric heterochromatin formation and maintenance in normal and malignant cells.
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Affiliation(s)
- Akihisa Osakabe
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Fumiya Adachi
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Yasuhiro Arimura
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Kazumitsu Maehara
- Department of Advanced Medical Initiatives, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan
| | - Yasuyuki Ohkawa
- Department of Advanced Medical Initiatives, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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49
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Jin J, Lian T, Gu C, Yu K, Gao YQ, Su XD. The effects of cytosine methylation on general transcription factors. Sci Rep 2016; 6:29119. [PMID: 27385050 PMCID: PMC4935894 DOI: 10.1038/srep29119] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/15/2016] [Indexed: 12/24/2022] Open
Abstract
DNA methylation on CpG sites is the most common epigenetic modification. Recently, methylation in a non-CpG context was found to occur widely on genomic DNA. Moreover, methylation of non-CpG sites is a highly controlled process, and its level may vary during cellular development. To study non-CpG methylation effects on DNA/protein interactions, we have chosen three human transcription factors (TFs): glucocorticoid receptor (GR), brain and muscle ARNT-like 1 (BMAL1) - circadian locomotor output cycles kaput (CLOCK) and estrogen receptor (ER) with methylated or unmethylated DNA binding sequences, using single-molecule and isothermal titration calorimetry assays. The results demonstrated that these TFs interact with methylated DNA with different effects compared with their cognate DNA sequences. The effects of non-CpG methylation on transcriptional regulation were validated by cell-based luciferase assay at protein level. The mechanisms of non-CpG methylation influencing DNA-protein interactions were investigated by crystallographic analyses and molecular dynamics simulation. With BisChIP-seq assays in HEK-293T cells, we found that GR can recognize highly methylated sites within chromatin in cells. Therefore, we conclude that non-CpG methylation of DNA can provide a mechanism for regulating gene expression through directly affecting the binding of TFs.
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Affiliation(s)
- Jianshi Jin
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
- State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China
| | - Tengfei Lian
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
- State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China
| | - Chan Gu
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Kai Yu
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
- State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China
| | - Yi Qin Gao
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Xiao-Dong Su
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
- State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China
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Ngo TTM, Yoo J, Dai Q, Zhang Q, He C, Aksimentiev A, Ha T. Effects of cytosine modifications on DNA flexibility and nucleosome mechanical stability. Nat Commun 2016; 7:10813. [PMID: 26905257 PMCID: PMC4770088 DOI: 10.1038/ncomms10813] [Citation(s) in RCA: 150] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 01/24/2016] [Indexed: 12/15/2022] Open
Abstract
Cytosine can undergo modifications, forming 5-methylcytosine (5-mC) and its oxidized products 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine (5-fC) and 5-carboxylcytosine (5-caC). Despite their importance as epigenetic markers and as central players in cellular processes, it is not well understood how these modifications influence physical properties of DNA and chromatin. Here we report a comprehensive survey of the effect of cytosine modifications on DNA flexibility. We find that even a single copy of 5-fC increases DNA flexibility markedly. 5-mC reduces and 5-hmC enhances flexibility, and 5-caC does not have a measurable effect. Molecular dynamics simulations show that these modifications promote or dampen structural fluctuations, likely through competing effects of base polarity and steric hindrance, without changing the average structure. The increase in DNA flexibility increases the mechanical stability of the nucleosome and vice versa, suggesting a gene regulation mechanism where cytosine modifications change the accessibility of nucleosomal DNA through their effects on DNA flexibility.
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Affiliation(s)
- Thuy T M Ngo
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jejoong Yoo
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Qing Dai
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA.,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA.,Institute for Biophysical Dynamic, The University of Chicago, Chicago, Illinois 60637, USA
| | - Qiucen Zhang
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA.,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA.,Institute for Biophysical Dynamic, The University of Chicago, Chicago, Illinois 60637, USA.,Howard Hughes Medical Institute, Chicago, Illinois 60637, USA
| | - Aleksei Aksimentiev
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Taekjip Ha
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,Howard Hughes Medical Institute, Baltimore, Maryland 21205, USA.,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, Maryland 21205, USA.,Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21205, USA.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21205, USA
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