1
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Zhu T, Tong H, Du Z, Beck S, Teschendorff AE. An improved epigenetic counter to track mitotic age in normal and precancerous tissues. Nat Commun 2024; 15:4211. [PMID: 38760334 PMCID: PMC11101651 DOI: 10.1038/s41467-024-48649-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 05/09/2024] [Indexed: 05/19/2024] Open
Abstract
The cumulative number of stem cell divisions in a tissue, known as mitotic age, is thought to be a major determinant of cancer-risk. Somatic mutational and DNA methylation (DNAm) clocks are promising tools to molecularly track mitotic age, yet their relationship is underexplored and their potential for cancer risk prediction in normal tissues remains to be demonstrated. Here we build and validate an improved pan-tissue DNAm counter of total mitotic age called stemTOC. We demonstrate that stemTOC's mitotic age proxy increases with the tumor cell-of-origin fraction in each of 15 cancer-types, in precancerous lesions, and in normal tissues exposed to major cancer risk factors. Extensive benchmarking against 6 other mitotic counters shows that stemTOC compares favorably, specially in the preinvasive and normal-tissue contexts. By cross-correlating stemTOC to two clock-like somatic mutational signatures, we confirm the mitotic-like nature of only one of these. Our data points towards DNAm as a promising molecular substrate for detecting mitotic-age increases in normal tissues and precancerous lesions, and hence for developing cancer-risk prediction strategies.
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Affiliation(s)
- Tianyu Zhu
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institute for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Huige Tong
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institute for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Zhaozhen Du
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institute for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Stephan Beck
- Medical Genomics Group, UCL Cancer Institute, University College London, 72 Huntley Street, WC1E 6BT, London, UK
| | - Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institute for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China.
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2
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Briffa A, Hollwey E, Shahzad Z, Moore JD, Lyons DB, Howard M, Zilberman D. Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations. Cell Syst 2023; 14:953-967.e17. [PMID: 37944515 DOI: 10.1016/j.cels.2023.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 07/18/2023] [Accepted: 10/13/2023] [Indexed: 11/12/2023]
Abstract
Methylation of CG dinucleotides (mCGs), which regulates eukaryotic genome functions, is epigenetically propagated by Dnmt1/MET1 methyltransferases. How mCG is established and transmitted across generations despite imperfect enzyme fidelity is unclear. Whether mCG variation in natural populations is governed by genetic or epigenetic inheritance also remains mysterious. Here, we show that MET1 de novo activity, which is enhanced by existing proximate methylation, seeds and stabilizes mCG in Arabidopsis thaliana genes. MET1 activity is restricted by active demethylation and suppressed by histone variant H2A.Z, producing localized mCG patterns. Based on these observations, we develop a stochastic mathematical model that precisely recapitulates mCG inheritance dynamics and predicts intragenic mCG patterns and their population-scale variation given only CG site spacing. Our results demonstrate that intragenic mCG establishment, inheritance, and variance constitute a unified epigenetic process, revealing that intragenic mCG undergoes large, millennia-long epigenetic fluctuations and can therefore mediate evolution on this timescale.
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Affiliation(s)
- Amy Briffa
- Department of Computational and Systems Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Elizabeth Hollwey
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK; Institute of Science and Technology, 3400 Klosterneuburg, Austria
| | - Zaigham Shahzad
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK; Department of Life Sciences, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
| | - Jonathan D Moore
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - David B Lyons
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Martin Howard
- Department of Computational and Systems Biology, John Innes Centre, Norwich NR4 7UH, UK.
| | - Daniel Zilberman
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK; Institute of Science and Technology, 3400 Klosterneuburg, Austria.
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3
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Hollwey E, Briffa A, Howard M, Zilberman D. Concepts, mechanisms and implications of long-term epigenetic inheritance. Curr Opin Genet Dev 2023; 81:102087. [PMID: 37441873 DOI: 10.1016/j.gde.2023.102087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023]
Abstract
Many modes and mechanisms of epigenetic inheritance have been elucidated in eukaryotes. Most of them are relatively short-term, generally not exceeding one or a few organismal generations. However, emerging evidence indicates that one mechanism, cytosine DNA methylation, can mediate epigenetic inheritance over much longer timescales, which are mostly or completely inaccessible in the laboratory. Here we discuss the evidence for, and mechanisms and implications of, such long-term epigenetic inheritance. We argue that compelling evidence supports the long-term epigenetic inheritance of gene body methylation, at least in the model angiosperm Arabidopsis thaliana, and that variation in such methylation can therefore serve as an epigenetic basis for phenotypic variation in natural populations.
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Affiliation(s)
| | - Amy Briffa
- Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Martin Howard
- Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Daniel Zilberman
- Institute of Science and Technology, 3400 Klosterneuburg, Austria.
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4
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Ren H, Taylor RB, Downing TL, Read EL. Locally correlated kinetics of post-replication DNA methylation reveals processivity and region specificity in DNA methylation maintenance. J R Soc Interface 2022; 19:20220415. [PMID: 36285438 PMCID: PMC9597173 DOI: 10.1098/rsif.2022.0415] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
DNA methylation occurs predominantly on cytosine-phosphate-guanine (CpG) dinucleotides in the mammalian genome, and the methylation landscape is maintained over mitotic cell division. It has been posited that coupling of maintenance methylation activity among neighbouring CpGs is critical to stability over cellular generations; however, the mechanism is unclear. We used mathematical models and stochastic simulation to analyse data from experiments that probe genome-wide methylation of nascent DNA post-replication in cells. We find that DNA methylation maintenance rates on individual CpGs are locally correlated, and the degree of this correlation varies by genomic regional context. By using theory of protein diffusion along DNA, we show that exponential decay of methylation rate correlation with genomic distance is consistent with enzyme processivity. Our results provide quantitative evidence of genome-wide methyltransferase processivity in vivo. We further developed a method to disentangle different mechanistic sources of kinetic correlations. From the experimental data, we estimate that an individual methyltransferase methylates neighbour CpGs processively if they are 36 basepairs apart, on average. But other mechanisms of coupling dominate for longer inter-CpG distances. Our study demonstrates that quantitative insights into enzymatic mechanisms can be obtained from replication-associated, cell-based genome-wide measurements, by combining data-driven statistical analyses with hypothesis-driven mathematical modelling.
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Affiliation(s)
- Honglei Ren
- NSF-Simons Center for Multiscale Cell Fate, University of California, Irvine, CA 92697, USA,Center for Complex Biological Systems, University of California, Irvine, CA 92697, USA
| | - Robert B. Taylor
- Center for Complex Biological Systems, University of California, Irvine, CA 92697, USA,Department of Physics, University of California, Irvine, CA 92697, USA
| | - Timothy L. Downing
- NSF-Simons Center for Multiscale Cell Fate, University of California, Irvine, CA 92697, USA,Center for Complex Biological Systems, University of California, Irvine, CA 92697, USA,Department of Biomedical Engineering, University of California, Irvine, CA 92697, USA,Department of Microbiology and Molecular Genetics, University of California, Irvine, CA 92697, USA
| | - Elizabeth L. Read
- NSF-Simons Center for Multiscale Cell Fate, University of California, Irvine, CA 92697, USA,Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA 92697, USA,Center for Complex Biological Systems, University of California, Irvine, CA 92697, USA
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5
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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] [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.
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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
- *Correspondence: Gilles Salbert,
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6
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The relative fitness of the de novo variants in general Lithuanian population vs. in individuals with intellectual disability. Eur J Hum Genet 2022; 30:332-338. [PMID: 34363065 PMCID: PMC8904440 DOI: 10.1038/s41431-021-00915-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 05/20/2021] [Accepted: 05/20/2021] [Indexed: 11/08/2022] Open
Abstract
The effect of a variant on an organism is always multifaceted and can be considered from multiple perspectives-biochemical, medical, or evolutionary. However, the relationship between the effects of amino acid substitution on protein activity, human health, and an individual's evolutionary fitness is not trivial. We uncover that the general Lithuanian population is characterized by a "mirror reflection" of the de novo variant fitness effect, confirming the theory of neutrality. Meanwhile, in the group of individuals with intellectual disability, compared with the reference exome de novo variants significantly changed the composition of the amino acid. Therefore, it predicts that, both in terms of the number of amino acids and changes in their relative fitness, the structure of the proteins encoded by the studied amino acids undergo significant changes following the de novo variant, leading to possible changes in protein function associated with phenotypic traits. These results suggest that the analysis of relative fitness of exome sequences with de novo variants can predict the future phenotype. Therefore even in those cases, then only a few of all functional prediction analysis tools predict a variant as damaging, the negative relative fitness or even adaptability of the genome variant should be carefully evaluated considering both its direct function and the global background of the possible disease-associated mechanism regardless of the phenotype being studied.
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7
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Lasri A, Sturrock M. The influence of methylation status on a stochastic model of MGMT dynamics in glioblastoma: Phenotypic selection can occur with and without a downshift in promoter methylation status. J Theor Biol 2021; 521:110662. [PMID: 33684406 DOI: 10.1016/j.jtbi.2021.110662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 01/02/2023]
Abstract
Glioblastoma originates in the brain and is one of the most aggressive cancer types. Glioblastoma represents 15% of all brain tumours, with a median survival of 15 months. Although the current standard of care for such a tumour (the Stupp protocol) has shown positive results for the prognosis of patients, O-6-methylguanine-DNA methyltransferase (MGMT) driven drug resistance has been an issue of increasing concern and hence requires innovative approaches. In addition to the well established drug resistance factors such as tumour location and blood brain barriers, it is also important to understand how the genetic and epigenetic dynamics of the glioblastoma cells can play a role. One important aspect of this is the study of methylation status of MGMT following administration of temozolomide. In this paper, we extend our previously published model that simulated MGMT expression in glioblastoma cells to incorporate the promoter methylation status of MGMT. This methylation status has clinical significance and is used as a marker for patient outcomes. Using this model, we investigate the causative relationship between temozolomide treatment and the methylation status of the MGMT promoter in a population of cells. In addition by constraining the model to relevant biological data using Approximate Bayesian Computation, we were able to identify parameter regimes that yield different possible modes of resistances, namely, phenotypic selection of MGMT, a downshift in the methylation status of the MGMT promoter or both simultaneously. We analysed each of the parameter sets associated with the different modes of resistance, presenting representative solutions as well as discovering some similarities between them as well as unique requirements for each of them. Finally, we used them to devise optimal strategies for inhibiting MGMT expression with the aim of minimising live glioblastoma cell numbers.
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Affiliation(s)
- Ayoub Lasri
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, York house, Dublin, Ireland.
| | - Marc Sturrock
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, York house, Dublin, Ireland
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8
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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.
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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
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9
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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: 54] [Impact Index Per Article: 13.5] [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.
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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.
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10
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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.
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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
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11
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Teschendorff AE. A comparison of epigenetic mitotic-like clocks for cancer risk prediction. Genome Med 2020; 12:56. [PMID: 32580750 PMCID: PMC7315560 DOI: 10.1186/s13073-020-00752-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 06/10/2020] [Indexed: 12/19/2022] Open
Abstract
Background DNA methylation changes that accrue in the stem cell pool of an adult tissue in line with the cumulative number of cell divisions may contribute to the observed variation in cancer risk among tissues and individuals. Thus, the construction of epigenetic “mitotic” clocks that can measure the lifetime number of stem cell divisions is of paramount interest. Methods Building upon a dynamic model of DNA methylation gain in unmethylated CpG-rich regions, we here derive a novel mitotic clock (“epiTOC2”) that can directly estimate the cumulative number of stem cell divisions in a tissue. We compare epiTOC2 to a different mitotic model, based on hypomethylation at solo-WCGW sites (“HypoClock”), in terms of their ability to measure mitotic age of normal adult tissues and predict cancer risk. Results Using epiTOC2, we estimate the intrinsic stem cell division rate for different normal tissue types, demonstrating excellent agreement (Pearson correlation = 0.92, R2 = 0.85, P = 3e−6) with those derived from experiment. In contrast, HypoClock’s estimates do not (Pearson correlation = 0.30, R2 = 0.09, P = 0.29). We validate these results in independent datasets profiling normal adult tissue types. While both epiTOC2 and HypoClock correctly predict an increased mitotic rate in cancer, epiTOC2 is more robust and significantly better at discriminating preneoplastic lesions characterized by chronic inflammation, a major driver of tissue turnover and cancer risk. Our data suggest that DNA methylation loss at solo-WCGWs is significant only when cells are under high replicative stress and that epiTOC2 is a better mitotic age and cancer risk prediction model for normal adult tissues. Conclusions These results have profound implications for our understanding of epigenetic clocks and for developing cancer risk prediction or early detection assays. We propose that measurement of DNAm at the 163 epiTOC2 CpGs in adult pre-neoplastic lesions, and potentially in serum cell-free DNA, could provide the basis for building feasible pre-diagnostic or cancer risk assays. epiTOC2 is freely available from 10.5281/zenodo.2632938
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Affiliation(s)
- Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institute for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China. .,UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK.
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12
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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: 78] [Impact Index Per Article: 19.5] [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.
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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.
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13
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Ye Y, Yang Z, Lei J. DNA Methylation Heterogeneity Induced by Collaborations Between Enhancers. J Comput Biol 2020; 27:1668-1677. [PMID: 32311277 DOI: 10.1089/cmb.2019.0413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
During mammalian embryo development, reprogramming of DNA methylation plays important roles in the erasure of parental epigenetic memory and the establishment of naive pluripotent cells. Multiple enzymes that regulate the processes of methylation and demethylation work together to shape the pattern of genome-scale DNA methylation and guide the process of cell differentiation. Recent availability of methylome information from single-cell whole genome bisulfite sequencing (scBS-seq) provides an opportunity to study DNA methylation dynamics in the whole genome in individual cells, which reveal the heterogeneous methylation distributions of enhancers in embryo stem cells. In this study, we developed a computational model of enhancer methylation inheritance to study the dynamics of genome-scale DNA methylation reprogramming during exit from pluripotency. The model enables us to track genome-scale DNA methylation reprogramming at single-cell level during the embryo development process and reproduce the DNA methylation heterogeneity reported by scBS-seq. Model simulations show that DNA methylation heterogeneity is an intrinsic property driven by cell division along the development process, and the collaboration between neighboring enhancers is required for heterogeneous methylation. Our study suggests that the mechanism of genome-scale oscillation might not be necessary for the DNA methylation heterogeneity during exit from pluripotency.
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Affiliation(s)
- Yusong Ye
- School of Mathematics and Systems Science and LMIB, Beihang University, Beijing, China
| | - Zhuoqin Yang
- School of Mathematics and Systems Science and LMIB, Beihang University, Beijing, China
| | - Jinzhi Lei
- Zhou Pei-Yuan Center for Applied Mathematics, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
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14
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Grosser K, Metzler D. Modeling methylation dynamics with simultaneous changes in CpG islands. BMC Bioinformatics 2020; 21:115. [PMID: 32183713 PMCID: PMC7079395 DOI: 10.1186/s12859-020-3438-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 03/02/2020] [Indexed: 11/24/2022] Open
Abstract
Background In vertebrate genomes, CpG sites can be clustered into CpG islands, and the amount of methylation in a CpG island can change due to gene regulation processes. Thus, single regulatory events can simultaneously change the methylation states of many CpG sites within a CpG island. This should be taken into account when quantifying the amount of change in methylation, for example in form of a branch length in a phylogeny of cell types. Results We propose a probabilistic model (the IWE-SSE model) of methylation dynamics that accounts for simultaneous methylation changes in multiple CpG sites belonging to the same CpG island. We further propose a Markov-chain Monte-Carlo (MCMC) method to fit this model to methylation data from cell type phylogenies and apply this method to available data from murine haematopoietic cells and from human cell lines. Combined with simulation studies, these analyses show that accounting for CpG island wide methylation changes has a strong effect on the inferred branch lengths and leads to a significantly better model fit for the methylation data from murine haematopoietic cells and human cell lines. Conclusion The MCMC based parameter estimation method for the IWE-SSE model in combination with our MCMC based inference method allows to quantify the amount of methylation changes at single CpG sites as well as on entire CpG islands. Accounting for changes affecting entire islands can lead to more accurate branch length estimation in the presence of simultaneous methylation change.
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Affiliation(s)
- Konrad Grosser
- Department of Biology, Ludwigs-Maximilians Universität München, Großhaderner Straße 2, Planegg, 82152, Germany
| | - Dirk Metzler
- Department of Biology, Ludwigs-Maximilians Universität München, Großhaderner Straße 2, Planegg, 82152, Germany.
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15
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Yu M, Hazelton WD, Luebeck GE, Grady WM. Epigenetic Aging: More Than Just a Clock When It Comes to Cancer. Cancer Res 2019; 80:367-374. [PMID: 31694907 DOI: 10.1158/0008-5472.can-19-0924] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 08/26/2019] [Accepted: 10/24/2019] [Indexed: 12/13/2022]
Abstract
The incidence of cancer, adjusted for secular trends, is directly related to age, and advanced chronologic age is one of the most significant risk factors for cancer. Organismal aging is associated with changes at the molecular, cellular, and tissue levels and is affected by both genetic and environmental factors. The specific mechanisms through which these age-associated molecular changes contribute to the increased risk of aging-related disease, such as cancer, are incompletely understood. DNA methylation, a prominent epigenetic mark, also changes over a lifetime as part of an "epigenetic aging" process. Here, we give an update and review of epigenetic aging, in particular, the phenomena of epigenetic drift and epigenetic clock, with regard to its implication in cancer etiology. We discuss the discovery of the DNA methylation-based biomarkers for biological tissue age and the construction of various epigenetic age estimators for human clinical outcomes and health/life span. Recent studies in various types of cancer point to the significance of epigenetic aging in tumorigenesis and its potential use for cancer risk prediction. Future studies are needed to assess the potential clinical impact of strategies focused on lowering cancer risk by preventing premature aging or promoting healthy aging.
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Affiliation(s)
- Ming Yu
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.
| | - William D Hazelton
- Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Georg E Luebeck
- Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - William M Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington. .,Division of Gastroenterology, Department of Medicine, University of Washington, Seattle, Washington.,GI Cancer Prevention Program, Seattle Cancer Care Alliance, Seattle, Washington
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16
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Luck A, Giehr P, Nordstrom K, Walter J, Wolf V. Hidden Markov Modelling Reveals Neighborhood Dependence of Dnmt3a and 3b Activity. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019; 16:1598-1609. [PMID: 31027045 DOI: 10.1109/tcbb.2019.2910814] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
DNA methylation is an epigenetic mark whose important role in development has been widely recognized. This epigenetic modification results in heritable information not encoded by the DNA sequence. The underlying mechanisms controlling DNA methylation are only partly understood. Several mechanistic models of enzyme activities responsible for DNA methylation have been proposed. Here, we extend existing Hidden Markov Models (HMMs) for DNA methylation by describing the occurrence of spatial methylation patterns over time and propose several models with different neighborhood dependences. Furthermore, we investigate correlations between the neighborhood dependence and other genomic information. We perform numerical analysis of the HMMs applied to comprehensive hairpin and non-hairpin bisulfite sequencing measurements and accurately predict wild-type data. We find evidence that the activities of Dnmt3a and Dnmt3b responsible for de novo methylation depend on 5' (left) but not on 3' (right) neighboring CpGs in a sequencing string.
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17
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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.
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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
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18
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Potabattula R, Dittrich M, Schorsch M, Hahn T, Haaf T, El Hajj N. Male obesity effects on sperm and next-generation cord blood DNA methylation. PLoS One 2019; 14:e0218615. [PMID: 31246962 PMCID: PMC6597061 DOI: 10.1371/journal.pone.0218615] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 06/05/2019] [Indexed: 12/20/2022] Open
Abstract
The prevalence of metabolic disorders, in particular obesity has dramatically increased worldwide. Genetic variants explain only a minor part of the obesity epidemic induced by physical inactivity and over-nutrition. Epidemiological studies in humans and animal models indicate that epigenetic changes associated with adverse parental and/or intrauterine factors may contribute to the missing heritability of metabolic disorders. Possible adverse paternal effects are likely transmitted by sperm to the next-generation. To investigate this hypothesis, we have systematically analyzed the effects of male body mass index (BMI) on sperm epigenome and its association with next-generation fetal cord blood (FCB) DNA methylation. Methylation levels of maternally imprinted (PEG1, PEG4, PEG5, and PEG10), paternally imprinted (H19-IG DMR, IGF2-DMR0, and MEG3-IG DMR) regions, and obesity-related non-imprinted HIF3A gene were quantified by bisulphite pyrosequencing in sperm samples of 294 human donors undergoing in vitro fertilization or intracytoplasmic sperm injection, and in 113 FCBs of the resulting offspring. Multivariable regression analyses revealed that MEG3 intergenic differentially methylated region (IG DMR) showed positive correlation between sperm methylation and donor’s BMI. A gender-specific correlation between paternal BMI and FCB methylation was observed for MEG3-IG DMR, HIF3A, and IGF2-DMR0. The former two genes displayed same directional nominal association (as sperm) between paternal BMI and FCB methylation in male offspring. Hypomethylation of IGF2-DMR0 with increased paternal BMI was observed in FCBs from female offsprings. Our results suggest that male obesity is nominally associated with modification of sperm DNA methylome in humans, which may affect the epigenome of the next-generation. Nevertheless, it is important to note that none of the associated p-values survived multiple testing adjustments. Future work should test the effect of associated methylation aberrations in the offspring as DNA methylation was shown to control expression and/or imprint establishment across the studied genes.
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Affiliation(s)
- Ramya Potabattula
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
- * E-mail: (RP); , (NEH)
| | - Marcus Dittrich
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | | | | | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - Nady El Hajj
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
- College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Doha, Qatar
- * E-mail: (RP); , (NEH)
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19
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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.
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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
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20
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Van Egeren D, Madsen T, Michor F. Fitness variation in isogenic populations leads to a novel evolutionary mechanism for crossing fitness valleys. Commun Biol 2018; 1:151. [PMID: 30272027 PMCID: PMC6158234 DOI: 10.1038/s42003-018-0160-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 08/28/2018] [Indexed: 12/14/2022] Open
Abstract
Individuals in a population often have different fitnesses even when they have identical genotypes, but the effect of this variation on the evolution of a population through complicated fitness landscapes is unknown. Here, we investigate how populations with non-genetic fitness variation cross fitness valleys, common barriers to adaptation in rugged fitness landscapes in which a population must pass through a deleterious intermediate to arrive at a final advantageous stage. We develop a stochastic computational model describing the dynamics of an asexually reproducing population crossing a fitness valley, in which individuals of the same evolutionary stage can have variable fitnesses. We find that fitness variation that persists over multiple generations increases the rate of valley crossing through a novel evolutionary mechanism different from previously characterized mechanisms such as stochastic tunneling. By reducing the strength of selection against deleterious intermediates, persistent fitness variation allows for faster adaptation through rugged fitness landscapes.
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Affiliation(s)
- Debra Van Egeren
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Thomas Madsen
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, 02215, USA
| | - Franziska Michor
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, 02215, USA.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA.
- The Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.
- The Broad Institute of Harvard and MIT, Cambridge, MA, 02139, USA.
- The Ludwig Center at Harvard, Boston, MA, 02115, USA.
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21
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Potabattula R, Dittrich M, Böck J, Haertle L, Müller T, Hahn T, Schorsch M, Hajj NE, Haaf T. Allele-specific methylation of imprinted genes in fetal cord blood is influenced by cis-acting genetic variants and parental factors. Epigenomics 2018; 10:1315-1326. [PMID: 30238782 PMCID: PMC6240887 DOI: 10.2217/epi-2018-0059] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Aim: To examine the effects of genetic variation, parental age and BMI on parental allele-specific methylation of imprinted genes in fetal cord blood samples. Methodology: We have developed SNP genotyping and deep bisulphite sequencing assays for six imprinted genes to determine parental allele-specific methylation patterns in diploid somatic tissues. Results: Multivariate linear regression analyses revealed a negative correlation of paternal age with paternal MEG3 allele methylation in fetal cord blood. Methylation of the maternal PEG3 allele showed a positive correlation with maternal age. Paternal BMI was positively correlated with paternal MEST allele methylation. In addition to parental origin, allele-specific methylation of most imprinted genes was largely dependent on the underlying SNP haplotype. Conclusion: Our study supports the idea that parental factors can have an impact, although of small effect size, on the epigenome of the next generation, providing an additional layer of complexity to phenotypic diversity.
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Affiliation(s)
- Ramya Potabattula
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany
| | - Marcus Dittrich
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany.,Department of Bioinformatics, Julius Maximilians University, 97074 Würzburg, Germany
| | - Julia Böck
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany
| | - Larissa Haertle
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany
| | - Tobias Müller
- Department of Bioinformatics, Julius Maximilians University, 97074 Würzburg, Germany
| | | | | | - Nady El Hajj
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany
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22
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Abstract
Esophageal adenocarcinoma (EAC) develops from Barrett's esophagus (BE), a condition where the normal squamous epithelia is replaced by specialized intestinal metaplasia in response to chronic gastroesophageal acid reflux. In a minority of individuals, BE can progress to low- and high-grade dysplasia and eventually to intra-mucosal and then invasive carcinoma. BE provides researchers with a unique model to characterize the process by which a carcinoma arises from its precursor lesion. Molecular studies of BE have demonstrated that it is not simply a metaplastic tissue, but rather it harbors frequent alterations that are also present in dysplastic BE and in EAC. Both BE and EAC are characterized by loss of heterozygosity, aneuploidy, specific genetic mutations, and clonal diversity. Epigenetic abnormalities, primary alterations in DNA methylation, are also frequently seen in BE and EAC. Candidate gene and array-based approaches have demonstrated that numerous tumor suppressor genes exhibit aberrant promoter methylation, and some of these altered genes are associated with the neoplastic progression of BE. It has also been shown that the BE and EAC epigenomes are characterized by hypomethylation of intragenic and non-coding regions Recent studies have also provided new insight into the evolutionary forces underlying the molecular alterations seen in BE and EAC and into the molecular pathogenesis of EAC.
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Affiliation(s)
- William M. Grady
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA,University of Washington School of Medicine, Department of Internal Medicine, Seattle, WA
| | - Ming Yu
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA
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23
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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.
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24
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Zhu Y, Lu H, Zhang D, Li M, Sun X, Wan L, Yu D, Tian Y, Jin H, Lin A, Gao F, Lai M. Integrated analyses of multi-omics reveal global patterns of methylation and hydroxymethylation and screen the tumor suppressive roles of HADHB in colorectal cancer. Clin Epigenetics 2018; 10:30. [PMID: 29507648 PMCID: PMC5833094 DOI: 10.1186/s13148-018-0458-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 02/14/2018] [Indexed: 12/15/2022] Open
Abstract
Background DNA methylation is an important epigenetic modification, associated with gene expression. 5-Methylcytosine and 5-hydroxymethylcytosine are two epigenetic hallmarks that maintain the equilibrium of epigenetic reprogramming. Disequilibrium in genomic methylation leads to carcinogenesis. The purpose of this study was to elucidate the epigenetic mechanisms of DNA methylation and hydroxymethylation in the carcinogenesis of colorectal cancer. Methods Genome-wide patterns of DNA methylation and hydroxymethylation in six paired colorectal tumor tissues and corresponding normal tissues were determined using immunoprecipitation and sequencing. Transcriptional expression was determined by RNA sequencing (RNA-Seq). Groupwise differential methylation regions (DMR), differential hydroxymethylation regions (DhMR), and differentially expressed gene (DEG) regions were identified. Epigenetic biomarkers were screened by integrating DMR, DhMR, and DEGs and confirmed using functional analysis. Results We identified a genome-wide distinct hydroxymethylation pattern that could be used as an epigenetic biomarker for clearly differentiating colorectal tumor tissues from normal tissues. We identified 59,249 DMRs, 187,172 DhMRs, and 948 DEGs by comparing between tumors and normal tissues. After cross-matching genes containing DMRs or DhMRs with DEGs, we screened seven genes that were aberrantly regulated by DNA methylation in tumors. Furthermore, hypermethylation of the HADHB gene was persistently found to be correlated with downregulation of its transcription in colorectal cancer (CRC). These findings were confirmed in other patients of colorectal cancer. Tumor functional analysis indicated that HADHB reduced cancer cell migration and invasiveness. These findings suggested its possible role as a tumor suppressor gene (TSG). Conclusion This study reveals the global patterns of methylation and hydroxymethylation in CRC. Several CRC-associated genes were screened with multi-omic analysis. Aberrant methylation and hydroxymethylation were found to be in the carcinogenesis of CRC. Electronic supplementary material The online version of this article (10.1186/s13148-018-0458-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yimin Zhu
- 1Department of Epidemiology and Biostatistics, School of Public Health, Zhejiang University, Hangzhou, 310058 China
| | - Hanlin Lu
- 2BGI-Shenzhen, Shenzhen, 518083 China.,3Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
| | - Dandan Zhang
- 4Key Laboratory of Disease Proteomics of Zhejiang Province and Department of Pathology, School of Medicine, Zhejiang University, Hangzhou, 310058 China
| | - Meiyan Li
- 2BGI-Shenzhen, Shenzhen, 518083 China
| | - Xiaohui Sun
- 1Department of Epidemiology and Biostatistics, School of Public Health, Zhejiang University, Hangzhou, 310058 China
| | - Ledong Wan
- 4Key Laboratory of Disease Proteomics of Zhejiang Province and Department of Pathology, School of Medicine, Zhejiang University, Hangzhou, 310058 China
| | - Dan Yu
- 4Key Laboratory of Disease Proteomics of Zhejiang Province and Department of Pathology, School of Medicine, Zhejiang University, Hangzhou, 310058 China
| | - Yiping Tian
- 4Key Laboratory of Disease Proteomics of Zhejiang Province and Department of Pathology, School of Medicine, Zhejiang University, Hangzhou, 310058 China
| | - Hongchuan Jin
- 5Laboratory of Cancer Biology, Provincial Key Lab of Biotherapy in Zhejiang, Sir Runrun Shaw Hospital, Medical School of Zhejiang University, Hangzhou, China
| | - Aifen Lin
- Human Tissue Bank/Medical Research Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, Zhejiang 317000 China
| | - Fei Gao
- 2BGI-Shenzhen, Shenzhen, 518083 China.,3Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
| | - Maode Lai
- 4Key Laboratory of Disease Proteomics of Zhejiang Province and Department of Pathology, School of Medicine, Zhejiang University, Hangzhou, 310058 China.,7Department of Pathology, School of Medicine, Zhejiang University, 866 Yuhangtang Road, Zhejiang, Hangzhou 310058 China
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25
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Linking DNA Damage and Age-Related Promoter DNA Hyper-Methylation in the Intestine. Genes (Basel) 2018; 9:genes9010017. [PMID: 29303998 PMCID: PMC5793170 DOI: 10.3390/genes9010017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 12/21/2017] [Accepted: 12/21/2017] [Indexed: 12/22/2022] Open
Abstract
Aberrant DNA methylation in stem cells is a hallmark of aging and tumor development. Here, we explore whether and how DNA damage repair might impact on these time-dependent changes, in particular in proliferative intestinal stem cells. We introduce a 3D multiscale computer model of intestinal crypts enabling simulation of aberrant DNA and histone methylation of gene promoters during aging. We assume histone state-dependent activity of de novo DNA methyltransferases (DNMTs) and methylation-dependent binding of maintenance DNMTs to CpGs. We simulate aging with and without repeated DNA repair. Motivated by recent findings on the histone demethylase KDM2b, we consider that DNA repair is associated with chromatin opening and improved recruitment of de novo DNMTs. Our results suggest that methylation-dependent binding of maintenance DNMTs to CpGs, establishing bistable DNA methylation states, is a prerequisite to promoter hyper-methylation following DNA repair. With this, the transient increase in de novo DNMT activity during repair can induce switches from low to high methylation states. These states remain stable after repair, leading to an epigenetic drift. The switches are most frequent in genes with H3K27me3 modified promoters. Our model provides a mechanistic explanation on how even successful DNA repair might confer long term changes of the epigenome.
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26
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Luebeck EG, Curtius K, Hazelton WD, Maden S, Yu M, Thota PN, Patil DT, Chak A, Willis JE, Grady WM. Identification of a key role of widespread epigenetic drift in Barrett's esophagus and esophageal adenocarcinoma. Clin Epigenetics 2017; 9:113. [PMID: 29046735 PMCID: PMC5644061 DOI: 10.1186/s13148-017-0409-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 09/24/2017] [Indexed: 12/13/2022] Open
Abstract
Background Recent studies have identified age-related changes in DNA methylation patterns in normal and cancer tissues in a process that is called epigenetic drift. However, the evolving patterns, functional consequences, and dynamics of epigenetic drift during carcinogenesis remain largely unexplored. Here we analyze the evolution of epigenetic drift patterns during progression from normal squamous esophagus tissue to Barrett’s esophagus (BE) to esophageal adenocarcinoma (EAC) using 173 tissue samples from 100 (nonfamilial) BE patients, along with publically available datasets including The Cancer Genome Atlas (TCGA). Results Our analysis reveals extensive methylomic drift between normal squamous esophagus and BE tissues in nonprogressed BE patients, with differential drift affecting 4024 (24%) of 16,984 normally hypomethylated cytosine-guanine dinucleotides (CpGs) occurring in CpG islands. The majority (63%) of islands that include drift CpGs are associated with gene promoter regions. Island CpGs that drift have stronger pairwise correlations than static islands, reflecting collective drift consistent with processive DNA methylation maintenance. Individual BE tissues are extremely heterogeneous in their distribution of methylomic drift and encompass unimodal low-drift to bimodal high-drift patterns, reflective of differences in BE tissue age. Further analysis of longitudinally collected biopsy samples from 20 BE patients confirm the time-dependent evolution of these drift patterns. Drift patterns in EAC are similar to those in BE, but frequently exhibit enhanced bimodality and advanced mode drift. To better understand the observed drift patterns, we developed a multicellular stochastic model at the CpG island level. Importantly, we find that nonlinear feedback in the model between mean island methylation and CpG methylation rates is able to explain the widely heterogeneous collective drift patterns. Using matched gene expression and DNA methylation data in EAC from TCGA and other publically available data, we also find that advanced methylomic drift is correlated with significant transcriptional repression of ~ 200 genes in important regulatory and developmental pathways, including several checkpoint and tumor suppressor-like genes. Conclusions Taken together, our findings suggest that epigenetic drift evolution acts to significantly reduce the expression of developmental genes that may alter tissue characteristics and improve functional adaptation during BE to EAC progression. Electronic supplementary material The online version of this article (10.1186/s13148-017-0409-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- E Georg Luebeck
- Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
| | - Kit Curtius
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ UK
| | - William D Hazelton
- Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
| | - Sean Maden
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
| | - Ming Yu
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
| | - Prashanthi N Thota
- Department of Gastroenterology, Digestive Disease & Surgery Institute, Cleveland Clinic, Cleveland, OH 44195 USA
| | - Deepa T Patil
- Department of Pathology, Cleveland Clinic, Cleveland, OH 44195 USA
| | - Amitabh Chak
- University Hospitals Case Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106 USA
| | - Joseph E Willis
- University Hospitals Case Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106 USA
| | - William M Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA.,Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195 USA
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27
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Anckaert E, Fair T. DNA methylation reprogramming during oogenesis and interference by reproductive technologies: Studies in mouse and bovine models. Reprod Fertil Dev 2017; 27:739-54. [PMID: 25976160 DOI: 10.1071/rd14333] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 04/01/2015] [Indexed: 12/24/2022] Open
Abstract
The use of assisted reproductive technology (ART) to overcome fertility problems has continued to increase since the birth of the first baby conceived by ART over 30 years ago. Similarly, embryo transfer is widely used as a mechanism to advance genetic gain in livestock. Despite repeated optimisation of ART treatments, pre- and postnatal outcomes remain compromised. Epigenetic mechanisms play a fundamental role in successful gametogenesis and development. The best studied of these is DNA methylation; the appropriate establishment of DNA methylation patterns in gametes and early embryos is essential for healthy development. Superovulation studies in the mouse indicate that specific ARTs are associated with normal imprinting establishment in oocytes, but abnormal imprinting maintenance in embryos. A similar limited impact of ART on oocytes has been reported in cattle, whereas the majority of embryo-focused studies have used cloned embryos, which do exhibit aberrant DNA methylation. The present review discusses the impact of ART on oocyte and embryo DNA methylation with regard to data available from mouse and bovine models.
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Affiliation(s)
- Ellen Anckaert
- Follicle Biology Laboratory and Center for Reproductive Medicine, UZ Brussel, Vrije Universiteit Brussel, Laarbeeklaan 101, Brussels 1090, Belgium
| | - Trudee Fair
- School of Agriculture and Food Sciences, University College Dublin, Belfield, Dublin 4, Ireland
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28
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Atsem S, Reichenbach J, Potabattula R, Dittrich M, Nava C, Depienne C, Böhm L, Rost S, Hahn T, Schorsch M, Haaf T, El Hajj N. Paternal age effects on sperm FOXK1 and KCNA7 methylation and transmission into the next generation. Hum Mol Genet 2016; 25:4996-5005. [PMID: 28171595 PMCID: PMC5418740 DOI: 10.1093/hmg/ddw328] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 09/16/2016] [Accepted: 09/21/2016] [Indexed: 01/27/2023] Open
Abstract
Children of older fathers carry an increased risk for developing autism and other disorders. To elucidate the underlying mechanisms, we investigated the correlation of sperm DNA methylation with paternal age and its impact on the epigenome of the offspring. Methylation levels of nine candidate genes and LINE-1 repeats were quantified by bisulfite pyrosequencing in sperm DNA of 162 donors and 191 cord blood samples of resulting children (conceived by IVF/ICSI with the same sperm samples). Four genes showed a significant negative correlation between sperm methylation and paternal age. For FOXK1 and KCNA7, the age effect on the sperm epigenome was replicated in an independent cohort of 188 sperm samples. For FOXK1, paternal age also significantly correlated with foetal cord blood (FCB) methylation. Deep bisulfite sequencing and allele-specific pyrosequencing allowed us to distinguish between maternal and paternal alleles in FCB samples with an informative SNP. FCB methylation of the paternal FOXK1 allele was negatively correlated with paternal age, whereas maternal allele was unaffected by maternal age. Since FOXK1 duplication has been associated with autism, we studied blood FOXK1 methylation in 74 children with autism and 41 age-matched controls. The FOXK1 promoter showed a trend for accelerated demethylation in the autism group. Dual luciferase reporter assay revealed that FOXK1 methylation influences gene expression. Collectively, our study demonstrates that age-related DNA methylation changes in sperm can be transmitted to the next generation and may contribute to the increased disease risk in offspring of older fathers.
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Affiliation(s)
- Stefanie Atsem
- Institute of Human Genetics, Julius-Maximilians University, Würzburg, Germany
| | - Juliane Reichenbach
- Institute of Human Genetics, Julius-Maximilians University, Würzburg, Germany
| | - Ramya Potabattula
- Institute of Human Genetics, Julius-Maximilians University, Würzburg, Germany
| | - Marcus Dittrich
- Institute of Human Genetics, Julius-Maximilians University, Würzburg, Germany
| | - Caroline Nava
- INSERM, U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France
| | - Christel Depienne
- INSERM, U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France
- Département de Médicine translationnelle et Neurogénétique, IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France
| | - Lena Böhm
- Institute of Human Genetics, Julius-Maximilians University, Würzburg, Germany
| | - Simone Rost
- Institute of Human Genetics, Julius-Maximilians University, Würzburg, Germany
| | | | | | - Thomas Haaf
- Institute of Human Genetics, Julius-Maximilians University, Würzburg, Germany
| | - Nady El Hajj
- Institute of Human Genetics, Julius-Maximilians University, Würzburg, Germany
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29
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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.
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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
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30
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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
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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.
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31
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Giehr P, Kyriakopoulos C, Ficz G, Wolf V, Walter J. The Influence of Hydroxylation on Maintaining CpG Methylation Patterns: A Hidden Markov Model Approach. PLoS Comput Biol 2016; 12:e1004905. [PMID: 27224554 PMCID: PMC4880293 DOI: 10.1371/journal.pcbi.1004905] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 04/07/2016] [Indexed: 01/11/2023] Open
Abstract
DNA methylation and demethylation are opposing processes that when in balance create stable patterns of epigenetic memory. The control of DNA methylation pattern formation by replication dependent and independent demethylation processes has been suggested to be influenced by Tet mediated oxidation of 5mC. Several alternative mechanisms have been proposed suggesting that 5hmC influences either replication dependent maintenance of DNA methylation or replication independent processes of active demethylation. Using high resolution hairpin oxidative bisulfite sequencing data, we precisely determine the amount of 5mC and 5hmC and model the contribution of 5hmC to processes of demethylation in mouse ESCs. We develop an extended hidden Markov model capable of accurately describing the regional contribution of 5hmC to demethylation dynamics. Our analysis shows that 5hmC has a strong impact on replication dependent demethylation, mainly by impairing methylation maintenance.
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Affiliation(s)
- Pascal Giehr
- Department of Biological Sciences, UdS, Saarbrücken, Saarland, Germany
| | | | - Gabriella Ficz
- Barts Cancer Institute, Queen Mary University, London, United Kingdom
| | - Verena Wolf
- Computer Science Department, UdS, Saarbrücken, Saarland, Germany
- * E-mail: (VW); (JW)
| | - Jörn Walter
- Department of Biological Sciences, UdS, Saarbrücken, Saarland, Germany
- * E-mail: (VW); (JW)
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32
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Curtius K, Wong CJ, Hazelton WD, Kaz AM, Chak A, Willis JE, Grady WM, Luebeck EG. A Molecular Clock Infers Heterogeneous Tissue Age Among Patients with Barrett's Esophagus. PLoS Comput Biol 2016; 12:e1004919. [PMID: 27168458 PMCID: PMC4864310 DOI: 10.1371/journal.pcbi.1004919] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 04/15/2016] [Indexed: 02/07/2023] Open
Abstract
Biomarkers that drift differentially with age between normal and premalignant tissues, such as Barrett’s esophagus (BE), have the potential to improve the assessment of a patient’s cancer risk by providing quantitative information about how long a patient has lived with the precursor (i.e., dwell time). In the case of BE, which is a metaplastic precursor to esophageal adenocarcinoma (EAC), such biomarkers would be particularly useful because EAC risk may change with BE dwell time and it is generally not known how long a patient has lived with BE when a patient is first diagnosed with this condition. In this study we first describe a statistical analysis of DNA methylation data (both cross-sectional and longitudinal) derived from tissue samples from 50 BE patients to identify and validate a set of 67 CpG dinucleotides in 51 CpG islands that undergo age-related methylomic drift. Next, we describe how this information can be used to estimate a patient’s BE dwell time. We introduce a Bayesian model that incorporates longitudinal methylomic drift rates, patient age, and methylation data from individually paired BE and normal squamous tissue samples to estimate patient-specific BE onset times. Our application of the model to 30 sporadic BE patients’ methylomic profiles first exposes a wide heterogeneity in patient-specific BE onset times. Furthermore, independent application of this method to a cohort of 22 familial BE (FBE) patients reveals significantly earlier mean BE onset times. Our analysis supports the conjecture that differential methylomic drift occurs in BE (relative to normal squamous tissue) and hence allows quantitative estimation of the time that a BE patient has lived with BE. Barrett’s Esophagus (BE) is a metaplastic precursor to esophageal adenocarcinoma (EAC). When a patient is diagnosed with BE, it is generally not known how long he/she has had this condition because BE is asymptomatic. While the question of how long a premalignant tissue or lesion has been resident in an organ (dwell time) may not be of importance for cases where curative interventions are readily available (such as adenomas in the colon), for BE, curative interventions are either costly or carry patient risks. Knowledge of a precursor’s dwell time may therefore be advantageous in determining the cancer risk due to the stepwise accumulation of critical mutations in the precursor. In this study, we create a molecular clock model that infers patient-specific BE onsets from DNA methylation data. We show that there is considerable variation in the predicted BE onset times which translates, using mathematical modeling of EAC, into large variation in individual EAC risks. We make the case that, notwithstanding other known risk factors such as chronological age, gender, reflux status, etc., knowledge of biological tissue age can provide valuable patient-specific risk information when a patient is first diagnosed with BE.
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Affiliation(s)
- Kit Curtius
- Division of Gastroenterology, University of Washington School of Medicine, Seattle, Washington, United States of America
- Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail: (KC); (EGL)
| | - Chao-Jen Wong
- Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - William D. Hazelton
- Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Andrew M. Kaz
- Division of Gastroenterology, University of Washington School of Medicine, Seattle, Washington, United States of America
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Gastroenterology Section, VA Puget Sound Health Care System, Seattle, Washington, United States of America
| | - Amitabh Chak
- University Hospitals Case Medical Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Joseph E. Willis
- University Hospitals Case Medical Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - William M. Grady
- Division of Gastroenterology, University of Washington School of Medicine, Seattle, Washington, United States of America
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - E. Georg Luebeck
- Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail: (KC); (EGL)
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33
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Hajj NE, Kuhtz J, Haaf T. Limiting Dilution Bisulfite Pyrosequencing®: A Method for Methylation Analysis of Individual DNA Molecules in a Single or a Few Cells. Methods Mol Biol 2016; 1315:221-39. [PMID: 26103903 DOI: 10.1007/978-1-4939-2715-9_17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Bisulfite-based methods for DNA methylation analysis of small amounts of DNA from a limited number of cells are technologically challenging. Degradation of genomic DNA by bisulfite treatment, contamination with foreign DNA, and biases in the amplification of individual DNA molecules can generate results, which are not representative of the starting sample. Limiting dilution (LD) bisulfite Pyrosequencing(®) (BSP) is a relatively simple technique to circumvent these problems. The bisulfite-treated DNA of a single or a few cells is diluted to an extent, that only a single DNA target molecule is present in the reaction. Then each individual DNA molecule in the starting sample is separately amplified and analyzed by Pyrosequencing. This allows the detection of rare alleles that are easily masked when pools of DNA target molecules are analyzed. Amplicons containing a heterozygous single nucleotide polymorphism (SNP) allow one to delineate the parental origin of the recovered molecules in addition to their methylation status. The number of cells (DNA target molecules) in the starting sample determines the dilution level and the number of reactions that have to be performed. LD-BSP allows methylation analysis of small cell pools (i.e., 5-10 microdissected cells) and even individual cells. The primers and PCR conditions described here have been successfully employed to analyze the methylation status of up to eight target genes in individual 2-16 cell embryos, germinal vesicle (GV) oocytes, and haploid sperms.
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Affiliation(s)
- Nady El Hajj
- Institute of Human Genetics, Julius-Maximilians University Würzburg, Würzburg, 97074, Germany
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34
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Chowdhury B, McGovern A, Cui Y, Choudhury SR, Cho IH, Cooper B, Chevassut T, Lossie AC, Irudayaraj J. The hypomethylating agent Decitabine causes a paradoxical increase in 5-hydroxymethylcytosine in human leukemia cells. Sci Rep 2015; 5:9281. [PMID: 25901663 PMCID: PMC4894448 DOI: 10.1038/srep09281] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 02/19/2015] [Indexed: 12/20/2022] Open
Abstract
The USFDA approved "epigenetic drug", Decitabine, exerts its effect by hypomethylating DNA, demonstrating the pivotal role aberrant genome-wide DNA methylation patterns play in cancer ontology. Using sensitive technologies in a cellular model of Acute Myeloid Leukemia, we demonstrate that while Decitabine reduces the global levels of 5-methylcytosine (5mC), it results in paradoxical increase of 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) levels. Hitherto, the only biological mechanism known to generate 5hmC, 5fC and 5caC, involving oxidation of 5mC by members of Ten-Eleven-Translocation (TET) dioxygenase family, was not observed to undergo any alteration during DAC treatment. Using a multi-compartmental model of DNA methylation, we show that partial selectivity of TET enzymes for hemi-methylated CpG dinucleotides could lead to such alterations in 5hmC content. Furthermore, we investigated the binding of TET1-catalytic domain (CD)-GFP to DNA by Fluorescent Correlation Spectroscopy in live cells and detected the gradual increase of the DNA bound fraction of TET1-CD-GFP after treatment with Decitabine. Our study provides novel insights on the therapeutic activity of DAC in the backdrop of the newly discovered derivatives of 5mC and suggests that 5hmC has the potential to serve as a biomarker for monitoring the clinical success of patients receiving DAC.
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Affiliation(s)
- Basudev Chowdhury
- Department of Biological Sciences, Purdue University, West Lafayette 47907, IN
- Bindley Biosciences Center, Discovery Park, Purdue University, West Lafayette 47907, IN
| | - Andrew McGovern
- Department of Healthcare Management and Policy, University of Surrey, Guildford, GY2 7XH, UK
- Brighton and Sussex Medical School, Falmer, Brighton, East Sussex, BN1 9PS, UK
| | - Yi Cui
- Bindley Biosciences Center, Discovery Park, Purdue University, West Lafayette 47907, IN
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907
| | - Samrat Roy Choudhury
- Bindley Biosciences Center, Discovery Park, Purdue University, West Lafayette 47907, IN
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907
| | - Il-Hoon Cho
- Bindley Biosciences Center, Discovery Park, Purdue University, West Lafayette 47907, IN
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907
| | - Bruce Cooper
- Bindley Biosciences Center, Discovery Park, Purdue University, West Lafayette 47907, IN
| | - Timothy Chevassut
- Brighton and Sussex Medical School, Falmer, Brighton, East Sussex, BN1 9PS, UK
| | - Amy C. Lossie
- Bindley Biosciences Center, Discovery Park, Purdue University, West Lafayette 47907, IN
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - Joseph Irudayaraj
- Bindley Biosciences Center, Discovery Park, Purdue University, West Lafayette 47907, IN
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907
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35
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Black AJ, Ross JV. Computation of epidemic final size distributions. J Theor Biol 2014; 367:159-165. [PMID: 25497476 DOI: 10.1016/j.jtbi.2014.11.029] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 11/24/2014] [Accepted: 11/27/2014] [Indexed: 11/17/2022]
Abstract
We develop a new methodology for the efficient computation of epidemic final size distributions for a broad class of Markovian models. We exploit a particular representation of the stochastic epidemic process to derive a method which is both computationally efficient and numerically stable. The algorithms we present are also physically transparent and so allow us to extend this method from the basic SIR model to a model with a phase-type infectious period and another with waning immunity. The underlying theory is applicable to many Markovian models where we wish to efficiently calculate hitting probabilities.
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Affiliation(s)
- Andrew J Black
- School of Mathematical Sciences, The University of Adelaide, Adelaide SA 5005, Australia.
| | - J V Ross
- School of Mathematical Sciences, The University of Adelaide, Adelaide SA 5005, Australia
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36
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Przybilla J, Rohlf T, Loeffler M, Galle J. Understanding epigenetic changes in aging stem cells--a computational model approach. Aging Cell 2014; 13:320-8. [PMID: 24428552 PMCID: PMC4331773 DOI: 10.1111/acel.12177] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2013] [Indexed: 12/29/2022] Open
Abstract
During aging, a decline in stem cell function is observed in many tissues. This decline is accompanied by complex changes of the chromatin structure among them changes in histone modifications and DNA methylation which both affect transcription of a tissue-specific subset of genes. A mechanistic understanding of these age-associated processes, their interrelations and environmental dependence is currently lacking. Here, we discuss related questions on the molecular, cellular, and population level. We combine an individual cell-based model of stem cell populations with a model of epigenetic regulation of transcription. The novel model enables to simulate age-related changes of trimethylation of lysine 4 at histone H3 and of DNA methylation. These changes entail expression changes of genes that induce age-related phenotypes (ARPs) of cells. We compare age-related changes of regulatory states in quiescent stem cells occupying a niche with those observed in proliferating cells. Moreover, we analyze the impact of the activity of the involved epigenetic modifiers on these changes. We find that epigenetic aging strongly affects stem cell heterogeneity and that homing at stem cell niches retards epigenetic aging. Our model provides a mechanistic explanation how increased stem cell proliferation can lead to progeroid phenotypes. Adapting our model to properties observed for aged hematopoietic stem cell (HSC) clones, we predict that the hematopoietic ARP activates young HSCs and thereby retards aging of the entire HSC population. In addition, our model suggests that the experimentally observed high interindividual variance in HSC numbers originates in a variance of histone methyltransferase activity.
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Affiliation(s)
- Jens Przybilla
- Interdisciplinary Center for Bioinformatics University Leipzig Haertelstr. 16‐1804107Leipzig Germany
| | - Thimo Rohlf
- Interdisciplinary Center for Bioinformatics University Leipzig Haertelstr. 16‐1804107Leipzig Germany
- Max‐Planck‐Institute for Mathematics in the Sciences Inselstr. 2204103 Leipzig Germany
| | - Markus Loeffler
- Interdisciplinary Center for Bioinformatics University Leipzig Haertelstr. 16‐1804107Leipzig Germany
- Institute for Medical Informatics, Statistics and Epidemiology University Leipzig Haertelstr. 16‐1804107Leipzig Germany
| | - Joerg Galle
- Interdisciplinary Center for Bioinformatics University Leipzig Haertelstr. 16‐1804107Leipzig Germany
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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.
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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
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Wodarz D, Boland CR, Goel A, Komarova NL. Methylation kinetics and CpG-island methylator phenotype status in colorectal cancer cell lines. Biol Direct 2013; 8:14. [PMID: 23758948 PMCID: PMC3691599 DOI: 10.1186/1745-6150-8-14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 05/24/2013] [Indexed: 12/31/2022] Open
Abstract
Background Hypermethylation of CpG islands is thought to contribute to carcinogenesis through the inactivation of tumor suppressor genes. Tumor cells with relatively high levels of CpG island methylation are considered CpG island methylator phenotypes (CIMP). The mechanisms that are responsible for regulating the activity of de novo methylation are not well understood. Results We quantify and compare de novo methylation kinetics in CIMP and non-CIMP colon cancer cell lines in the context of different loci, following 5-aza-2’deoxycytidine (5-AZA)-mediated de-methylation of cells. In non-CIMP cells, a relatively fast rate of re-methylation is observed that starts with a certain time delay after cessation of 5-AZA treatment. CIMP cells, on the other hand, start re-methylation without a time delay but at a significantly slower rate. A mathematical model can account for these counter-intuitive results by assuming negative feedback regulation of de novo methylation activity and by further assuming that this regulation is corrupted in CIMP cells. This model further suggests that when methylation levels have grown back to physiological levels, de novo methylation activity ceases in non-CIMP cells, while it continues at a constant low level in CIMP cells. Conclusions We propose that the faster rate of re-methylation observed in non-CIMP compared to CIMP cells in our study could be a consequence of feedback-mediated regulation of DNA methyl transferase activity. Testing this hypothesis will involve the search for specific feedback regulatory mechanisms involved in the activation of de novo methylation. Reviewers’ report This article was reviewed by Georg Luebeck, Tomasz Lipniacki, and Anna Marciniak-Czochra
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Affiliation(s)
- Dominik Wodarz
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
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Przybilla J, Buske P, Binder H, Galle J. Histone modifications control DNA methylation profiles during ageing and tumour expansion. FRONTIERS IN LIFE SCIENCE 2013. [DOI: 10.1080/21553769.2013.854279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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40
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Anckaert E, De Rycke M, Smitz J. Culture of oocytes and risk of imprinting defects. Hum Reprod Update 2012; 19:52-66. [DOI: 10.1093/humupd/dms042] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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41
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Diederich M, Hansmann T, Heinzmann J, Barg-Kues B, Herrmann D, Aldag P, Baulain U, Reinhard R, Kues W, Weißgerber C, Haaf T, Niemann H. DNA methylation and mRNA expression profiles in bovine oocytes derived from prepubertal and adult donors. Reproduction 2012; 144:319-30. [DOI: 10.1530/rep-12-0134] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The developmental capacity of oocytes from prepubertal cattle is reduced compared with their adult counterparts, and epigenetic mechanisms are thought to be involved herein. Here, we analyzed DNA methylation in three developmentally important, nonimprinted genes (SLC2A1, PRDX1, ZAR1) and two satellite sequences, i.e. ‘bovine testis satellite I’ (BTS) and ‘Bos taurus alpha satellite I’ (BTαS). In parallel, mRNA expression of the genes was determined by quantitative real-time PCR. Oocytes were retrieved from prepubertal calves and adult cows twice per week over a 3-week period by ultrasound-guided follicular aspiration after treatment with FSH and/or IGF1. Both immature and in vitro matured prepubertal and adult oocytes showed a distinct hypomethylation profile of the three genes without differences between the two types of donors. The methylation status of the BTS sequence changed according to the age and treatment while the methylation status of BTαS sequence remained largely unchanged across the different age and treatment groups. Relative transcript abundance of the selected genes was significantly different in immature and in vitro matured oocytes; only minor changes related to origin and treatment were observed. In conclusion, methylation levels of the investigated satellite sequences were high (>50%) in all groups and showed significant variation depending on the age, treatment, or in vitro maturation. To what extent this is involved in the acquisition of developmental competence of bovine oocytes needs further study.
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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]
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43
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Hansmann T, Pliushch G, Leubner M, Kroll P, Endt D, Gehrig A, Preisler-Adams S, Wieacker P, Haaf T. Constitutive promoter methylation of BRCA1 and RAD51C in patients with familial ovarian cancer and early-onset sporadic breast cancer. Hum Mol Genet 2012; 21:4669-79. [PMID: 22843497 PMCID: PMC3471399 DOI: 10.1093/hmg/dds308] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Genetic defects in breast cancer (BC) susceptibility genes, most importantly BRCA1 and BRCA2, account for ∼40% of hereditary BC and ovarian cancer (OC). Little is known about the contribution of constitutive (soma-wide) epimutations to the remaining cases. We developed bisulfite pyrosequencing assays to screen >600 affected BRCA1/BRCA2 mutation-negative patients from the German Consortium for Hereditary Breast and Ovarian Cancer for constitutive hypermethylation of ATM, BRCA1, BRCA2, RAD51C, PTEN and TP53 in blood cells. In a second step, patients with ≥6% promoter methylation were analyzed by bisulfite plasmid sequencing to demonstrate the presence of hypermethylated alleles (epimutations), indicative of epigenetic gene silencing. Altogether we identified nine (1.4%) patients with constitutive BRCA1 and three (0.5%) with RAD51C hypermethylation. Epimutations were found in both sporadic cases, in particular in 2 (5.5%) of 37 patients with early-onset BC, and familial cases, in particular 4 (10%) of 39 patients with OC. Hypermethylation was always confined to one of the two parental alleles in a subset (12–40%) of the analyzed cells. Because epimutations occurred in cell types from different embryonal layers, they most likely originated in single cells during early somatic development. We propose that analogous to germline genetic mutations constitutive epimutations may serve as the first hit of tumor development. Because the role of constitutive epimutations in cancer development is likely to be largely underestimated, future strategies for effective testing of susceptibility to BC and OC should include an epimutation screen.
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Affiliation(s)
- Tamara Hansmann
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany
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44
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Przybilla J, Galle J, Rohlf T. Is adult stem cell aging driven by conflicting modes of chromatin remodeling? Bioessays 2012; 34:841-8. [PMID: 22821708 DOI: 10.1002/bies.201100190] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Epigenetic control of gene expression by chromatin remodeling is critical for adult stem cell function. A decline in stem cell function is observed during aging, which is accompanied by changes in the chromatin structure that are currently unexplained. Here, we hypothesize that these epigenetic changes originate from the limited cellular capability to inherit epigenetic information. We suggest that spontaneous loss of histone modification, due to fluctuations over short time scales, gives rise to long-term changes in DNA methylation and, accordingly, in gene expression. These changes are assumed to impair stem cell function and, thus, to contribute to aging. We discuss cell replication as a major source of fluctuations in histone modification patterns. Gene silencing by our proposed mechanism can be interpreted as a manifestation of the conflict between the stem cell plasticity required for tissue regeneration and the permanent silencing of potentially deleterious genomic sequences.
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Affiliation(s)
- Jens Przybilla
- Interdisciplinary Center for Bioinformatics, University Leipzig, Leipzig, Germany
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45
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Rohlf T, Steiner L, Przybilla J, Prohaska S, Binder H, Galle J. Modeling the dynamic epigenome: from histone modifications towards self-organizing chromatin. Epigenomics 2012; 4:205-19. [PMID: 22449191 DOI: 10.2217/epi.11.117] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Epigenetic mechanisms play an important role in regulating and stabilizing functional states of living cells. However, in spite of an increasing amount of experimental data, models of transcriptional regulation by epigenetic processes, in particular by histone modifications, are rather rare. In this article, we focus on epigenetic modes of transcriptional regulation based on histone modifications and their potential dynamical interplay with DNA methylation and higher-order chromatin structure. The main purpose of this article is to review recent formal modeling approaches to the dynamics and propagation of histone modifications and to relate them to available experimental data. We evaluate their assumptions with respect to recruitment of relevant modifiers, establishment and processing of modifications, and compare the emerging stability properties and memory effects. Theoretical predictions that await experimental validation are highlighted and potential extensions of these models towards multiscale models of self-organizing chromatin are discussed.
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Affiliation(s)
- Thimo Rohlf
- Interdisciplinary Centre for Bioinformatics, University Leipzig, D-04107 Leipzig, Härtelstr. 16-18, Germany
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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.
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Affiliation(s)
- Andrew P McGovern
- Medical Research Building, Brighton and Sussex Medical School, University of Sussex, Falmer, Brighton BN1 9PS, UK
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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: 288] [Impact Index Per Article: 24.0] [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.
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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
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Schneider E, Mayer S, El Hajj N, Jensen LR, Kuss AW, Zischler H, Kondova I, Bontrop RE, Navarro B, Fuchs E, Zechner U, Haaf T. Methylation and expression analyses of the 7q autism susceptibility locus genes MEST , COPG2, and TSGA14 in human and anthropoid primate cortices. Cytogenet Genome Res 2012; 136:278-87. [PMID: 22456293 DOI: 10.1159/000337298] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2012] [Indexed: 12/11/2022] Open
Abstract
The autism susceptibility locus on human chromosome 7q32 contains the maternally imprinted MEST and the non-imprinted COPG2 and TSGA14 genes. Autism is a disorder of the 'social brain' that has been proposed to be due to an overbalance of paternally expressed genes. To study regulation of the 7q32 locus during anthropoid primate evolution, we analyzed the methylation and expression patterns of MEST, COPG2, and TSGA14 in human, chimpanzee, Old World monkey (baboon and rhesus macaque), and New World monkey (marmoset) cortices. In all human and anthropoid primate cortices, the MEST promoter was hemimethylated, as expected for a differentially methylated imprinting control region, whereas the COPG2 and TSGA14 promoters were completely demethylated, typical for transcriptionally active non-imprinted genes. The MEST gene also showed comparable mRNA expression levels in all analyzed species. In contrast, COPG2 expression was downregulated in the human cortex compared to chimpanzee, Old and New World monkeys. TSGA14 either showed no differential regulation in the human brain compared to chimpanzee and marmoset or a slight upregulation compared to baboon. The human-specific downregulation supports a role for COPG2 in the development of a 'social brain'. Promoter methylation patterns appear to be more stable during evolution than gene expression patterns, suggesting that other mechanisms may be more important for inter-primate differences in gene expression.
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Affiliation(s)
- E Schneider
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
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Galetzka D, Hansmann T, El Hajj N, Weis E, Irmscher B, Ludwig M, Schneider-Rätzke B, Kohlschmidt N, Beyer V, Bartsch O, Zechner U, Spix C, Haaf T. Monozygotic twins discordant for constitutive BRCA1 promoter methylation, childhood cancer and secondary cancer. Epigenetics 2012; 7:47-54. [PMID: 22207351 PMCID: PMC3329502 DOI: 10.4161/epi.7.1.18814] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
We describe monozygotic twins discordant for childhood leukemia and secondary thyroid carcinoma. We used bisulfite pyrosequencing to compare the constitutive promoter methylation of BRCA1 and several other tumor suppressor genes in primary fibroblasts. The affected twin displayed an increased BRCA1 methylation (12%), compared with her sister (3%). Subsequent bisulfite plasmid sequencing demonstrated that 13% (6 of 47) BRCA1 alleles were fully methylated in the affected twin, whereas her sister displayed only single CpG errors without functional implications. This between-twin methylation difference was also found in irradiated fibroblasts and untreated saliva cells. The BRCA1 epimutation may have originated by an early somatic event in the affected twin: approximately 25% of her body cells derived from different embryonic cell lineages carry one epigenetically inactivated BRCA1 allele. This epimutation was associated with reduced basal protein levels and a higher induction of BRCA1 after DNA damage. In addition, we performed a genome-wide microarray analysis of both sisters and found several copy number variations, i.e., heterozygous deletion and reduced expression of the RSPO3 gene in the affected twin. This monozygotic twin pair represents an impressive example of epigenetic somatic mosaicism, suggesting a role for constitutive epimutations, maybe along with de novo genetic alterations in recurrent tumor development.
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Affiliation(s)
- Danuta Galetzka
- Institute of Human Genetics, University Medical Center, Mainz, Germany
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50
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Song Z, Zhang Q. Design, synthesis, and incorporation of fluorous 5-methylcytosines into oligonucleotides. J Org Chem 2011; 76:10263-8. [PMID: 22082055 DOI: 10.1021/jo2015399] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A palladium-catalyzed Negishi coupling reaction has been developed to synthesize fluorous 5-methylcytosines. These fluorous nucleosides are incorporated into the oligonucleotides that correspond to part of the promoter region of Oct4, a master gene that undergoes dynamic DNA demethylation during cellular reprogramming. The separation of the fluorous oligonucleotides from its nonfluorous analogues has been achieved through solid-phase extraction over fluorous silica, suggesting its potential use in probing DNA demethylation.
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Affiliation(s)
- Zhiquan Song
- Division of Chemical Biology and Medicinal Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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