1
|
Dabrowski JK, Yang EJ, Crofts SJC, Hillary RF, Simpson DJ, McCartney DL, Marioni RE, Kirschner K, Latorre-Crespo E, Chandra T. Probabilistic inference of epigenetic age acceleration from cellular dynamics. NATURE AGING 2024:10.1038/s43587-024-00700-5. [PMID: 39313745 DOI: 10.1038/s43587-024-00700-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 07/31/2024] [Indexed: 09/25/2024]
Abstract
The emergence of epigenetic predictors was a pivotal moment in geroscience, propelling the measurement and concept of biological aging into a quantitative era; however, while current epigenetic clocks show strong predictive power, they are data-driven in nature and are not based on the underlying biological mechanisms driving methylation dynamics. We show that predictions of these clocks are susceptible to several confounding non-age-related phenomena that make interpretation of these estimates and associations difficult. To address these limitations, we developed a probabilistic model describing methylation transitions at the cellular level. Our approach reveals two measurable components, acceleration and bias, which directly reflect perturbations of the underlying cellular dynamics. Acceleration is the proportional increase in the speed of methylation transitions across CpG sites, whereas bias corresponds to global changes in methylation levels. Using data from 15,900 participants from the Generation Scotland study, we develop a robust inference framework and show that these are two distinct processes confounding current epigenetic predictors. Our results show improved associations of acceleration and bias with physiological traits known to impact healthy aging, such as smoking and alcohol consumption, respectively. Furthermore, a genome-wide association study of epigenetic age acceleration identified seven genomic loci.
Collapse
Affiliation(s)
- Jan K Dabrowski
- School of Informatics, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, UK
| | - Emma J Yang
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, UK
| | - Samuel J C Crofts
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, UK
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Robert F Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | | | - Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Kristina Kirschner
- Cancer Research UK Scotland Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
- Department of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Eric Latorre-Crespo
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, UK.
- School of Cancer Sciences, University of Glasgow, Glasgow, UK.
| | - Tamir Chandra
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, UK.
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA.
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA.
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA.
| |
Collapse
|
2
|
Meyer DH, Schumacher B. Aging clocks based on accumulating stochastic variation. NATURE AGING 2024; 4:871-885. [PMID: 38724736 PMCID: PMC11186771 DOI: 10.1038/s43587-024-00619-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 03/28/2024] [Indexed: 05/15/2024]
Abstract
Aging clocks have provided one of the most important recent breakthroughs in the biology of aging, and may provide indicators for the effectiveness of interventions in the aging process and preventive treatments for age-related diseases. The reproducibility of accurate aging clocks has reinvigorated the debate on whether a programmed process underlies aging. Here we show that accumulating stochastic variation in purely simulated data is sufficient to build aging clocks, and that first-generation and second-generation aging clocks are compatible with the accumulation of stochastic variation in DNA methylation or transcriptomic data. We find that accumulating stochastic variation is sufficient to predict chronological and biological age, indicated by significant prediction differences in smoking, calorie restriction, heterochronic parabiosis and partial reprogramming. Although our simulations may not explicitly rule out a programmed aging process, our results suggest that stochastically accumulating changes in any set of data that have a ground state at age zero are sufficient for generating aging clocks.
Collapse
Affiliation(s)
- David H Meyer
- Institute for Genome Stability in Aging and Disease, University Hospital and University of Cologne, Cologne, Germany.
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
| | - Björn Schumacher
- Institute for Genome Stability in Aging and Disease, University Hospital and University of Cologne, Cologne, Germany.
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
| |
Collapse
|
3
|
Crofts SJC, Latorre-Crespo E, Chandra T. DNA methylation rates scale with maximum lifespan across mammals. NATURE AGING 2024; 4:27-32. [PMID: 38049585 PMCID: PMC10798888 DOI: 10.1038/s43587-023-00535-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 11/02/2023] [Indexed: 12/06/2023]
Abstract
DNA methylation rates have previously been found to broadly correlate with maximum lifespan in mammals, yet no precise relationship has been observed. We developed a statistically robust framework to compare methylation rates at conserved age-related sites across mammals. We found that methylation rates negatively scale with maximum lifespan in both blood and skin. The emergence of explicit scaling suggests that methylation rates are, or are linked to, an evolutionary constraint on maximum lifespan acting across diverse mammalian lineages.
Collapse
Affiliation(s)
- Samuel J C Crofts
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, UK
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Tamir Chandra
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, UK.
| |
Collapse
|
4
|
Hay AD, Kessler NJ, Gebert D, Takahashi N, Tavares H, Teixeira FK, Ferguson-Smith AC. Epigenetic inheritance is unfaithful at intermediately methylated CpG sites. Nat Commun 2023; 14:5336. [PMID: 37660134 PMCID: PMC10475082 DOI: 10.1038/s41467-023-40845-2] [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: 03/14/2023] [Accepted: 08/12/2023] [Indexed: 09/04/2023] Open
Abstract
DNA methylation at the CpG dinucleotide is considered a stable epigenetic mark due to its presumed long-term inheritance through clonal expansion. Here, we perform high-throughput bisulfite sequencing on clonally derived somatic cell lines to quantitatively measure methylation inheritance at the nucleotide level. We find that although DNA methylation is generally faithfully maintained at hypo- and hypermethylated sites, this is not the case at intermediately methylated CpGs. Low fidelity intermediate methylation is interspersed throughout the genome and within genes with no or low transcriptional activity, and is not coordinately maintained between neighbouring sites. We determine that the probabilistic changes that occur at intermediately methylated sites are likely due to DNMT1 rather than DNMT3A/3B activity. The observed lack of clonal inheritance at intermediately methylated sites challenges the current epigenetic inheritance model and has direct implications for both the functional relevance and general interpretability of DNA methylation as a stable epigenetic mark.
Collapse
Affiliation(s)
- Amir D Hay
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Noah J Kessler
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Daniel Gebert
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Nozomi Takahashi
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Hugo Tavares
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Felipe K Teixeira
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY, UK.
| | - Anne C Ferguson-Smith
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.
| |
Collapse
|
5
|
Turpin M, Salbert G. 5-methylcytosine turnover: Mechanisms and therapeutic implications in cancer. Front Mol Biosci 2022; 9:976862. [PMID: 36060265 PMCID: PMC9428128 DOI: 10.3389/fmolb.2022.976862] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 07/26/2022] [Indexed: 12/04/2022] Open
Abstract
DNA methylation at the fifth position of cytosine (5mC) is one of the most studied epigenetic mechanisms essential for the control of gene expression and for many other biological processes including genomic imprinting, X chromosome inactivation and genome stability. Over the last years, accumulating evidence suggest that DNA methylation is a highly dynamic mechanism driven by a balance between methylation by DNMTs and TET-mediated demethylation processes. However, one of the main challenges is to understand the dynamics underlying steady state DNA methylation levels. In this review article, we give an overview of the latest advances highlighting DNA methylation as a dynamic cycling process with a continuous turnover of cytosine modifications. We describe the cooperative actions of DNMT and TET enzymes which combine with many additional parameters including chromatin environment and protein partners to govern 5mC turnover. We also discuss how mathematical models can be used to address variable methylation levels during development and explain cell-type epigenetic heterogeneity locally but also at the genome scale. Finally, we review the therapeutic implications of these discoveries with the use of both epigenetic clocks as predictors and the development of epidrugs that target the DNA methylation/demethylation machinery. Together, these discoveries unveil with unprecedented detail how dynamic is DNA methylation during development, underlying the establishment of heterogeneous DNA methylation landscapes which could be altered in aging, diseases and cancer.
Collapse
Affiliation(s)
- Marion Turpin
- Sp@rte Team, UMR6290 CNRS, Institute of Genetics and Development of Rennes, Rennes, France
- University of Rennes 1, Rennes, France
| | - Gilles Salbert
- Sp@rte Team, UMR6290 CNRS, Institute of Genetics and Development of Rennes, Rennes, France
- University of Rennes 1, Rennes, France
| |
Collapse
|
6
|
Ocañas SR, Ansere VA, Tooley KB, Hadad N, Chucair-Elliott AJ, Stanford DR, Rice S, Wronowski B, Pham KD, Hoffman JM, Austad SN, Stout MB, Freeman WM. Differential Regulation of Mouse Hippocampal Gene Expression Sex Differences by Chromosomal Content and Gonadal Sex. Mol Neurobiol 2022; 59:4669-4702. [PMID: 35589920 PMCID: PMC9119800 DOI: 10.1007/s12035-022-02860-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 04/25/2022] [Indexed: 01/23/2023]
Abstract
Common neurological disorders, like Alzheimer's disease (AD), multiple sclerosis (MS), and autism, display profound sex differences in prevalence and clinical presentation. However, sex differences in the brain with health and disease are often overlooked in experimental models. Sex effects originate, directly or indirectly, from hormonal or sex chromosomal mechanisms. To delineate the contributions of genetic sex (XX v. XY) versus gonadal sex (ovaries v. testes) to the epigenomic regulation of hippocampal sex differences, we used the Four Core Genotypes (FCG) mouse model which uncouples chromosomal and gonadal sex. Transcriptomic and epigenomic analyses of ~ 12-month-old FCG mouse hippocampus, revealed genomic context-specific regulatory effects of genotypic and gonadal sex on X- and autosome-encoded gene expression and DNA modification patterns. X-chromosomal epigenomic patterns, classically associated with X-inactivation, were established almost entirely by genotypic sex, independent of gonadal sex. Differences in X-chromosome methylation were primarily localized to gene regulatory regions including promoters, CpG islands, CTCF binding sites, and active/poised chromatin, with an inverse relationship between methylation and gene expression. Autosomal gene expression demonstrated regulation by both genotypic and gonadal sex, particularly in immune processes. These data demonstrate an important regulatory role of sex chromosomes, independent of gonadal sex, on sex-biased hippocampal transcriptomic and epigenomic profiles. Future studies will need to further interrogate specific CNS cell types, identify the mechanisms by which sex chromosomes regulate autosomes, and differentiate organizational from activational hormonal effects.
Collapse
Affiliation(s)
- Sarah R Ocañas
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13thStreet, Oklahoma City, OK, 73104, USA
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Victor A Ansere
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13thStreet, Oklahoma City, OK, 73104, USA
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Kyla B Tooley
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13thStreet, Oklahoma City, OK, 73104, USA
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | | | - Ana J Chucair-Elliott
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13thStreet, Oklahoma City, OK, 73104, USA
| | - David R Stanford
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13thStreet, Oklahoma City, OK, 73104, USA
| | - Shannon Rice
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13thStreet, Oklahoma City, OK, 73104, USA
| | - Benjamin Wronowski
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Kevin D Pham
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13thStreet, Oklahoma City, OK, 73104, USA
| | - Jessica M Hoffman
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Steven N Austad
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Michael B Stout
- Aging & Metabolism Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Willard M Freeman
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13thStreet, Oklahoma City, OK, 73104, USA.
- Oklahoma City Veterans Affairs Medical Center, Oklahoma City, OK, USA.
| |
Collapse
|
7
|
Zagkos L, Roberts J, Auley MM. A mathematical model which examines age-related stochastic fluctuations in DNA maintenance methylation. Exp Gerontol 2021; 156:111623. [PMID: 34774717 DOI: 10.1016/j.exger.2021.111623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 10/30/2021] [Accepted: 11/04/2021] [Indexed: 10/19/2022]
Abstract
Due to its complexity and its ubiquitous nature the ageing process remains an enduring biological puzzle. Many molecular mechanisms and biochemical process have become synonymous with ageing. However, recent findings have pinpointed epigenetics as having a key role in ageing and healthspan. In particular age related changes to DNA methylation offer the possibility of monitoring the trajectory of biological ageing and could even be used to predict the onset of diseases such as cancer, Alzheimer's disease and cardiovascular disease. At the molecular level emerging evidence strongly suggests the regulatory processes which govern DNA methylation are subject to intracellular stochasticity. It is challenging to fully understand the impact of stochasticity on DNA methylation levels at the molecular level experimentally. An ideal solution is to use mathematical models to capture the essence of the stochasticity and its outcomes. In this paper we present a novel stochastic model which accounts for specific methylation levels within a gene promoter. Uncertainty of the eventual site-specific methylation levels for different values of methylation age, depending on the initial methylation levels were analysed. Our model predicts the observed bistable levels in CpG islands. In addition, simulations with various levels of noise indicate that uncertainty predominantly spreads through the hypermethylated region of stability, especially for large values of input noise. A key outcome of the model is that CpG islands with high to intermediate methylation levels tend to be more susceptible to dramatic DNA methylation changes due to increasing methylation age.
Collapse
Affiliation(s)
- Loukas Zagkos
- Department of Mathematics, School of Science and Engineering, University of Chester, Thornton Science Park, Chester CH2 4NU, UK; Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, St Mary's Campus, London W2 1PG, UK.
| | - Jason Roberts
- Department of Mathematics, School of Science and Engineering, University of Chester, Thornton Science Park, Chester CH2 4NU, UK
| | - Mark Mc Auley
- Department of Chemical Engineering, School of Science and Engineering, University of Chester, Thornton Science Park, Chester CH2 4NU, UK
| |
Collapse
|
8
|
Zhao C, Zhang N, Zhang Y, Tuersunjiang N, Gao S, Liu W, Zhang Y. A DNA methylation state transition model reveals the programmed epigenetic heterogeneity in human pre-implantation embryos. Genome Biol 2020; 21:277. [PMID: 33198783 PMCID: PMC7667739 DOI: 10.1186/s13059-020-02189-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 10/27/2020] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND During mammalian early embryogenesis, expression and epigenetic heterogeneity emerge before the first cell fate determination, but the programs causing such determinate heterogeneity are largely unexplored. RESULTS Here, we present MethylTransition, a novel DNA methylation state transition model, for characterizing methylation changes during one or a few cell cycles at single-cell resolution. MethylTransition involves the creation of a transition matrix comprising three parameters that represent the probabilities of DNA methylation-modifying activities in order to link the methylation states before and after a cell cycle. We apply MethylTransition to single-cell DNA methylome data from human pre-implantation embryogenesis and elucidate that the DNA methylation heterogeneity that emerges at promoters during this process is largely an intrinsic output of a program with unique probabilities of DNA methylation-modifying activities. Moreover, we experimentally validate the effect of the initial DNA methylation on expression heterogeneity in pre-implantation mouse embryos. CONCLUSIONS Our study reveals the programmed DNA methylation heterogeneity during human pre-implantation embryogenesis through a novel mathematical model and provides valuable clues for identifying the driving factors of the first cell fate determination during this process.
Collapse
Affiliation(s)
- Chengchen Zhao
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Science and Technology, Tongji University, Shanghai, 200092 China
| | - Naiqian Zhang
- School of Mathematics and Statistics, Shandong University at Weihai, Weihai, 264209 China
| | - Yalin Zhang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Science and Technology, Tongji University, Shanghai, 200092 China
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Tongji University, Shanghai, 200092 China
| | - Nuermaimaiti Tuersunjiang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Science and Technology, Tongji University, Shanghai, 200092 China
| | - Shaorong Gao
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Science and Technology, Tongji University, Shanghai, 200092 China
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Tongji University, Shanghai, 200092 China
| | - Wenqiang Liu
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Science and Technology, Tongji University, Shanghai, 200092 China
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Tongji University, Shanghai, 200092 China
| | - Yong Zhang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Science and Technology, Tongji University, Shanghai, 200092 China
| |
Collapse
|
9
|
Modeling DNA Methylation Profiles through a Dynamic Equilibrium between Methylation and Demethylation. Biomolecules 2020; 10:biom10091271. [PMID: 32899254 PMCID: PMC7564540 DOI: 10.3390/biom10091271] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 12/30/2022] Open
Abstract
DNA methylation is a heritable epigenetic mark that plays a key role in regulating gene expression. Mathematical modeling has been extensively applied to unravel the regulatory mechanisms of this process. In this study, we aimed to investigate DNA methylation by performing a high-depth analysis of particular loci, and by subsequent modeling of the experimental results. In particular, we performed an in-deep DNA methylation profiling of two genomic loci surrounding the transcription start site of the D-Aspartate Oxidase and the D-Serine Oxidase genes in different samples (n = 51). We found evidence of cell-to-cell differences in DNA methylation status. However, these cell differences were maintained between different individuals, which indeed showed very similar DNA methylation profiles. Therefore, we hypothesized that the observed pattern of DNA methylation was the result of a dynamic balance between DNA methylation and demethylation, and that this balance was identical between individuals. We hence developed a simple mathematical model to test this hypothesis. Our model reliably captured the characteristics of the experimental data, suggesting that DNA methylation and demethylation work together in determining the methylation state of a locus. Furthermore, our model suggested that the methylation status of neighboring cytosines plays an important role in this balance.
Collapse
|
10
|
Wang Q, Yu G, Ming X, Xia W, Xu X, Zhang Y, Zhang W, Li Y, Huang C, Xie H, Zhu B, Xie W. Imprecise DNMT1 activity coupled with neighbor-guided correction enables robust yet flexible epigenetic inheritance. Nat Genet 2020; 52:828-839. [PMID: 32690947 DOI: 10.1038/s41588-020-0661-y] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 06/08/2020] [Indexed: 12/18/2022]
Abstract
The epigenome, including DNA methylation, is stably propagated during mitotic division. However, single-cell clonal expansion produces heterogeneous methylomes, thus raising the question of how the DNA methylome remains stable despite constant epigenetic drift. Here, we report that a clonal population of DNA (cytosine-5)-methyltransferase 1 (DNMT1)-only cells produces a heterogeneous methylome, which is robustly propagated on cell expansion and differentiation. Our data show that DNMT1 has imprecise maintenance activity and possibly possesses weak de novo activity, leading to spontaneous 'epimutations'. However, these epimutations tend to be corrected through a neighbor-guided mechanism, which is likely to be enabled by the environment-sensitive de novo activity ('tuner') and maintenance activity ('stabilizer') of DNMT1. By generating base-resolution maps of de novo and maintenance activities, we find that H3K9me2/3-marked regions show enhanced de novo activity, and CpG islands have both poor maintenance and de novo activities. The imprecise epigenetic machinery coupled with neighbor-guided correction may be a fundamental mechanism underlying robust yet flexible epigenetic inheritance.
Collapse
Affiliation(s)
- Qiujun Wang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China
| | - Guang Yu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China
| | - Xuan Ming
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Weikun Xia
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China
| | - Xiguang Xu
- Epigenomics and Computational Biology Lab, Fralin Life Sciences Institute at Virginia Tech, Blacksburg, VA, USA.,Department of Biological Sciences, Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, USA
| | - Yu Zhang
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Wenhao Zhang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China
| | - Yuanyuan Li
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Chunyi Huang
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Hehuang Xie
- Epigenomics and Computational Biology Lab, Fralin Life Sciences Institute at Virginia Tech, Blacksburg, VA, USA.,Department of Biological Sciences, Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, USA
| | - Bing Zhu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. .,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, Tsinghua University, Beijing, China. .,School of Life Sciences, Tsinghua University, Beijing, China.
| |
Collapse
|
11
|
A Mathematical Model for Inheritance of DNA Methylation Patterns in Somatic Cells. Bull Math Biol 2020; 82:84. [PMID: 32613387 DOI: 10.1007/s11538-020-00765-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 06/10/2020] [Indexed: 12/22/2022]
Abstract
DNA methylation is an essential epigenetic mechanism used by cells to regulate gene expression. Interestingly, DNA replication, a function necessary for cell division, disrupts the methylation pattern. Since perturbed methylation patterns are associated with aberrant gene expression and many diseases, including cancer, restoration of the correct pattern following DNA replication is crucial. However, the exact mechanisms of this restoration remain under investigation. DNA methyltransferases (Dnmts) perform methylation by adding a methyl group to cytosines at CpG sites in the DNA. These CpG sites are found in regions of high density, termed CpG islands (CGIs), and regions of low density in the genome. Nearly, every CpG site in a CGI has the same state, either methylated or unmethylated, and almost all CpG sites in regions of low CpG density are methylated. We propose a stochastic model for the dynamics of the post-replicative restoration of methylation patterns. The model considers the recruitment of Dnmts and demethylating enzymes to regions of hyper- and hypomethylation, respectively. The model also includes the interaction between Dnmt1 and PCNA, an enzyme that localizes Dnmt1 to the replication complex. Using our model, we predict that the methylation of regions of DNA can be bistable. Further, we predict that recruitment mechanisms maintain methylation in CGIs, whereas the Dnmt1-PCNA interaction maintains methylation in low-density regions.
Collapse
|
12
|
Storey K, Leder K, Hawkins-Daarud A, Swanson K, Ahmed AU, Rockne RC, Foo J. Glioblastoma Recurrence and the Role of O 6-Methylguanine-DNA Methyltransferase Promoter Methylation. JCO Clin Cancer Inform 2020; 3:1-12. [PMID: 30758983 DOI: 10.1200/cci.18.00062] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Tumor recurrence in glioblastoma multiforme (GBM) is often attributed to acquired resistance to the standard chemotherapeutic agent, temozolomide (TMZ). Promoter methylation of the DNA repair gene MGMT (O6-methylguanine-DNA methyltransferase) has been associated with sensitivity to TMZ, whereas increased expression of MGMT has been associated with TMZ resistance. Clinical studies have observed a downward shift in MGMT methylation percentage from primary to recurrent stage tumors; however, the evolutionary processes that drive this shift and more generally the emergence and growth of TMZ-resistant tumor subpopulations are still poorly understood. Here, we develop a mathematical model, parameterized using clinical and experimental data, to investigate the role of MGMT methylation in TMZ resistance during the standard treatment regimen for GBM-surgery, chemotherapy, and radiation. We first found that the observed downward shift in MGMT promoter methylation status between detection and recurrence cannot be explained solely by evolutionary selection. Next, our model suggests that TMZ has an inhibitory effect on maintenance methylation of MGMT after cell division. Finally, incorporating this inhibitory effect, we study the optimal number of TMZ doses per adjuvant cycle for patients with GBM with high and low levels of MGMT methylation at diagnosis.
Collapse
Affiliation(s)
- Katie Storey
- University of Minnesota Twin Cities, Minneapolis, MN
| | - Kevin Leder
- University of Minnesota Twin Cities, Minneapolis, MN
| | | | | | - Atique U Ahmed
- Northwestern University Feinberg School of Medicine, Chicago, IL
| | | | - Jasmine Foo
- University of Minnesota Twin Cities, Minneapolis, MN
| |
Collapse
|
13
|
Ginno PA, Gaidatzis D, Feldmann A, Hoerner L, Imanci D, Burger L, Zilbermann F, Peters AHFM, Edenhofer F, Smallwood SA, Krebs AR, Schübeler D. A genome-scale map of DNA methylation turnover identifies site-specific dependencies of DNMT and TET activity. Nat Commun 2020; 11:2680. [PMID: 32471981 PMCID: PMC7260214 DOI: 10.1038/s41467-020-16354-x] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 04/24/2020] [Indexed: 12/21/2022] Open
Abstract
DNA methylation is considered a stable epigenetic mark, yet methylation patterns can vary during differentiation and in diseases such as cancer. Local levels of DNA methylation result from opposing enzymatic activities, the rates of which remain largely unknown. Here we developed a theoretical and experimental framework enabling us to infer methylation and demethylation rates at 860,404 CpGs in mouse embryonic stem cells. We find that enzymatic rates can vary as much as two orders of magnitude between CpGs with identical steady-state DNA methylation. Unexpectedly, de novo and maintenance methylation activity is reduced at transcription factor binding sites, while methylation turnover is elevated in transcribed gene bodies. Furthermore, we show that TET activity contributes substantially more than passive demethylation to establishing low methylation levels at distal enhancers. Taken together, our work unveils a genome-scale map of methylation kinetics, revealing highly variable and context-specific activity for the DNA methylation machinery.
Collapse
Affiliation(s)
- Paul Adrian Ginno
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Dimos Gaidatzis
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Angelika Feldmann
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Leslie Hoerner
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Dilek Imanci
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Lukas Burger
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | | | - Antoine H F M Peters
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Faculty of Sciences, University of Basel, Basel, Switzerland
| | - Frank Edenhofer
- Leopold-Franzens-University Innsbruck & CMBI, Innsbruck, Austria
| | | | - Arnaud R Krebs
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- EMBL Heidelberg, Heidelberg, Germany
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
- Faculty of Sciences, University of Basel, Basel, Switzerland.
| |
Collapse
|
14
|
Busto-Moner L, Morival J, Ren H, Fahim A, Reitz Z, Downing TL, Read EL. Stochastic modeling reveals kinetic heterogeneity in post-replication DNA methylation. PLoS Comput Biol 2020; 16:e1007195. [PMID: 32275652 PMCID: PMC7176288 DOI: 10.1371/journal.pcbi.1007195] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 04/22/2020] [Accepted: 01/20/2020] [Indexed: 01/17/2023] Open
Abstract
DNA methylation is a heritable epigenetic modification that plays an essential role in mammalian development. Genomic methylation patterns are dynamically maintained, with DNA methyltransferases mediating inheritance of methyl marks onto nascent DNA over cycles of replication. A recently developed experimental technique employing immunoprecipitation of bromodeoxyuridine labeled nascent DNA followed by bisulfite sequencing (Repli-BS) measures post-replication temporal evolution of cytosine methylation, thus enabling genome-wide monitoring of methylation maintenance. In this work, we combine statistical analysis and stochastic mathematical modeling to analyze Repli-BS data from human embryonic stem cells. We estimate site-specific kinetic rate constants for the restoration of methyl marks on >10 million uniquely mapped cytosines within the CpG (cytosine-phosphate-guanine) dinucleotide context across the genome using Maximum Likelihood Estimation. We find that post-replication remethylation rate constants span approximately two orders of magnitude, with half-lives of per-site recovery of steady-state methylation levels ranging from shorter than ten minutes to five hours and longer. Furthermore, we find that kinetic constants of maintenance methylation are correlated among neighboring CpG sites. Stochastic mathematical modeling provides insight to the biological mechanisms underlying the inference results, suggesting that enzyme processivity and/or collaboration can produce the observed kinetic correlations. Our combined statistical/mathematical modeling approach expands the utility of genomic datasets and disentangles heterogeneity in methylation patterns arising from replication-associated temporal dynamics versus stable cell-to-cell differences.
Collapse
Affiliation(s)
- Luis Busto-Moner
- Institut Químic de Sarrià, Universitat Ramon Llull, Barcelona, Spain
- Dept. of Chemical & Biomolecular Engineering, University of California, Irvine, California, United States of America
| | - Julien Morival
- Department of Biomedical Engineering, University of California, Irvine, Irvine, California, United States of America
| | - Honglei Ren
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, California, United States of America
| | - Arjang Fahim
- Department of Biomedical Engineering, University of California, Irvine, Irvine, California, United States of America
| | - Zachary Reitz
- Department of Biomedical Engineering, University of California, Irvine, Irvine, California, United States of America
| | - Timothy L. Downing
- Department of Biomedical Engineering, University of California, Irvine, Irvine, California, United States of America
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California, Irvine, Irvine, California, United States of America
| | - Elizabeth L. Read
- Dept. of Chemical & Biomolecular Engineering, University of California, Irvine, California, United States of America
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California, Irvine, Irvine, California, United States of America
| |
Collapse
|
15
|
Lei J, Nie Q, Chen DB. A single-cell epigenetic model for paternal psychological stress-induced transgenerational reprogramming in offspring. Biol Reprod 2019; 98:846-855. [PMID: 29506130 DOI: 10.1093/biolre/ioy050] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 02/25/2018] [Indexed: 12/16/2022] Open
Abstract
Experimental evidence shows that parental psychological stress affects the long-term health of offspring in an inheritable fashion. Although epigenetic mechanisms, including DNA methylation, miRNA, and histone modifications, are involved in transgenerational programming, the underlining mechanisms of transgenerational inheritance remain unsolved. Here, we present a single-cell-based computational model for transgenerational inheritance for investigating the long-term dynamics of phenotype changes in response to parental stress. The model is based on a recent study that has identified the imprinted sperm gene Sfmbt2 as a key target, and incorporates crosstalks among drastically different time scales in mammalian development, including DNA methylation, transcription, cell division, and population dynamics. Computational analysis of the model suggests a positive feedback to DNA methylation in the promoter region of sperm Sfmbt2 gene that provides a possible mechanism to mediate the parental psychological stress reprogramming in offspring. This approach provides a modeling framework for the understanding of the roles that epigenetics play in transgenerational inheritance.
Collapse
Affiliation(s)
- Jinzhi Lei
- Zhou Pei-Yuan Center for Applied Mathematics, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
| | - Qing Nie
- Department of Mathematics, Department of Developmental and Cell Biology, Center for Mathematical and Computational Biology, University of California, Irvine, Irvine, California, USA
| | - Dong-Bao Chen
- Department of Obstetrics and Gynecology, University of California Irvine, Irvine, California, USA
| |
Collapse
|
16
|
Mc Auley MT, Mooney KM, Salcedo-Sora JE. Computational modelling folate metabolism and DNA methylation: implications for understanding health and ageing. Brief Bioinform 2019; 19:303-317. [PMID: 28007697 DOI: 10.1093/bib/bbw116] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Indexed: 11/12/2022] Open
Abstract
Dietary folates have a key role to play in health, as deficiencies in the intake of these B vitamins have been implicated in a wide variety of clinical conditions. The reason for this is folates function as single carbon donors in the synthesis of methionine and nucleotides. Moreover, folates have a vital role to play in the epigenetics of mammalian cells by supplying methyl groups for DNA methylation reactions. Intriguingly, a growing body of experimental evidence suggests that DNA methylation status could be a central modulator of the ageing process. This has important health implications because the methylation status of the human genome could be used to infer age-related disease risk. Thus, it is imperative we further our understanding of the processes which underpin DNA methylation and how these intersect with folate metabolism and ageing. The biochemical and molecular mechanisms, which underpin these processes, are complex. However, computational modelling offers an ideal framework for handling this complexity. A number of computational models have been assembled over the years, but to date, no model has represented the full scope of the interaction between the folate cycle and the reactions, which governs the DNA methylation cycle. In this review, we will discuss several of the models, which have been developed to represent these systems. In addition, we will present a rationale for developing a combined model of folate metabolism and the DNA methylation cycle.
Collapse
Affiliation(s)
- Mark T Mc Auley
- Department of Chemical Engineering, Thornton Science Park, University of Chester, UK
| | - Kathleen M Mooney
- Faculty of Health and Social Care, Edge Hill University, Ormskirk, Lancashire, UK
| | | |
Collapse
|
17
|
Zagkos L, Auley MM, Roberts J, Kavallaris NI. Mathematical models of DNA methylation dynamics: Implications for health and ageing. J Theor Biol 2019; 462:184-193. [DOI: 10.1016/j.jtbi.2018.11.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 11/01/2018] [Accepted: 11/09/2018] [Indexed: 12/24/2022]
|
18
|
Abstract
Fundamental differences exist between males and females, encompassing anatomy, physiology, behaviour, and genetics. Such differences undoubtedly play a part in the well documented, yet poorly understood, disparity in disease susceptibility between the sexes. Although traditionally attributed to gonadal sex hormone effects, recent work has begun to shed more light on the contribution of genetics - and in particular the sex chromosomes - to these sexual dimorphisms. Here, we explore the accumulating evidence for a significant genetic component to mammalian sexual dimorphism through the paradigm of sex chromosome evolution. The differences between the extant X and Y chromosomes, at both a sequence and regulatory level, arose across 166 million years. A functional result of these differences is cell autonomous sexual dimorphism. By understanding the process that changed a pair of homologous ancestral autosomes into the extant mammalian X and Y, we believe it easier to consider the mechanisms that may contribute to hormone-independent male-female differences. We highlight key roles for genes with homologues present on both sex chromosomes, where the X-linked copy escapes X chromosome inactivation. Finally, we summarise current experimental paradigms and suggest areas for developments to further increase our understanding of cell autonomous sexual dimorphism in the context of health and disease.
Collapse
Affiliation(s)
- Daniel M Snell
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - James M A Turner
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
| |
Collapse
|
19
|
Meyer KN, Lacey MR. Modeling Methylation Patterns with Long Read Sequencing Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 15:1379-1389. [PMID: 28682263 DOI: 10.1109/tcbb.2017.2721943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Variation in cytosine methylation at CpG dinucleotides is often observed in genomic regions, and analysis typically focuses on estimating the proportion of methylated sites observed in a given region and comparing these levels across samples to determine association with conditions of interest. While sites are tacitly treated as independent, when observed at the level of individual molecules methylation patterns exhibit strong evidence of local spatial dependence. We previously developed a neighboring sites model to account for correlation and clustering behavior observed in two tandem repeat regions in a collection of ovarian carcinomas. We now introduce extensions of the model that account for the effect of distance between sites as well as asymmetric correlation in de novo methylation and demethylation rates. We apply our models to published data from a whole genome bisulfite sequencing experiment using long reads, estimating model parameters for a selection of CpG-dense regions spanning between 21 and 67 sites. Our methods detect evidence of local spatial correlation as a function of site-to-site distance and demonstrate the added value of employing long read sequencing data in epigenetic research.
Collapse
|
20
|
Laubach ZM, Perng W, Dolinoy DC, Faulk CD, Holekamp KE, Getty T. Epigenetics and the maintenance of developmental plasticity: extending the signalling theory framework. Biol Rev Camb Philos Soc 2018; 93:1323-1338. [PMID: 29356358 DOI: 10.1111/brv.12396] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Revised: 12/20/2017] [Accepted: 12/22/2017] [Indexed: 12/12/2022]
Abstract
Developmental plasticity, a phenomenon of importance in both evolutionary biology and human studies of the developmental origins of health and disease (DOHaD), enables organisms to respond to their environment based on previous experience without changes to the underlying nucleotide sequence. Although such phenotypic responses should theoretically improve an organism's fitness and performance in its future environment, this is not always the case. Herein, we first discuss epigenetics as an adaptive mechanism of developmental plasticity and use signaling theory to provide an evolutionary context for DOHaD phenomena within a generation. Next, we utilize signalling theory to identify determinants of adaptive developmental plasticity, detect sources of random variability - also known as process errors that affect maintenance of an epigenetic signal (DNA methylation) over time, and discuss implications of these errors for an organism's health and fitness. Finally, we apply life-course epidemiology conceptual models to inform study design and analytical strategies that are capable of parsing out the potential effects of process errors in the relationships among an organism's early environment, DNA methylation, and phenotype in a future environment. Ultimately, we hope to foster cross-talk and interdisciplinary collaboration between evolutionary biology and DOHaD epidemiology, which have historically remained separate despite a shared interest in developmental plasticity.
Collapse
Affiliation(s)
- Zachary M Laubach
- Department of Integrative Biology, Michigan State University, 288 Farm Lane, East Lansing, MI, 48824, U.S.A.,Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, 288 Farm Lane, East Lansing, MI, 48824, U.S.A.,BEACON, NSF Center for the Study of Evolution in Action, Michigan State University, 567 Wilson Road, East Lansing, MI, 48824, U.S.A
| | - Wei Perng
- Department of Nutritional Sciences, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI, 48109-2029, U.S.A.,Department of Epidemiology, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI, 48109-2029, U.S.A
| | - Dana C Dolinoy
- Department of Nutritional Sciences, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI, 48109-2029, U.S.A.,Department of Environmental Health Sciences, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI, 48109-2029, U.S.A
| | - Christopher D Faulk
- Department of Animal Sciences, University of Minnesota, 495B AnSc/VetMed, 1988 Fitch Avenue, St. Paul, MN, 55108, U.S.A
| | - Kay E Holekamp
- Department of Integrative Biology, Michigan State University, 288 Farm Lane, East Lansing, MI, 48824, U.S.A.,Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, 288 Farm Lane, East Lansing, MI, 48824, U.S.A.,BEACON, NSF Center for the Study of Evolution in Action, Michigan State University, 567 Wilson Road, East Lansing, MI, 48824, U.S.A
| | - Thomas Getty
- Department of Integrative Biology, Michigan State University, 288 Farm Lane, East Lansing, MI, 48824, U.S.A.,Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, 288 Farm Lane, East Lansing, MI, 48824, U.S.A.,BEACON, NSF Center for the Study of Evolution in Action, Michigan State University, 567 Wilson Road, East Lansing, MI, 48824, U.S.A
| |
Collapse
|
21
|
Abstract
The last decade has been marked by an increased interest in relating epigenetic mechanisms to complex human behaviors, although this interest has not been balanced, accentuating various types of affective and primarily ignoring cognitive functioning. Recent animal model data support the view that epigenetic processes play a role in learning and memory consolidation and help transmit acquired memories even across generations. In this review, we provide an overview of various types of epigenetic mechanisms in the brain (DNA methylation, histone modification, and noncoding RNA action) and discuss their impact proximally on gene transcription, protein synthesis, and synaptic plasticity and distally on learning, memory, and other cognitive functions. Of particular importance are observations that neuronal activation regulates the dynamics of the epigenome's functioning under precise timing, with subsequent alterations in the gene expression profile. In turn, epigenetic regulation impacts neuronal action, closing the circle and substantiating the signaling pathways that underlie, at least partially, learning, memory, and other cognitive processes.
Collapse
|
22
|
Sneppen K, Dodd IB. Nucleosome dynamics and maintenance of epigenetic states of CpG islands. Phys Rev E 2016; 93:062417. [PMID: 27415308 DOI: 10.1103/physreve.93.062417] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Indexed: 01/02/2023]
Abstract
Methylation of mammalian DNA occurs primarily at CG dinucleotides. These CpG sites are located nonrandomly in the genome, tending to occur within high density clusters of CpGs (islands) or within large regions of low CpG density. Cluster methylation tends to be bimodal, being dominantly unmethylated or mostly methylated. For CpG clusters near promoters, low methylation is associated with transcriptional activity, while high methylation is associated with gene silencing. Alternative CpG methylation states are thought to be stable and heritable, conferring localized epigenetic memory that allows transient signals to create long-lived gene expression states. Positive feedback where methylated CpG sites recruit enzymes that methylate nearby CpGs, can produce heritable bistability but does not easily explain that as clusters increase in size or density they change from being primarily methylated to primarily unmethylated. Here, we show that an interaction between the methylation state of a cluster and its occupancy by nucleosomes provides a mechanism to generate these features and explain genome wide systematics of CpG islands.
Collapse
Affiliation(s)
- Kim Sneppen
- Center for Models of Life, Niels Bohr Institute, Blegdamsvej 17, 2100 Copenhagen, Denmark
| | - Ian B Dodd
- Department of Molecular and Cellular Biology, University of Adelaide, Adelaide SA 5005, Australia
| |
Collapse
|
23
|
von Meyenn F, Iurlaro M, Habibi E, Liu NQ, Salehzadeh-Yazdi A, Santos F, Petrini E, Milagre I, Yu M, Xie Z, Kroeze LI, Nesterova TB, Jansen JH, Xie H, He C, Reik W, Stunnenberg HG. Impairment of DNA Methylation Maintenance Is the Main Cause of Global Demethylation in Naive Embryonic Stem Cells. Mol Cell 2016; 62:848-861. [PMID: 27237052 PMCID: PMC4914828 DOI: 10.1016/j.molcel.2016.04.025] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/04/2016] [Accepted: 04/21/2016] [Indexed: 12/20/2022]
Abstract
Global demethylation is part of a conserved program of epigenetic reprogramming to naive pluripotency. The transition from primed hypermethylated embryonic stem cells (ESCs) to naive hypomethylated ones (serum-to-2i) is a valuable model system for epigenetic reprogramming. We present a mathematical model, which accurately predicts global DNA demethylation kinetics. Experimentally, we show that the main drivers of global demethylation are neither active mechanisms (Aicda, Tdg, and Tet1-3) nor the reduction of de novo methylation. UHRF1 protein, the essential targeting factor for DNMT1, is reduced upon transition to 2i, and so is recruitment of the maintenance methylation machinery to replication foci. Concurrently, there is global loss of H3K9me2, which is needed for chromatin binding of UHRF1. These mechanisms synergistically enforce global DNA hypomethylation in a replication-coupled fashion. Our observations establish the molecular mechanism for global demethylation in naive ESCs, which has key parallels with those operating in primordial germ cells and early embryos. Impaired DNA methylation maintenance is the cause of global demethylation in naive ESCs Loss of H3K9me2 and UHRF1 lead to impaired maintenance targeting to replication foci TET enzymes are not required for global demethylation Mathematical model accurately predicts global 5mC and 5hmC during epigenetic resetting
Collapse
Affiliation(s)
| | - Mario Iurlaro
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Ehsan Habibi
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525GA Nijmegen, the Netherlands
| | - Ning Qing Liu
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525GA Nijmegen, the Netherlands
| | - Ali Salehzadeh-Yazdi
- Hematology-Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Fátima Santos
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Edoardo Petrini
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Inês Milagre
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Miao Yu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Zhenqing Xie
- Virginia Bioinformatics Institute and Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24060, USA
| | - Leonie I Kroeze
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Nijmegen Medical Centre and Radboudumc Institute for Molecular Life Sciences (RIMLS), 6525GA Nijmegen, the Netherlands
| | - Tatyana B Nesterova
- Developmental Epigenetics Group, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Joop H Jansen
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Nijmegen Medical Centre and Radboudumc Institute for Molecular Life Sciences (RIMLS), 6525GA Nijmegen, the Netherlands
| | - Hehuang Xie
- Virginia Bioinformatics Institute and Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24060, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Wolf Reik
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525GA Nijmegen, the Netherlands.
| |
Collapse
|
24
|
Yuan L, Chan GC, Beeler D, Janes L, Spokes KC, Dharaneeswaran H, Mojiri A, Adams WJ, Sciuto T, Garcia-Cardeña G, Molema G, Kang PM, Jahroudi N, Marsden PA, Dvorak A, Regan ER, Aird WC. A role of stochastic phenotype switching in generating mosaic endothelial cell heterogeneity. Nat Commun 2016; 7:10160. [PMID: 26744078 PMCID: PMC5154372 DOI: 10.1038/ncomms10160] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 11/10/2015] [Indexed: 01/20/2023] Open
Abstract
Previous studies have shown that biological noise may drive dynamic phenotypic mosaicism in isogenic unicellular organisms. However, there is no evidence for a similar mechanism operating in metazoans. Here we show that the endothelial-restricted gene, von Willebrand factor (VWF), is expressed in a mosaic pattern in the capillaries of many vascular beds and in the aorta. In capillaries, the mosaicism is dynamically regulated, with VWF switching between ON and OFF states during the lifetime of the animal. Clonal analysis of cultured endothelial cells reveals that dynamic mosaic heterogeneity is controlled by a low-barrier, noise-sensitive bistable switch that involves random transitions in the DNA methylation status of the VWF promoter. Finally, the hearts of VWF-null mice demonstrate an abnormal endothelial phenotype as well as cardiac dysfunction. Together, these findings suggest a novel stochastic phenotype switching strategy for adaptive homoeostasis in the adult vasculature.
Collapse
Affiliation(s)
- Lei Yuan
- Center for Vascular Biology Research, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA.,Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA
| | - Gary C Chan
- Center for Vascular Biology Research, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA.,Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA
| | - David Beeler
- Center for Vascular Biology Research, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA.,Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA
| | - Lauren Janes
- Center for Vascular Biology Research, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA.,Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA
| | - Katherine C Spokes
- Center for Vascular Biology Research, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA.,Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA
| | - Harita Dharaneeswaran
- Center for Vascular Biology Research, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA.,Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA
| | - Anahita Mojiri
- Department of Medicine, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - William J Adams
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA
| | - Tracey Sciuto
- Center for Vascular Biology Research, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA.,Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA
| | - Guillermo Garcia-Cardeña
- Center for Excellence in Vascular Biology, Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02215, USA
| | - Grietje Molema
- Department of Pathology and Medical Biology, Medical Biology Section, University Medical Center Groningen, University of Groningen, 9700 AB Groningen, The Netherlands
| | - Peter M Kang
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA.,Cardiovascular Institute, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA
| | - Nadia Jahroudi
- Department of Medicine, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Philip A Marsden
- Department of Medicine, University of Toronto, Toronto, Ontario M5G 2C4, Canada.,St. Michaels's Hospital, Toronto, Ontario M5B 1W8, Canada
| | - Ann Dvorak
- Center for Vascular Biology Research, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA.,Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA
| | - Erzsébet Ravasz Regan
- Center for Vascular Biology Research, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA.,Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA
| | - William C Aird
- Center for Vascular Biology Research, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA.,Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA
| |
Collapse
|
25
|
Vincent ZL, Mitchell MD, Ponnampalam AP. Regulation of TIMP-1 in Human Placenta and Fetal Membranes by lipopolysaccharide and demethylating agent 5-aza-2'-deoxycytidine. Reprod Biol Endocrinol 2015; 13:136. [PMID: 26691525 PMCID: PMC4687108 DOI: 10.1186/s12958-015-0132-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 12/09/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND An appropriate transcriptional profile in the placenta and fetal membranes is required for successful pregnancy; any variations may lead to inappropriate timing of birth. Epigenetic regulation through reversible modification of chromatin has emerged as a fundamental mechanism for the control of gene expression in a range of biological systems and can be modified by pharmacological intervention, thus providing novel therapeutic avenues. TIMP-1 is an endogenous inhibitor of MMPs, and hence is intimately involved in maintaining the integrity of the fetal membranes until labor. OBJECTIVE AND METHODS To determine if TIMP-1 is regulated by DNA methylation in gestational tissues we employed an in vitro model in which gestational tissue explants were treated with demethylating agent 5-aza-2'-deoxycytidine (AZA) and lipopolysaccharide (LPS). RESULTS Quantitative Real-Time PCR (qRT-PCR) revealed that TIMP-1 transcription was significantly increased by combined treatment of AZA and LPS, but not LPS alone, in villous, amnion and choriodecidua explants after 24 and 48 hrs, whilst western blotting showed protein production was stimulated after 24 hrs only. Upon interrogation of the TIMP-1 promoter using Sequenom EpiTyper MassARRAY, we discovered sex-specific differential methylation, in part explained by x-linked methylation in females. Increased TIMP-1 in the presence of LPS was potentiated by AZA treatment, signifying that a change in chromatin structure, but not in DNA methylation at the promoter region, is required for transcriptional activators to access the promoter region of TIMP-1. CONCLUSIONS Collectively, these observations support a potential role for pharmacological agents that modify chromatin structure to be utilized in the therapeutic targeting of TIMP-1 to prevent premature rupture of the fetal membranes in an infectious setting.
Collapse
Affiliation(s)
- Zoë L Vincent
- Liggins Institute, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
- Gravida: National Centre for Growth and Development, Palmerston North, New Zealand
| | - Murray D Mitchell
- Liggins Institute, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
- University of Queensland Centre for Clinical Research, Brisbane, Australia
| | - Anna P Ponnampalam
- Liggins Institute, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.
- Gravida: National Centre for Growth and Development, Palmerston North, New Zealand.
- The Heart Foundation, Auckland, New Zealand.
| |
Collapse
|
26
|
Ferguson LR, Chen H, Collins AR, Connell M, Damia G, Dasgupta S, Malhotra M, Meeker AK, Amedei A, Amin A, Ashraf SS, Aquilano K, Azmi AS, Bhakta D, Bilsland A, Boosani CS, Chen S, Ciriolo MR, Fujii H, Guha G, Halicka D, Helferich WG, Keith WN, Mohammed SI, Niccolai E, Yang X, Honoki K, Parslow VR, Prakash S, Rezazadeh S, Shackelford RE, Sidransky D, Tran PT, Yang ES, Maxwell CA. Genomic instability in human cancer: Molecular insights and opportunities for therapeutic attack and prevention through diet and nutrition. Semin Cancer Biol 2015; 35 Suppl:S5-S24. [PMID: 25869442 PMCID: PMC4600419 DOI: 10.1016/j.semcancer.2015.03.005] [Citation(s) in RCA: 195] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 03/08/2015] [Accepted: 03/13/2015] [Indexed: 02/06/2023]
Abstract
Genomic instability can initiate cancer, augment progression, and influence the overall prognosis of the affected patient. Genomic instability arises from many different pathways, such as telomere damage, centrosome amplification, epigenetic modifications, and DNA damage from endogenous and exogenous sources, and can be perpetuating, or limiting, through the induction of mutations or aneuploidy, both enabling and catastrophic. Many cancer treatments induce DNA damage to impair cell division on a global scale but it is accepted that personalized treatments, those that are tailored to the particular patient and type of cancer, must also be developed. In this review, we detail the mechanisms from which genomic instability arises and can lead to cancer, as well as treatments and measures that prevent genomic instability or take advantage of the cellular defects caused by genomic instability. In particular, we identify and discuss five priority targets against genomic instability: (1) prevention of DNA damage; (2) enhancement of DNA repair; (3) targeting deficient DNA repair; (4) impairing centrosome clustering; and, (5) inhibition of telomerase activity. Moreover, we highlight vitamin D and B, selenium, carotenoids, PARP inhibitors, resveratrol, and isothiocyanates as priority approaches against genomic instability. The prioritized target sites and approaches were cross validated to identify potential synergistic effects on a number of important areas of cancer biology.
Collapse
Affiliation(s)
| | - Helen Chen
- Department of Pediatrics, University of British Columbia, Michael Cuccione Childhood Cancer Research Program, Child and Family Research Institute, Vancouver, Canada
| | - Andrew R Collins
- Department of Nutrition, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Marisa Connell
- Department of Pediatrics, University of British Columbia, Michael Cuccione Childhood Cancer Research Program, Child and Family Research Institute, Vancouver, Canada
| | - Giovanna Damia
- Department of Oncology, Instituti di Ricovero e Cura a Carattere Scientifico-Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Santanu Dasgupta
- Department of Cellular and Molecular Biology, The University of Texas Health Science Center at Tyler, Tyler, United States
| | | | - Alan K Meeker
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Amedeo Amedei
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Amr Amin
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates; Faculty of Science, Cairo University, Cairo, Egypt
| | - S Salman Ashraf
- Department of Chemistry, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Katia Aquilano
- Department of Biology, Università di Roma Tor Vergata, Rome, Italy
| | - Asfar S Azmi
- Department of Biology, University of Rochester, Rochester, United States
| | - Dipita Bhakta
- School of Chemical and BioTechnology, SASTRA University, Thanjavur, Tamil Nadu, India
| | - Alan Bilsland
- Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Chandra S Boosani
- Department of BioMedical Sciences, Creighton University, Omaha, NE, United States
| | - Sophie Chen
- Department of Research & Development, Ovarian and Prostate Cancer Research Trust Laboratory, Guildford, Surrey, United Kingdom
| | | | - Hiromasa Fujii
- Department of Orthopaedic Surgery, Nara Medical University, Kashihara, Nara, Japan
| | - Gunjan Guha
- School of Chemical and BioTechnology, SASTRA University, Thanjavur, Tamil Nadu, India
| | | | - William G Helferich
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - W Nicol Keith
- Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Sulma I Mohammed
- Department of Comparative Pathobiology and Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, United States
| | - Elena Niccolai
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Xujuan Yang
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Kanya Honoki
- Department of Orthopaedic Surgery, Nara Medical University, Kashihara, Nara, Japan
| | | | - Satya Prakash
- School of Pharmacy, University College Cork, Cork, Ireland
| | - Sarallah Rezazadeh
- Department of Biology, University of Rochester, Rochester, United States
| | - Rodney E Shackelford
- Department of Pathology, Louisiana State University Health Shreveport, Shreveport, LA, United States
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Phuoc T Tran
- Departments of Radiation Oncology & Molecular Radiation Sciences, Oncology and Urology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Eddy S Yang
- Department of Radiation Oncology, University of Alabama at Birmingham School of Medicine, Birmingham, AL, United States
| | - Christopher A Maxwell
- Department of Pediatrics, University of British Columbia, Michael Cuccione Childhood Cancer Research Program, Child and Family Research Institute, Vancouver, Canada.
| |
Collapse
|
27
|
Couldrey C, Brauning R, Henderson HV, McEwan JC. Genome-wide DNA methylation analysis: no evidence for stable hemimethylation in the sheep muscle genome. Anim Genet 2015; 46:185-9. [PMID: 25662407 DOI: 10.1111/age.12268] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2014] [Indexed: 11/28/2022]
Abstract
The importance of maintaining DNA methylation patterns and faithful transmission of these patterns during cell division to ensure appropriate gene expression has been known for many decades now. It has largely been assumed that the symmetrical nature of CpG motifs, the most common site for DNA methylation in mammals, together with the presence of maintenance methylases able to methylate newly synthesised DNA, ensures that there is concordance of methylation on both strands. However, although this assumption is compelling in theory, little experimental evidence exists that either supports or refutes this assumption. Here, we have undertaken a genome-wide single-nucleotide resolution analysis to determine the frequency with which hemimethylated CpG sites exist in sheep muscle tissue. Analysis of multiple independent samples provides strong evidence that stably maintained hemimethylation is a very rare occurrence, at least in this tissue. Given the rarity of stably maintained hemimethylation, next-generation sequencing data from both DNA strands may be carefully combined to increase the accuracy with which DNA methylation can be measured at single-nucleotide resolution.
Collapse
Affiliation(s)
- C Couldrey
- Ruakura Research Centre, AgResearch Ltd., 10 Bisley Road, Hamilton, New Zealand
| | | | | | | |
Collapse
|
28
|
Eissenberg JC. Epigenetics: modifying the genetic blueprint. MISSOURI MEDICINE 2014; 111:428-433. [PMID: 25438366 PMCID: PMC6172102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The sequence of the human genome represents our genetic blueprint. While it is now possible to draw direct connections between specific DNA sequences and specific physical features and to predict disease risk, the effects of certain genes can be masked by a process called "epigenetics." Here, I summarize our current understanding of epigenetics and it affects gene expression, with impacts on health and aging.
Collapse
|
29
|
Zeng J, Nagrajan HK, Yi SV. Fundamental diversity of human CpG islands at multiple biological levels. Epigenetics 2014; 9:483-91. [PMID: 24419148 PMCID: PMC4121359 DOI: 10.4161/epi.27654] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
CpG islands (CGIs) are commonly used as genomic markers to study the patterns and regulatory consequences of DNA methylation. Interestingly, recent studies reveal a substantial diversity among CGIs: long and short CGIs, for example, exhibit contrasting patterns of gene expression complexity and nucleosome occupancy. Evolutionary origins of CGIs are also highly heterogeneous. In order to systematically evaluate potential diversities among CGIs and ultimately to illuminate the link between diversity of CGIs and their epigenetic variation, we analyzed the nucleotide-resolution DNA methylation maps (methylomes) of multiple cellular origins. We discover novel ‘clusters’ of CGIs according to their patterns of DNA methylation; the stably hypomethylated CGI cluster (cluster I), sperm-hypomethylated CGI cluster (cluster II), and variably methylated CGI cluster (cluster III). These epigenomic CGI clusters are strikingly distinct at multiple biological features including genomic, evolutionary, and functional characteristics. At the genomic level, the stably hypomethylated CGI cluster tends to be longer and harbors many more CpG dinucleotides than those in other clusters. They are also frequently associated with promoters, while CGI clusters II and III mostly reside in intragenic or intergenic regions and exhibit highly tissue-specific DNA methylation. Functional ontology terms and transcriptional profiles co-vary with CGI clusters, indicating that the regulatory functions of CGIs are tightly linked to their heterogeneity. Finally, CGIs associated with distinctive biological processes, such as diseases, aging, and imprinting, occur disproportionately across CGI clusters. These new findings provide an effective means to combine existing knowledge on CGIs into a genomic context while bringing new insights that elucidate the significance of DNA methylation across different biological conditions and demography.
Collapse
Affiliation(s)
- Jia Zeng
- School of Biology; Georgia Institute of Technology; Atlanta, GA USA
| | - Hema K Nagrajan
- School of Biology; Georgia Institute of Technology; Atlanta, GA USA
| | - Soojin V Yi
- School of Biology; Georgia Institute of Technology; Atlanta, GA USA
| |
Collapse
|
30
|
Haerter JO, Lövkvist C, Dodd IB, Sneppen K. Collaboration between CpG sites is needed for stable somatic inheritance of DNA methylation states. Nucleic Acids Res 2013; 42:2235-44. [PMID: 24288373 PMCID: PMC3936770 DOI: 10.1093/nar/gkt1235] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Inheritance of 5-methyl cytosine modification of CpG (CG/CG) DNA sequences is needed to maintain early developmental decisions in vertebrates. The standard inheritance model treats CpGs as independent, with methylated CpGs maintained by efficient methylation of hemimethylated CpGs produced after DNA replication, and unmethylated CpGs maintained by an absence of de novo methylation. By stochastic simulations of CpG islands over multiple cell cycles and systematic sampling of reaction parameters, we show that the standard model is inconsistent with many experimental observations. In contrast, dynamic collaboration between CpGs can provide strong error-tolerant somatic inheritance of both hypermethylated and hypomethylated states of a cluster of CpGs, reproducing observed stable bimodal methylation patterns. Known recruitment of methylating enzymes by methylated CpGs could provide the necessary collaboration, but we predict that recruitment of demethylating enzymes by unmethylated CpGs strengthens inheritance and allows CpG islands to remain hypomethylated within a sea of hypermethylation.
Collapse
Affiliation(s)
- Jan O Haerter
- Center for Models of Life, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, DK-2100 Copenhagen, Denmark and Department of Molecular and Biomedical Sciences (Biochemistry), University of Adelaide, SA 5005, Australia
| | | | | | | |
Collapse
|
31
|
Hormoz S. Stem cell population asymmetry can reduce rate of replicative aging. J Theor Biol 2013; 331:19-27. [PMID: 23623948 DOI: 10.1016/j.jtbi.2013.04.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Revised: 04/11/2013] [Accepted: 04/16/2013] [Indexed: 01/17/2023]
Abstract
Cycling tissues such as the intestinal epithelium, germ line, and hair follicles, require a constant flux of differentiated cells. These tissues are maintained by a population of stem cells, which generate differentiated progenies and self-renew. Asymmetric division of each stem cell into one stem cell and one differentiated cell can accomplish both tasks. However, in mammalian cycling tissues, some stem cells divide symmetrically into two differentiated cells and are replaced by a neighbor that divides symmetrically into two stem cells. Besides this heterogeneity in fate (population asymmetry), stem cells also exhibit heterogenous proliferation-rates; in the long run, however, all stem cells proliferate at the same average rate (equipotency). We construct and simulate a mathematical model based on these experimental observations. We show that the complex steady-state dynamics of population-asymmetric stem cells reduces the rate of replicative aging of the tissue-potentially lowering the incidence of somatic mutations and genetics diseases such as cancer. Essentially, slow-dividing stem cells proliferate and purge the population of the fast-dividing - older - cells which had undertaken the majority of the tissue-generation burden. As the number of slow-dividing cells grows, their cycling-rate increases, eventually turning them into fast-dividers, which are themselves replaced by newly emerging slow-dividers. Going beyond current experiments, we propose a mechanism for equipotency that can potentially halve the rate of replicative aging. Our results highlight the importance of a population-level understanding of stem cells, and may explain the prevalence of population asymmetry in a wide variety of cycling tissues.
Collapse
Affiliation(s)
- Sahand Hormoz
- Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, USA.
| |
Collapse
|
32
|
de Andrés MC, Kingham E, Imagawa K, Gonzalez A, Roach HI, Wilson DI, Oreffo ROC. Epigenetic regulation during fetal femur development: DNA methylation matters. PLoS One 2013; 8:e54957. [PMID: 23383012 PMCID: PMC3557259 DOI: 10.1371/journal.pone.0054957] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Accepted: 12/18/2012] [Indexed: 01/09/2023] Open
Abstract
Epigenetic modifications are heritable changes in gene expression without changes in DNA sequence. DNA methylation has been implicated in the control of several cellular processes including differentiation, gene regulation, development, genomic imprinting and X-chromosome inactivation. Methylated cytosine residues at CpG dinucleotides are commonly associated with gene repression; conversely, strategic loss of methylation during development could lead to activation of lineage-specific genes. Evidence is emerging that bone development and growth are programmed; although, interestingly, bone is constantly remodelled throughout life. Using human embryonic stem cells, human fetal bone cells (HFBCs), adult chondrocytes and STRO-1+ marrow stromal cells from human bone marrow, we have examined a spectrum of developmental stages of femur development and the role of DNA methylation therein. Using pyrosequencing methodology we analysed the status of methylation of genes implicated in bone biology; furthermore, we correlated these methylation levels with gene expression levels using qRT-PCR and protein distribution during fetal development evaluated using immunohistochemistry. We found that during fetal femur development DNA methylation inversely correlates with expression of genes including iNOS (NOS2) and COL9A1, but not catabolic genes including MMP13 and IL1B. Furthermore, significant demethylation was evident in the osteocalcin promoter between the fetal and adult developmental stages. Increased TET1 expression and decreased expression of DNA (cytosine-5-)-methyltransferase 1 (DNMT1) in adult chondrocytes compared to HFBCs could contribute to the loss of methylation observed during fetal development. HFBC multipotency confirms these cells to be an ideal developmental system for investigation of DNA methylation regulation. In conclusion, these findings demonstrate the role of epigenetic regulation, specifically DNA methylation, in bone development, informing and opening new possibilities in development of strategies for bone repair/tissue engineering.
Collapse
Affiliation(s)
- María C. de Andrés
- Bone and Joint Research Group, University of Southampton, Southampton, United Kingdom
- Centre for Human Development, Stem Cells and Regeneration Human Development and Health, Institute of Developmental Sciences, University of Southampton, Southampton, United Kingdom
- Instituto de Investigación Sanitaria-Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain
| | - Emmajayne Kingham
- Bone and Joint Research Group, University of Southampton, Southampton, United Kingdom
- Centre for Human Development, Stem Cells and Regeneration Human Development and Health, Institute of Developmental Sciences, University of Southampton, Southampton, United Kingdom
| | - Kei Imagawa
- Bone and Joint Research Group, University of Southampton, Southampton, United Kingdom
- Centre for Human Development, Stem Cells and Regeneration Human Development and Health, Institute of Developmental Sciences, University of Southampton, Southampton, United Kingdom
- Tohoku University School of Medicine, Sendai, Japan
| | - Antonio Gonzalez
- Instituto de Investigación Sanitaria-Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain
| | - Helmtrud I. Roach
- Bone and Joint Research Group, University of Southampton, Southampton, United Kingdom
- Centre for Human Development, Stem Cells and Regeneration Human Development and Health, Institute of Developmental Sciences, University of Southampton, Southampton, United Kingdom
| | - David I. Wilson
- Centre for Human Development, Stem Cells and Regeneration Human Development and Health, Institute of Developmental Sciences, University of Southampton, Southampton, United Kingdom
| | - Richard O. C. Oreffo
- Bone and Joint Research Group, University of Southampton, Southampton, United Kingdom
- Centre for Human Development, Stem Cells and Regeneration Human Development and Health, Institute of Developmental Sciences, University of Southampton, Southampton, United Kingdom
- Stem Cell Unit, Department of Anatomy, College of Medicine, King Saud University, Riyadh, Kingdom of Saudi Arabia
- * E-mail:
| |
Collapse
|
33
|
Normal DNA methylation dynamics in DICER1-deficient mouse embryonic stem cells. PLoS Genet 2012; 8:e1002919. [PMID: 22969435 PMCID: PMC3435250 DOI: 10.1371/journal.pgen.1002919] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Accepted: 07/09/2012] [Indexed: 11/19/2022] Open
Abstract
Reduced DNA methylation has been reported in DICER1-deficient mouse ES cells. Reductions seen at pericentric satellite repeats have suggested that siRNAs are required for the proper assembly of heterochromatin. More recent studies have postulated that the reduced methylation is an indirect effect: the loss of Mir290 cluster miRNAs leads to upregulation of the transcriptional repressor RBL2 that targets the downregulation of DNA methyltransferase (Dnmt) genes. However, the observations have been inconsistent. We surmised that the inconsistency could be related to cell line “age,” given that DNA methylation is lost progressively with passage in DNMT-deficient ES cells. We therefore subjected Dicer1−/− ES cells to two experimental regimes to rigorously test the level of functional DNMT activity. First, we cultured them for a prolonged period. If DNMT activity was reduced, further losses of methylation would occur. Second, we measured their DNMT activity in a rebound DNA methylation assay: DNA methylation was stripped from Cre/loxP conditionally mutant Dicer1 ES cells using a shRNA targeting Dnmt1 mRNA. Cre expression then converted these cells to Dicer1−/−, allowing for DNMT1 recovery and forcing the cells to remethylate in the absence of RNAi. In both cases, we found functional DNMT activity to be normal. Finally, we also show that the level of RBL2 protein is not at excess levels in Dicer1−/− ES cells as has been assumed. These studies reveal that reduced functional DNMT activity is not a salient feature of DICER1-deficient ES cells. We suggest that the reduced DNA methylation sometimes observed in these cells could be due to stochastic alterations in DNA methylation patterns that could offer growth or survival advantages in culture, or to the dysregulation of pathways acting in opposition to the DNMT pathway. In mammalian cells, DNA methylation is required for the maintenance of genome stability. Recent studies have shown that the genome-wide levels of DNA methylation can be reduced in DICER1-deficient mouse embryonic stem (ES) cells, suggesting that the activity of DNA methylating enzymes (DNMTs) may be regulated by small RNA molecules. The enzyme DICER1 catalyses the production of these small RNAs that serve as sequence-specific guides for modifying chromatin or transcription. However, these observations of defective DNA methylation have been inconsistent. We surmised that this inconsistency could be due to cell line “age,” because it can take many cell divisions before reduced DNMT activity may result in loss of DNA methylation. To test this idea, we rigorously assayed the functional level of DNMT activity in DICER1-deficient ES cells. First, we tested their ability to maintain DNA methylation over prolonged culture. Second, we tested their ability to rebound in DNA methylation after first stripping it from the genome. In both cases functional DNMT activity was entirely normal. We suggest that losses of DNA methylation sometimes seen in DICER1-deficient ES cells is stochastic and could involve cell line adaptation.
Collapse
|
34
|
DNA Hypomethylation and Hemimethylation in Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 754:31-56. [DOI: 10.1007/978-1-4419-9967-2_2] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
35
|
McGovern AP, Powell BE, Chevassut TJT. A dynamic multi-compartmental model of DNA methylation with demonstrable predictive value in hematological malignancies. J Theor Biol 2012; 310:14-20. [PMID: 22728673 DOI: 10.1016/j.jtbi.2012.06.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 06/12/2012] [Accepted: 06/13/2012] [Indexed: 11/19/2022]
Abstract
Recent advances have highlighted the central role of DNA methylation in leukemogenesis and have led to clinical trials of epigenetic therapy, notably hypomethylating agents, in myelodysplasia and acute myeloid leukemia. However, despite these advances, our understanding of the dynamic regulation of the methylome remains poor. We have attempted to address this shortcoming by producing a dynamic, six-compartmental model of DNA methylation levels based on the activity of the Dnmt methyltransferase proteins. In addition, the model incorporates the recently discovered Tet family proteins which enzymatically convert methylcytosine to hydroxymethylcytosine. A set of first order, partial differential equations comprise the model and were solved via numerical integration. The model is able to predict the relative abundances of unmethylated, hemimethylated, fully methylated, and hydroxymethylated CpG dyads in the DNA of cells with fully functional Dnmt and Tet proteins. In addition, the model accurately predicts the experimentally measured changes in these abundances with disruption of Dnmt function. Furthermore, the model reveals the mechanism whereby CpG islands are maintained in a hypomethylated state via local modulation of Dnmt and Tet activities without any requirement for active demethylation. We conclude that this model provides an accurate depiction of the major epigenetic processes involving modification of DNA.
Collapse
Affiliation(s)
- Andrew P McGovern
- Medical Research Building, Brighton and Sussex Medical School, University of Sussex, Falmer, Brighton BN1 9PS, UK
| | | | | |
Collapse
|
36
|
Arand J, Spieler D, Karius T, Branco MR, Meilinger D, Meissner A, Jenuwein T, Xu G, Leonhardt H, Wolf V, Walter J. In vivo control of CpG and non-CpG DNA methylation by DNA methyltransferases. PLoS Genet 2012; 8:e1002750. [PMID: 22761581 PMCID: PMC3386304 DOI: 10.1371/journal.pgen.1002750] [Citation(s) in RCA: 294] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Accepted: 04/20/2012] [Indexed: 12/14/2022] Open
Abstract
The enzymatic control of the setting and maintenance of symmetric and non-symmetric DNA methylation patterns in a particular genome context is not well understood. Here, we describe a comprehensive analysis of DNA methylation patterns generated by high resolution sequencing of hairpin-bisulfite amplicons of selected single copy genes and repetitive elements (LINE1, B1, IAP-LTR-retrotransposons, and major satellites). The analysis unambiguously identifies a substantial amount of regional incomplete methylation maintenance, i.e. hemimethylated CpG positions, with variant degrees among cell types. Moreover, non-CpG cytosine methylation is confined to ESCs and exclusively catalysed by Dnmt3a and Dnmt3b. This sequence position-, cell type-, and region-dependent non-CpG methylation is strongly linked to neighboring CpG methylation and requires the presence of Dnmt3L. The generation of a comprehensive data set of 146,000 CpG dyads was used to apply and develop parameter estimated hidden Markov models (HMM) to calculate the relative contribution of DNA methyltransferases (Dnmts) for de novo and maintenance DNA methylation. The comparative modelling included wild-type ESCs and mutant ESCs deficient for Dnmt1, Dnmt3a, Dnmt3b, or Dnmt3a/3b, respectively. The HMM analysis identifies a considerable de novo methylation activity for Dnmt1 at certain repetitive elements and single copy sequences. Dnmt3a and Dnmt3b contribute de novo function. However, both enzymes are also essential to maintain symmetrical CpG methylation at distinct repetitive and single copy sequences in ESCs.
Collapse
Affiliation(s)
- Julia Arand
- Department of Biological Sciences, Institute of Genetics/Epigenetics, University of Saarland, Saarbrücken, Germany
| | - David Spieler
- Department of Computer Science, University of Saarland, Saarbrücken, Germany
| | - Tommy Karius
- Department of Biological Sciences, Institute of Genetics/Epigenetics, University of Saarland, Saarbrücken, Germany
| | - Miguel R. Branco
- Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom
- Centre for Trophoblast Research, University of Cambridge, Cambridge, United Kingdom
| | - Daniela Meilinger
- Department of Biology II, LMU München, Biozentrum Martinsried, Martinsried, Germany
| | - Alexander Meissner
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | | | - Guoliang Xu
- Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Heinrich Leonhardt
- Department of Biology II, LMU München, Biozentrum Martinsried, Martinsried, Germany
| | - Verena Wolf
- Department of Computer Science, University of Saarland, Saarbrücken, Germany
| | - Jörn Walter
- Department of Biological Sciences, Institute of Genetics/Epigenetics, University of Saarland, Saarbrücken, Germany
| |
Collapse
|
37
|
Abstract
DNA hypomethylation was the initial epigenetic abnormality recognized in human tumors. However, for several decades after its independent discovery by two laboratories in 1983, it was often ignored as an unwelcome complication, with almost all of the attention on the hypermethylation of promoters of genes that are silenced in cancers (e.g., tumor-suppressor genes). Because it was subsequently shown that global hypomethylation of DNA in cancer was most closely associated with repeated DNA elements, cancer linked-DNA hypomethylation continued to receive rather little attention. DNA hypomethylation in cancer can no longer be considered an oddity, because recent high-resolution genome-wide studies confirm that DNA hypomethylation is the almost constant companion to hypermethylation of the genome in cancer, just usually (but not always) in different sequences. Methylation changes at individual CpG dyads in cancer can have a high degree of dependence not only on the regional context, but also on neighboring sites. DNA demethylation during carcinogenesis may involve hemimethylated dyads as intermediates, followed by spreading of the loss of methylation on both strands. In this review, active demethylation of DNA and the relationship of cancer-associated DNA hypomethylation to cancer stem cells are discussed. Evidence is accumulating for the biological significance and clinical relevance of DNA hypomethylation in cancer, and for cancer-linked demethylation and de novo methylation being highly dynamic processes.
Collapse
Affiliation(s)
- Melanie Ehrlich
- Hayward Genetics Program, Department of Biochemistry, Tulane Cancer Center, Tulane Medical School, 1430 TulaneAvenue, New Orleans, LA 70112, USA.
| |
Collapse
|
38
|
Teng M, Balch C, Liu Y, Li M, Huang THM, Wang Y, Nephew KP, Li L. The influence of cis-regulatory elements on DNA methylation fidelity. PLoS One 2012; 7:e32928. [PMID: 22412954 PMCID: PMC3295790 DOI: 10.1371/journal.pone.0032928] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Accepted: 02/05/2012] [Indexed: 12/22/2022] Open
Abstract
It is now established that, as compared to normal cells, the cancer cell genome has an overall inverse distribution of DNA methylation (“methylome”), i.e., predominant hypomethylation and localized hypermethylation, within “CpG islands” (CGIs). Moreover, although cancer cells have reduced methylation “fidelity” and genomic instability, accurate maintenance of aberrant methylomes that underlie malignant phenotypes remains necessary. However, the mechanism(s) of cancer methylome maintenance remains largely unknown. Here, we assessed CGI methylation patterns propagated over 1, 3, and 5 divisions of A2780 ovarian cancer cells, concurrent with exposure to the DNA cross-linking chemotherapeutic cisplatin, and observed cell generation-successive increases in total hyper- and hypo-methylated CGIs. Empirical Bayesian modeling revealed five distinct modes of methylation propagation: (1) heritable (i.e., unchanged) high- methylation (1186 probe loci in CGI microarray); (2) heritable (i.e., unchanged) low-methylation (286 loci); (3) stochastic hypermethylation (i.e., progressively increased, 243 loci); (4) stochastic hypomethylation (i.e., progressively decreased, 247 loci); and (5) considerable “random” methylation (582 loci). These results support a “stochastic model” of DNA methylation equilibrium deriving from the efficiency of two distinct processes, methylation maintenance and de novo methylation. A role for cis-regulatory elements in methylation fidelity was also demonstrated by highly significant (p<2.2×10−5) enrichment of transcription factor binding sites in CGI probe loci showing heritably high (118 elements) and low (47 elements) methylation, and also in loci demonstrating stochastic hyper-(30 elements) and hypo-(31 elements) methylation. Notably, loci having “random” methylation heritability displayed nearly no enrichment. These results demonstrate an influence of cis-regulatory elements on the nonrandom propagation of both strictly heritable and stochastically heritable CGIs.
Collapse
Affiliation(s)
- Mingxiang Teng
- Harbin Institute of Technology, School of Computer Science and Technology, Harbin, Heilongjiang, China
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Curt Balch
- Medical Sciences Program, Indiana University, Bloomington, Indiana, United States of America
- Indiana University Melvin and Bren Simon Cancer, Indianapolis, Indiana, United States of America
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Indiana University Melvin and Bren Simon Cancer, Indianapolis, Indiana, United States of America
| | - Meng Li
- Medical Sciences Program, Indiana University, Bloomington, Indiana, United States of America
| | - Tim H. M. Huang
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America
| | - Yadong Wang
- Harbin Institute of Technology, School of Computer Science and Technology, Harbin, Heilongjiang, China
- * E-mail: (YW); (KPN); (LL)
| | - Kenneth P. Nephew
- Medical Sciences Program, Indiana University, Bloomington, Indiana, United States of America
- Indiana University Melvin and Bren Simon Cancer, Indianapolis, Indiana, United States of America
- Departments of Cellular and Integrative Physiology and Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- * E-mail: (YW); (KPN); (LL)
| | - Lang Li
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Indiana University Melvin and Bren Simon Cancer, Indianapolis, Indiana, United States of America
- Indiana Institute of Personalized Medicine, Departments of Cellular and Integrative Physiology and Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- * E-mail: (YW); (KPN); (LL)
| |
Collapse
|
39
|
Mann JR, Mattiske DM. RNA interference in mammalian DNA methylation1This review is part of Special Issue entitled Asilomar Chromatin and has undergone the Journal’s usual peer review process. Biochem Cell Biol 2012; 90:70-7. [DOI: 10.1139/o11-050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
RNAi and Dicer-dependent siRNAs are required for constitutive heterochromatin formation in fission yeast and for establishing DNA methylation at repetitive elements in plants. In the mammalian male germ line, DICER1-independent piRNAs are required for the full establishment of DNA methylation of dispersed repetitive transposable elements. However, in other mammalian cell types, no clear picture has yet emerged of the role of RNAi in establishing heterochromatin and DNA methylation. In mouse embryonic stem cells, which remain viable on loss of DICER1 and ablation of RNAi, while no firm evidence has been obtained for defective heterochromatin formation, there are indications of defective DNA methylation. The latter has been attributed to an indirect effect of reduced DNA methyltransferase (DNMT) activity due to a loss of miRNA-mediated gene regulation. However, it is unclear whether the reductions in DNMT activity were sufficient to affect DNA methylation. We consider it equally likely that the defects in DNA methylation that can be observed in DICER1-deficient embryonic stem cells are the result of nonspecific effects related to RNAi loss aside from reduced DNMT activity.
Collapse
Affiliation(s)
- Jeffrey R. Mann
- Theme of Genetic Disorders, Murdoch Childrens Research Institute, The Royal Children’s Hospital, Parkville 3052, Victoria, Australia
| | - Deidre M. Mattiske
- Theme of Genetic Disorders, Murdoch Childrens Research Institute, The Royal Children’s Hospital, Parkville 3052, Victoria, Australia
| |
Collapse
|
40
|
Teven CM, Liu X, Hu N, Tang N, Kim SH, Huang E, Yang K, Li M, Gao JL, Liu H, Natale RB, Luther G, Luo Q, Wang L, Rames R, Bi Y, Luo J, Luu HH, Haydon RC, Reid RR, He TC. Epigenetic regulation of mesenchymal stem cells: a focus on osteogenic and adipogenic differentiation. Stem Cells Int 2011; 2011:201371. [PMID: 21772852 PMCID: PMC3137957 DOI: 10.4061/2011/201371] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Accepted: 04/27/2011] [Indexed: 12/20/2022] Open
Abstract
Stem cells are characterized by their capability to self-renew and terminally differentiate into multiple cell types. Somatic or adult stem cells have a finite self-renewal capacity and are lineage-restricted. The use of adult stem cells for therapeutic purposes has been a topic of recent interest given the ethical considerations associated with embryonic stem (ES) cells. Mesenchymal stem cells (MSCs) are adult stem cells that can differentiate into osteogenic, adipogenic, chondrogenic, or myogenic lineages. Owing to their ease of isolation and unique characteristics, MSCs have been widely regarded as potential candidates for tissue engineering and repair. While various signaling molecules important to MSC differentiation have been identified, our complete understanding of this process is lacking. Recent investigations focused on the role of epigenetic regulation in lineage-specific differentiation of MSCs have shown that unique patterns of DNA methylation and histone modifications play an important role in the induction of MSC differentiation toward specific lineages. Nevertheless, MSC epigenetic profiles reflect a more restricted differentiation potential as compared to ES cells. Here we review the effect of epigenetic modifications on MSC multipotency and differentiation, with a focus on osteogenic and adipogenic differentiation. We also highlight clinical applications of MSC epigenetics and nuclear reprogramming.
Collapse
Affiliation(s)
- Chad M Teven
- Molecular Oncology Laboratory, Department of Surgery, The University of Chicago Medical Center, 5841 South Maryland Avenue, Chicago, IL 60637, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Xie H, Wang M, de Andrade A, Bonaldo MDF, Galat V, Arndt K, Rajaram V, Goldman S, Tomita T, Soares MB. Genome-wide quantitative assessment of variation in DNA methylation patterns. Nucleic Acids Res 2011; 39:4099-108. [PMID: 21278160 PMCID: PMC3105398 DOI: 10.1093/nar/gkr017] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Genomic DNA methylation contributes substantively to transcriptional regulations that underlie mammalian development and cellular differentiation. Much effort has been made to decipher the molecular mechanisms governing the establishment and maintenance of DNA methylation patterns. However, little is known about genome-wide variation of DNA methylation patterns. In this study, we introduced the concept of methylation entropy, a measure of the randomness of DNA methylation patterns in a cell population, and exploited it to assess the variability in DNA methylation patterns of Alu repeats and promoters. A few interesting observations were made: (i) within a cell population, methylation entropy varies among genomic loci; (ii) among cell populations, the methylation entropies of most genomic loci remain constant; (iii) compared to normal tissue controls, some tumors exhibit greater methylation entropies; (iv) Alu elements with high methylation entropy are associated with high GC content but depletion of CpG dinucleotides and (v) Alu elements in the intronic regions or far from CpG islands are associated with low methylation entropy. We further identified 12 putative allelic-specific methylated genomic loci, including four Alu elements and eight promoters. Lastly, using subcloned normal fibroblast cells, we demonstrated the highly variable methylation patterns are resulted from low fidelity of DNA methylation inheritance.
Collapse
Affiliation(s)
- Hehuang Xie
- Falk Brain Tumor Center, Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago IL 60614-3394, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
42
|
A twin approach to unraveling epigenetics. Trends Genet 2011; 27:116-25. [PMID: 21257220 PMCID: PMC3063335 DOI: 10.1016/j.tig.2010.12.005] [Citation(s) in RCA: 223] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Revised: 12/09/2010] [Accepted: 12/13/2010] [Indexed: 01/07/2023]
Abstract
The regulation of gene expression plays a pivotal role in complex phenotypes, and epigenetic mechanisms such as DNA methylation are essential to this process. The availability of next-generation sequencing technologies allows us to study epigenetic variation at an unprecedented level of resolution. Even so, our understanding of the underlying sources of epigenetic variability remains limited. Twin studies have played an essential role in estimating phenotypic heritability, and these now offer an opportunity to study epigenetic variation as a dynamic quantitative trait. High monozygotic twin discordance rates for common diseases suggest that unexplained environmental or epigenetic factors could be involved. Recent genome-wide epigenetic studies in disease-discordant monozygotic twins emphasize the power of this design to successfully identify epigenetic changes associated with complex traits. We describe how large-scale epigenetic studies of twins can improve our understanding of how genetic, environmental and stochastic factors impact upon epigenetics, and how such studies can provide a comprehensive understanding of how epigenetic variation affects complex traits.
Collapse
|
43
|
Schär P, Fritsch O. DNA repair and the control of DNA methylation. PROGRESS IN DRUG RESEARCH. FORTSCHRITTE DER ARZNEIMITTELFORSCHUNG. PROGRES DES RECHERCHES PHARMACEUTIQUES 2011; 67:51-68. [PMID: 21141724 DOI: 10.1007/978-3-7643-8989-5_3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The successful establishment and stable maintenance of cell identity are critical for organismal development and tissue homeostasis. Cell identity is provided by epigenetic mechanisms that facilitate a selective readout of the genome. Operating at the level of chromatin, they establish defined gene expression programs during cell differentiation. Among the epigenetic modifications in mammalian chromatin, the 5'-methylation of cytosine in CpG dinucleotides is unique in that it affects the DNA rather than histones and the biochemistry of the DNA methylating enzymes offers a mechanistic explanation for stable inheritance. Yet, DNA methylation states appear to be more dynamic and their maintenance more complex than existing models predict. Also, methylation patterns are by far not always faithfully inherited, as best exemplified by human cancers. Often, these show widespread hypo- or hypermethylation across their genomes, reflecting an underlying epigenetic instability that may have contributed to carcinogenesis. The phenotype of unstable methylation in cancer illustrates the importance of quality control in the DNA methylation system and implies the existence of proof-reading mechanisms that enforce fidelity to DNA methylation in healthy tissue. Fidelity seems particularly important in islands of unmethylated CpG-rich sequences where an accurate maintenance of un- or differentially methylated states is critical for stable expression of nearby genes. Methylation proof-reading in such sequences requires a system capable of recognition and active demethylation of erroneously methylated CpGs. Active demethylation of 5-methylcytosine has been known to occur for long, but the underlying mechanisms have remained enigmatic and controversial. However, recent progress in this direction substantiates a role of DNA repair in such processes. This review will address general aspects of cytosine methylation stability in mammalian DNA and explore a putative role of DNA repair in methylation control.
Collapse
Affiliation(s)
- Primo Schär
- Institute of Biochemistry and Genetics, Department of Biomedicine, University of Basel, Mattenstrasse 28, CH-4058 Basel, Switzerland.
| | | |
Collapse
|
44
|
Khare T, Pal M, Petronis A. Understanding bipolar disorder: the epigenetic perspective. Curr Top Behav Neurosci 2011; 5:31-49. [PMID: 25236548 DOI: 10.1007/7854_2010_64] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Bipolar disease (BPD) is a complex major psychiatric disorder that affects between 1% and 2% of the population and exhibits ?85% heritability. This has made BPD an appealing target for genetic studies yet, despite numerous attempts, the genetic basis of this disease remains elusive. Recently, it has come to light that epigenetic factors may also influence the development of BPD. These factors act via stable but reversible modifications of DNA and chromatin structure. In this chapter, we revisit the epidemiological, clinical, and molecular findings in BPD and reanalyze them from the perspective of inherited and acquired epigenetic misregulation. Epigenetic research has great potential to enhance our understanding of the molecular basis of BPD.
Collapse
Affiliation(s)
- Tarang Khare
- The Krembil Family Epigenetics Laboratory, Centre for Addiction and Mental Health, 250 College Street, Toronto, Ontario, M5T 1R8, Canada,
| | | | | |
Collapse
|
45
|
Fu AQ, Genereux DP, Stöger R, Laird CD, Stephens M. Statistical inference of transmission fidelity of DNA methylation patterns over somatic cell divisions in mammals. Ann Appl Stat 2010. [DOI: 10.1214/09-aoas297] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
46
|
Fu AQ, Genereux DP, Stöger R, Laird CD, Stephens M. STATISTICAL INFERENCE OF TRANSMISSION FIDELITY OF DNA METHYLATION PATTERNS OVER SOMATIC CELL DIVISIONS IN MAMMALS. Ann Appl Stat 2010; 4:871-892. [PMID: 21625348 PMCID: PMC3103139 DOI: 10.1214/09-aoas297suppa] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We develop Bayesian inference methods for a recently-emerging type of epigenetic data to study the transmission fidelity of DNA methylation patterns over cell divisions. The data consist of parent-daughter double-stranded DNA methylation patterns with each pattern coming from a single cell and represented as an unordered pair of binary strings. The data are technically difficult and time-consuming to collect, putting a premium on an efficient inference method. Our aim is to estimate rates for the maintenance and de novo methylation events that gave rise to the observed patterns, while accounting for measurement error. We model data at multiple sites jointly, thus using whole-strand information, and considerably reduce confounding between parameters. We also adopt a hierarchical structure that allows for variation in rates across sites without an explosion in the effective number of parameters. Our context-specific priors capture the expected stationarity, or near-stationarity, of the stochastic process that generated the data analyzed here. This expected stationarity is shown to greatly increase the precision of the estimation. Applying our model to a data set collected at the human FMR1 locus, we find that measurement errors, generally ignored in similar studies, occur at a non-trivial rate (inappropriate bisulfite conversion error: 1.6% with 80% CI: 0.9-2.3%). Accounting for these errors has a substantial impact on estimates of key biological parameters. The estimated average failure of maintenance rate and daughter de novo rate decline from 0.04 to 0.024 and from 0.14 to 0.07, respectively, when errors are accounted for. Our results also provide evidence that de novo events may occur on both parent and daughter strands: the median parent and daughter de novo rates are 0.08 (80% CI: 0.04-0.13) and 0.07 (80% CI: 0.04-0.11), respectively.
Collapse
|
47
|
Reexpression of epigenetically silenced AML tumor suppressor genes by SUV39H1 inhibition. Oncogene 2009; 29:576-88. [PMID: 19881540 DOI: 10.1038/onc.2009.361] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Reexpression of hypermethylated tumor suppressor genes using DNA methyltransferase (DNMT) and histone deacetylase inhibitors occurs by a mechanism whereby promoter demethylation is the dominant event. In support of this model, we found in acute myeloid leukemia cells with hypermethylated p15INK4B and E-cadherin promoters that the DNMT inhibitor, 5-aza-2'-deoxycytidine, induced p15INK4B and E-cadherin expression, and decreased levels of DNA methylation, histone H3 lysine 9 (H3K9) methylation and SUV39H1 associated with p15INK4B and E-cadherin promoters. On the basis of these observations, we examined whether promoter demethylation was dominant to H3K9 demethylation in p15INK4B and E-cadherin reexpression. We observed that SUV39H1 short hairpin RNA and chaetocin, a SUV39H1 inhibitor, induced p15INK4B and E-cadherin expression and H3K9 demethylation without promoter demethylation. Reexpression of hypermethylated p15INK4B and E-cadherin required histone H3K9 demethylation that was achieved directly by inhibiting SUV39H1 expression or activity, or indirectly by decreasing the amount of SUV39H1 associated with the p15INK4B and E-cadherin promoters using 5-aza-2'-deoxycytidine. The results from this study highlight the potential of H3K9 methyltransferases as therapeutic targets for reactivating expression of hypermethylated genes.
Collapse
|
48
|
Patra SK, Bettuzzi S. Epigenetic DNA-(cytosine-5-carbon) modifications: 5-aza-2'-deoxycytidine and DNA-demethylation. BIOCHEMISTRY (MOSCOW) 2009; 74:613-9. [PMID: 19645665 DOI: 10.1134/s0006297909060042] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
DNA (cytosine-5-carbon) methylation is one of the hallmarks of mammalian chromatin modifications. Distinct methylation pattern can generate synergistic or antagonistic interaction affinities for CpG-islands associated with methylated or unmethylated cytosine binding proteins, which also may dictate histone modifications and dynamic transition between transcriptionally silent or transcriptionally active chromatin states. The enzymes and cofactors associated with DNA-methylation reactions are convincing in terms of chemistry and chemical thermodynamics. The mechanism of demethylation, the candidate enzyme(s) exhibiting direct demethylase activity, and associated cofactors are not firmly established. Use of azanucleosides, such as 5-azacytidine and 5-aza-2'-deoxycytidine (AzadC), in cell culture produces re-expression of certain genes, which otherwise were repressed in association with hypermethylated CpG-rich promoters. Hence the notion developed that AzadC is a demethylating agent. Here we discuss the broad global pictures with the following points: first, chemical definition and recent advances regarding the mechanism of DNA (cytosine-5-carbon) methylation ((Me)CpG-DNA or (Me)CpNpG-DNA formation) and (Me)CpG/(Me)CpNpG-DNA-demethylation, and then with the mechanistic basis of inactivation of DNA-methyltransferase 1 by AzadC. This will clarify that: (i) AzadC has nothing to do with DNA-demethylation; (ii) it cannot prevent even de novo methylation in non-replicating cells; (iii) it can only prevent replication coupled maintenance as well as de novo methylations. Finally, we would like to suggest that terming/designating AzadC as DNA-demethylating agent is a serious misuse of chemistry and chemical terminology.
Collapse
Affiliation(s)
- S K Patra
- Division of Biochemistry, Department of Experimental Medicine, University of Parma, Parma, Italy.
| | | |
Collapse
|
49
|
Abstract
DNA methylation patterns are set up early in mammalian development and are then copied during the division of somatic cells. A long-established model for the maintenance of these patterns explains some, but not all, of the data that are now available. We propose a new model that suggests that the maintenance of DNA methylation relies not only on the recognition of hemimethylated DNA by DNA methyltransferase 1 (DNMT1) but also on the localization of the DNMT3A and DNMT3B enzymes to specific chromatin regions that contain methylated DNA.
Collapse
|
50
|
Collas P. Epigenetic states in stem cells. Biochim Biophys Acta Gen Subj 2009; 1790:900-5. [DOI: 10.1016/j.bbagen.2008.10.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Revised: 10/09/2008] [Accepted: 10/12/2008] [Indexed: 12/01/2022]
|