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Schulz M, Teissandier A, De La Mata Santaella E, Armand M, Iranzo J, El Marjou F, Gestraud P, Walter M, Kinston S, Göttgens B, Greenberg MVC, Bourc'his D. DNA methylation restricts coordinated germline and neural fates in embryonic stem cell differentiation. Nat Struct Mol Biol 2024; 31:102-114. [PMID: 38177678 DOI: 10.1038/s41594-023-01162-w] [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: 11/22/2022] [Accepted: 10/26/2023] [Indexed: 01/06/2024]
Abstract
As embryonic stem cells (ESCs) transition from naive to primed pluripotency during early mammalian development, they acquire high DNA methylation levels. During this transition, the germline is specified and undergoes genome-wide DNA demethylation, while emergence of the three somatic germ layers is preceded by acquisition of somatic DNA methylation levels in the primed epiblast. DNA methylation is essential for embryogenesis, but the point at which it becomes critical during differentiation and whether all lineages equally depend on it is unclear. Here, using culture modeling of cellular transitions, we found that DNA methylation-free mouse ESCs with triple DNA methyltransferase knockout (TKO) progressed through the continuum of pluripotency states but demonstrated skewed differentiation abilities toward neural versus other somatic lineages. More saliently, TKO ESCs were fully competent for establishing primordial germ cell-like cells, even showing temporally extended and self-sustained capacity for the germline fate. By mapping chromatin states, we found that neural and germline lineages are linked by a similar enhancer dynamic upon exit from the naive state, defined by common sets of transcription factors, including methyl-sensitive ones, that fail to be decommissioned in the absence of DNA methylation. We propose that DNA methylation controls the temporality of a coordinated neural-germline axis of the preferred differentiation route during early development.
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Affiliation(s)
- Mathieu Schulz
- INSERM U934, CNRS UMR3215, Institut Curie, PSL Research University, Paris, France
| | - Aurélie Teissandier
- INSERM U934, CNRS UMR3215, Institut Curie, PSL Research University, Paris, France
| | | | - Mélanie Armand
- INSERM U934, CNRS UMR3215, Institut Curie, PSL Research University, Paris, France
| | - Julian Iranzo
- INSERM U934, CNRS UMR3215, Institut Curie, PSL Research University, Paris, France
| | - Fatima El Marjou
- INSERM U934, CNRS UMR3215, Institut Curie, PSL Research University, Paris, France
| | - Pierre Gestraud
- INSERM U900, MINES ParisTech, Institut Curie, PSL Research University, Paris, France
| | | | - Sarah Kinston
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Berthold Göttgens
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | | | - Deborah Bourc'his
- INSERM U934, CNRS UMR3215, Institut Curie, PSL Research University, Paris, France.
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2
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Kretschmer M, Fischer V, Gapp K. When Dad's Stress Gets under Kid's Skin-Impacts of Stress on Germline Cargo and Embryonic Development. Biomolecules 2023; 13:1750. [PMID: 38136621 PMCID: PMC10742275 DOI: 10.3390/biom13121750] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 11/24/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
Multiple lines of evidence suggest that paternal psychological stress contributes to an increased prevalence of neuropsychiatric and metabolic diseases in the progeny. While altered paternal care certainly plays a role in such transmitted disease risk, molecular factors in the germline might additionally be at play in humans. This is supported by findings on changes to the molecular make up of germ cells and suggests an epigenetic component in transmission. Several rodent studies demonstrate the correlation between paternal stress induced changes in epigenetic modifications and offspring phenotypic alterations, yet some intriguing cases also start to show mechanistic links in between sperm and the early embryo. In this review, we summarise efforts to understand the mechanism of intergenerational transmission from sperm to the early embryo. In particular, we highlight how stress alters epigenetic modifications in sperm and discuss the potential for these modifications to propagate modified molecular trajectories in the early embryo to give rise to aberrant phenotypes in adult offspring.
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Affiliation(s)
- Miriam Kretschmer
- Laboratory of Epigenetics and Neuroendocrinology, Department of Health Sciences and Technology, Institute for Neuroscience, ETH Zürich, 8057 Zürich, Switzerland; (M.K.); (V.F.)
- Neuroscience Center Zurich, ETH Zürich and University of Zürich, 8057 Zürich, Switzerland
| | - Vincent Fischer
- Laboratory of Epigenetics and Neuroendocrinology, Department of Health Sciences and Technology, Institute for Neuroscience, ETH Zürich, 8057 Zürich, Switzerland; (M.K.); (V.F.)
- Neuroscience Center Zurich, ETH Zürich and University of Zürich, 8057 Zürich, Switzerland
| | - Katharina Gapp
- Laboratory of Epigenetics and Neuroendocrinology, Department of Health Sciences and Technology, Institute for Neuroscience, ETH Zürich, 8057 Zürich, Switzerland; (M.K.); (V.F.)
- Neuroscience Center Zurich, ETH Zürich and University of Zürich, 8057 Zürich, Switzerland
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3
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Ruan Y, Wang J, Yu M, Wang F, Wang J, Xu Y, Liu L, Cheng Y, Yang R, Zhang C, Yang Y, Wang J, Wu W, Huang Y, Tian Y, Chen G, Zhang J, Jian R. A multi-omics integrative analysis based on CRISPR screens re-defines the pluripotency regulatory network in ESCs. Commun Biol 2023; 6:410. [PMID: 37059858 PMCID: PMC10104827 DOI: 10.1038/s42003-023-04700-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 03/13/2023] [Indexed: 04/16/2023] Open
Abstract
A comprehensive and precise definition of the pluripotency gene regulatory network (PGRN) is crucial for clarifying the regulatory mechanisms in embryonic stem cells (ESCs). Here, after a CRISPR/Cas9-based functional genomics screen and integrative analysis with other functional genomes, transcriptomes, proteomes and epigenome data, an expanded pluripotency-associated gene set is obtained, and a new PGRN with nine sub-classes is constructed. By integrating the DNA binding, epigenetic modification, chromatin conformation, and RNA expression profiles, the PGRN is resolved to six functionally independent transcriptional modules (CORE, MYC, PAF, PRC, PCGF and TBX). Spatiotemporal transcriptomics reveal activated CORE/MYC/PAF module activity and repressed PRC/PCGF/TBX module activity in both mouse ESCs (mESCs) and pluripotent cells of early embryos. Moreover, this module activity pattern is found to be shared by human ESCs (hESCs) and cancers. Thus, our results provide novel insights into elucidating the molecular basis of ESC pluripotency.
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Affiliation(s)
- Yan Ruan
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Jiaqi Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
- Department of Pathophysiology, College of High Altitude Military Medicine, Army Medical University, Chongqing, 400038, China
| | - Meng Yu
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
- Department of Joint Surgery, The First Affiliated Hospital, Army Medical University, Chongqing, 400038, China
| | - Fengsheng Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China
| | - Jiangjun Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
- Department of Cell Biology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Yixiao Xu
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Lianlian Liu
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Yuda Cheng
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Ran Yang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
- Department of Pathophysiology, College of High Altitude Military Medicine, Army Medical University, Chongqing, 400038, China
| | - Chen Zhang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Yi Yang
- Experimental Center of Basic Medicine, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - JiaLi Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Wei Wu
- Thoracic Surgery Department, Southwest Hospital, The First Hospital Affiliated to Army Medical University, Chongqing, 400038, China
| | - Yi Huang
- Biomedical Analysis Center, Army Medical University, Chongqing, 400038, China
| | - Yanping Tian
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Guangxing Chen
- Department of Joint Surgery, The First Affiliated Hospital, Army Medical University, Chongqing, 400038, China.
| | - Junlei Zhang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China.
| | - Rui Jian
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China.
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Kreibich E, Kleinendorst R, Barzaghi G, Kaspar S, Krebs AR. Single-molecule footprinting identifies context-dependent regulation of enhancers by DNA methylation. Mol Cell 2023; 83:787-802.e9. [PMID: 36758546 DOI: 10.1016/j.molcel.2023.01.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 11/21/2022] [Accepted: 01/16/2023] [Indexed: 02/11/2023]
Abstract
Enhancers are cis-regulatory elements that control the establishment of cell identities during development. In mammals, enhancer activation is tightly coupled with DNA demethylation. However, whether this epigenetic remodeling is necessary for enhancer activation is unknown. Here, we adapted single-molecule footprinting to measure chromatin accessibility and transcription factor binding as a function of the presence of methylation on the same DNA molecules. We leveraged natural epigenetic heterogeneity at active enhancers to test the impact of DNA methylation on their chromatin accessibility in multiple cell lineages. Although reduction of DNA methylation appears dispensable for the activity of most enhancers, we identify a class of cell-type-specific enhancers where DNA methylation antagonizes the binding of transcription factors. Genetic perturbations reveal that chromatin accessibility and transcription factor binding require active demethylation at these loci. Thus, in addition to safeguarding the genome from spurious activation, DNA methylation directly controls transcription factor occupancy at active enhancers.
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Affiliation(s)
- Elisa Kreibich
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany; Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Heidelberg, Germany
| | - Rozemarijn Kleinendorst
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Guido Barzaghi
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany; Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Heidelberg, Germany
| | - Sarah Kaspar
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Arnaud R Krebs
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.
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5
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Maintenance of methylation profile in imprinting control regions in human induced pluripotent stem cells. Clin Epigenetics 2022; 14:190. [PMID: 36578048 PMCID: PMC9798676 DOI: 10.1186/s13148-022-01410-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/14/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Parental imprinting is an epigenetic mechanism that leads to monoallelic expression of a subset of genes depending on their parental origin. Imprinting disorders (IDs), caused by disturbances of imprinted genes, are a set of rare congenital diseases that mainly affect growth, metabolism and development. To date, there is no accurate model to study the physiopathology of IDs or test therapeutic strategies. Human induced pluripotent stem cells (iPSCs) are a promising cellular approach to model human diseases and complex genetic disorders. However, aberrant hypermethylation of imprinting control regions (ICRs) may appear during the reprogramming process and subsequent culture of iPSCs. Therefore, we tested various conditions of reprogramming and culture of iPSCs and performed an extensive analysis of methylation marks at the ICRs to develop a cellular model that can be used to study IDs. RESULTS We assessed the methylation levels at seven imprinted loci in iPSCs before differentiation, at various passages of cell culture, and during chondrogenic differentiation. Abnormal methylation levels were found, with hypermethylation at 11p15 H19/IGF2:IG-DMR and 14q32 MEG3/DLK1:IG-DMR, independently of the reprogramming method and cells of origin. Hypermethylation at these two loci led to the loss of parental imprinting (LOI), with biallelic expression of the imprinted genes IGF2 and DLK1, respectively. The epiPS™ culture medium combined with culturing of the cells under hypoxic conditions prevented hypermethylation at H19/IGF2:IG-DMR (ICR1) and MEG3/DLK1:IG-DMR, as well as at other imprinted loci, while preserving the proliferation and pluripotency qualities of these iPSCs. CONCLUSIONS An extensive and quantitative analysis of methylation levels of ICRs in iPSCs showed hypermethylation of certain ICRs in human iPSCs, especially paternally methylated ICRs, and subsequent LOI of certain imprinted genes. The epiPS™ culture medium and culturing of the cells under hypoxic conditions prevented hypermethylation of ICRs in iPSCs. We demonstrated that the reprogramming and culture in epiPS™ medium allow the generation of control iPSCs lines with a balanced methylation and ID patient iPSCs lines with unbalanced methylation. Human iPSCs are therefore a promising cellular model to study the physiopathology of IDs and test therapies in tissues of interest.
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6
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DNA methyltransferases 3A and 3B target specific sequences during mouse gastrulation. Nat Struct Mol Biol 2022; 29:1252-1265. [PMID: 36510023 DOI: 10.1038/s41594-022-00885-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/02/2022] [Indexed: 12/14/2022]
Abstract
In mammalian embryos, DNA methylation is initialized to maximum levels in the epiblast by the de novo DNA methyltransferases DNMT3A and DNMT3B before gastrulation diversifies it across regulatory regions. Here we show that DNMT3A and DNMT3B are differentially regulated during endoderm and mesoderm bifurcation and study the implications in vivo and in meso-endoderm embryoid bodies. Loss of both Dnmt3a and Dnmt3b impairs exit from the epiblast state. More subtly, independent loss of Dnmt3a or Dnmt3b leads to small biases in mesoderm-endoderm bifurcation and transcriptional deregulation. Epigenetically, DNMT3A and DNMT3B drive distinct methylation kinetics in the epiblast, as can be predicted from their strand-specific sequence preferences. The enzymes compensate for each other in the epiblast, but can later facilitate lineage-specific methylation kinetics as their expression diverges. Single-cell analysis shows that differential activity of DNMT3A and DNMT3B combines with replication-linked methylation turnover to increase epigenetic plasticity in gastrulation. Together, these findings outline a dynamic model for the use of DNMT3A and DNMT3B sequence specificity during gastrulation.
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7
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Ors A, Chitsazan AD, Doe AR, Mulqueen RM, Ak C, Wen Y, Haverlack S, Handu M, Naldiga S, Saldivar J, Mohammed H. Estrogen regulates divergent transcriptional and epigenetic cell states in breast cancer. Nucleic Acids Res 2022; 50:11492-11508. [PMID: 36318267 PMCID: PMC9723652 DOI: 10.1093/nar/gkac908] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 09/20/2022] [Accepted: 10/20/2022] [Indexed: 12/12/2022] Open
Abstract
Breast cancers are known to be driven by the transcription factor estrogen receptor and its ligand estrogen. While the receptor's cis-binding elements are known to vary between tumors, heterogeneity of hormone signaling at a single-cell level is unknown. In this study, we systematically tracked estrogen response across time at a single-cell level in multiple cell line and organoid models. To accurately model these changes, we developed a computational tool (TITAN) that quantifies signaling gradients in single-cell datasets. Using this approach, we found that gene expression response to estrogen is non-uniform, with distinct cell groups expressing divergent transcriptional networks. Pathway analysis suggested the two most distinct signatures are driven separately by ER and FOXM1. We observed that FOXM1 was indeed activated by phosphorylation upon estrogen stimulation and silencing of FOXM1 attenuated the relevant gene signature. Analysis of scRNA-seq data from patient samples confirmed the existence of these divergent cell groups, with the FOXM1 signature predominantly found in ER negative cells. Further, multi-omic single-cell experiments indicated that the different cell groups have distinct chromatin accessibility states. Our results provide a comprehensive insight into ER biology at the single-cell level and potential therapeutic strategies to mitigate resistance to therapy.
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Affiliation(s)
| | | | - Aaron Reid Doe
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97201, USA
| | - Ryan M Mulqueen
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97201, USA
| | - Cigdem Ak
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97201, USA
| | - Yahong Wen
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97201, USA
| | - Syber Haverlack
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97201, USA
| | - Mithila Handu
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97201, USA
| | - Spandana Naldiga
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97201, USA
| | - Joshua C Saldivar
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97201, USA,Division of Oncological Sciences, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97201, USA
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8
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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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9
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Alata Jimenez N, Strobl-Mazzulla PH. Folate Carrier Deficiency Drives Differential Methylation and Enhanced Cellular Potency in the Neural Plate Border. Front Cell Dev Biol 2022; 10:834625. [PMID: 35912103 PMCID: PMC9326018 DOI: 10.3389/fcell.2022.834625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 06/07/2022] [Indexed: 11/28/2022] Open
Abstract
The neural plate border (NPB) of vertebrate embryos segregates from the neural and epidermal regions, and it is comprised of an intermingled group of multipotent progenitor cells. Folate is the precursor of S-adenosylmethionine, the main methyl donor for DNA methylation, and it is critical for embryonic development, including the specification of progenitors which reside in the NPB. Despite the fact that several intersecting signals involved in the specification and territorial restriction of NPB cells are known, the role of epigenetics, particularly DNA methylation, has been a matter of debate. Here, we examined the temporal and spatial distribution of the methyl source and analyzed the abundance of 5mC/5 hmC and their epigenetic writers throughout the segregation of the neural and NPB territories. Reduced representation bisulfite sequencing (RRBS) on Reduced Folate Carrier 1 (RFC1)-deficient embryos leads to the identification of differentially methylated regions (DMRs). In the RFC1-deficient embryos, we identified several DMRs in the Notch1 locus, and the spatiotemporal expression of Notch1 and its downstream target gene Bmp4 were expanded in the NPB. Cell fate analysis on folate deficient embryos revealed a significant increase in the number of cells coexpressing both neural (SOX2) and NPB (PAX7) markers, which may represent an enhancing effect in the cellular potential of those progenitors. Taken together, our findings propose a model where the RFC1 deficiency drives methylation changes in specific genomic regions that are correlated with a dysregulation of pathways involved in early development such as Notch1 and BMP4 signaling. These changes affect the potency of the progenitors residing in the juncture of the neural plate and NPB territories, thus driving them to a primed state.
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10
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Gabbutt C, Schenck RO, Weisenberger DJ, Kimberley C, Berner A, Househam J, Lakatos E, Robertson-Tessi M, Martin I, Patel R, Clark SK, Latchford A, Barnes CP, Leedham SJ, Anderson ARA, Graham TA, Shibata D. Fluctuating methylation clocks for cell lineage tracing at high temporal resolution in human tissues. Nat Biotechnol 2022; 40:720-730. [PMID: 34980912 PMCID: PMC9110299 DOI: 10.1038/s41587-021-01109-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 09/28/2021] [Indexed: 02/07/2023]
Abstract
Molecular clocks that record cell ancestry mutate too slowly to measure the short-timescale dynamics of cell renewal in adult tissues. Here, we show that fluctuating DNA methylation marks can be used as clocks in cells where ongoing methylation and demethylation cause repeated 'flip-flops' between methylated and unmethylated states. We identify endogenous fluctuating CpG (fCpG) sites using standard methylation arrays and develop a mathematical model to quantitatively measure human adult stem cell dynamics from these data. Small intestinal crypts were inferred to contain slightly more stem cells than the colon, with slower stem cell replacement in the small intestine. Germline APC mutation increased the number of replacements per crypt. In blood, we measured rapid expansion of acute leukemia and slower growth of chronic disease. Thus, the patterns of human somatic cell birth and death are measurable with fluctuating methylation clocks (FMCs).
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Affiliation(s)
- Calum Gabbutt
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Department of Cell and Developmental Biology, University College London, London, UK
- London Interdisciplinary Doctoral Training Programme (LIDo), London, UK
| | - Ryan O Schenck
- Integrated Mathematical Oncology Department, Moffitt Cancer Center, Tampa, FL, USA
- Intestinal Stem Cell Biology Lab, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Daniel J Weisenberger
- Department of Biochemistry and Molecular Medicine, University of Southern California, Los Angeles, CA, USA
| | - Christopher Kimberley
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Alison Berner
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Jacob Househam
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Eszter Lakatos
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Mark Robertson-Tessi
- Integrated Mathematical Oncology Department, Moffitt Cancer Center, Tampa, FL, USA
| | - Isabel Martin
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- St. Mark's Hospital, Harrow, London, UK
| | - Roshani Patel
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- St. Mark's Hospital, Harrow, London, UK
| | - Susan K Clark
- St. Mark's Hospital, Harrow, London, UK
- Department of Surgery and Cancer, Imperial College, London, UK
| | - Andrew Latchford
- St. Mark's Hospital, Harrow, London, UK
- Department of Surgery and Cancer, Imperial College, London, UK
| | - Chris P Barnes
- Department of Cell and Developmental Biology, University College London, London, UK
| | - Simon J Leedham
- Intestinal Stem Cell Biology Lab, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Trevor A Graham
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
| | - Darryl Shibata
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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11
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scTEM-seq: Single-cell analysis of transposable element methylation to link global epigenetic heterogeneity with transcriptional programs. Sci Rep 2022; 12:5776. [PMID: 35388081 PMCID: PMC8986802 DOI: 10.1038/s41598-022-09765-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 03/28/2022] [Indexed: 12/11/2022] Open
Abstract
Global changes in DNA methylation are observed in development and disease, and single-cell analyses are highlighting the heterogeneous regulation of these processes. However, technical challenges associated with single-cell analysis of DNA methylation limit these studies. We present single-cell transposable element methylation sequencing (scTEM-seq) for cost-effective estimation of average DNA methylation levels. By targeting high-copy SINE Alu elements, we achieve amplicon bisulphite sequencing with thousands of loci covered in each scTEM-seq library. Parallel transcriptome analysis is also performed to link global DNA methylation estimates with gene expression. We apply scTEM-seq to KG1a acute myeloid leukaemia (AML) cells, and primary AML cells. Our method reveals global DNA methylation heterogeneity induced by decitabine treatment of KG1a cells associated with altered expression of immune process genes. We also compare global DNA methylation estimates to expression of transposable elements and find a predominance of negative correlations. Finally, we observe co-ordinated upregulation of many transposable elements in a sub-set of decitabine treated cells. By linking global DNA methylation heterogeneity with transcription, scTEM-seq will refine our understanding of epigenetic regulation in cancer and beyond.
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12
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Laurent A, Madigou T, Bizot M, Turpin M, Palierne G, Mahé E, Guimard S, Métivier R, Avner S, Le Péron C, Salbert G. TET2-mediated epigenetic reprogramming of breast cancer cells impairs lysosome biogenesis. Life Sci Alliance 2022; 5:5/7/e202101283. [PMID: 35351824 PMCID: PMC8963717 DOI: 10.26508/lsa.202101283] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/11/2022] [Accepted: 03/14/2022] [Indexed: 11/24/2022] Open
Abstract
TET2-mediated oxidation of 5-methylcytosine establishes an antiviral state and contributes to MYC-dependent down-regulation of genes involved in lysosome biogenesis and function in breast cancer cells. Methylation and demethylation of cytosines in DNA are believed to act as keystones of cell-specific gene expression by controlling the chromatin structure and accessibility to transcription factors. Cancer cells have their own transcriptional programs, and we sought to alter such a cancer-specific program by enforcing expression of the catalytic domain (CD) of the methylcytosine dioxygenase TET2 in breast cancer cells. The TET2 CD decreased the tumorigenic potential of cancer cells through both activation and repression of a repertoire of genes that, interestingly, differed in part from the one observed upon treatment with the hypomethylating agent decitabine. In addition to promoting the establishment of an antiviral state, TET2 activated 5mC turnover at thousands of MYC-binding motifs and down-regulated a panel of known MYC-repressed genes involved in lysosome biogenesis and function. Thus, an extensive cross-talk between TET2 and the oncogenic transcription factor MYC establishes a lysosomal storage disease–like state that contributes to an exacerbated sensitivity to autophagy inducers.
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Affiliation(s)
- Audrey Laurent
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Thierry Madigou
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Maud Bizot
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Marion Turpin
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Gaëlle Palierne
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Elise Mahé
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Sarah Guimard
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Raphaël Métivier
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Stéphane Avner
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Christine Le Péron
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Gilles Salbert
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
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13
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Silverthorne T, Oh ES, Stinchcombe AR. Promoter methylation in a mixed feedback loop circadian clock model. Phys Rev E 2022; 105:034411. [PMID: 35428061 DOI: 10.1103/physreve.105.034411] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 02/27/2022] [Indexed: 06/14/2023]
Abstract
We investigate how epigenetic modifications to clock gene promoters affect transcriptomic activity in the circadian clock. Motivated by experimental observations that link DNA methylation with the behavior of the clock, we introduce and analyze an extension of the mixed feedback loop (MFL) model of François and Hakim. We extend the original model to include an additional methylated promoter state and allow for reversible protein sequestration, an important feature for circadian applications. First, working with the general form of the MFL model, we find that the qualitative behavior of the model is dictated by the promoter state with the highest transcription rate. We then build on the work of Kim and Forger, who analyzed the stability of the mammalian circadian clock by using a reduced form of the MFL model. We present a rigorous procedure for translating between the MFL model and the reduction of Kim and Forger. We then propose a model reduction more appropriate for the study of oscillatory promoter states, making use of a fully coupled quasi-steady-state approximation rather than the standard partially uncoupled quasi-steady-state approach. Working with the novel reduced form of the model, we find substantial differences in the transcription function and show that, although methylation contributes to period control, excessive methylation can abolish rhythmicity. Altogether our results show that even in a minimal clock model, DNA methylation has a nontrivial influence on the system's ability to oscillate.
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Affiliation(s)
- Turner Silverthorne
- Department of Mathematics, University of Toronto, Toronto, M5S 2E4 Ontario, Canada
- The Krembil Family Epigenetics Laboratory, The Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, M5T 1R8 Ontario, Canada
| | - Edward Saehong Oh
- The Krembil Family Epigenetics Laboratory, The Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, M5T 1R8 Ontario, Canada
| | - Adam R Stinchcombe
- Department of Mathematics, University of Toronto, Toronto, M5S 2E4 Ontario, Canada
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14
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Kusi M, Zand M, Lin LL, Chen M, Lopez A, Lin CL, Wang CM, Lucio ND, Kirma NB, Ruan J, Huang THM, Mitsuya K. 2-Hydroxyglutarate destabilizes chromatin regulatory landscape and lineage fidelity to promote cellular heterogeneity. Cell Rep 2022; 38:110220. [PMID: 35021081 PMCID: PMC8811753 DOI: 10.1016/j.celrep.2021.110220] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 09/23/2021] [Accepted: 12/15/2021] [Indexed: 02/07/2023] Open
Abstract
The epigenome delineates lineage-specific transcriptional programs and restricts cell plasticity to prevent non-physiological cell fate transitions. Although cell diversification fosters tumor evolution and therapy resistance, upstream mechanisms that regulate the stability and plasticity of the cancer epigenome remain elusive. Here we show that 2-hydroxyglutarate (2HG) not only suppresses DNA repair but also mediates the high-plasticity chromatin landscape. A combination of single-cell epigenomics and multi-omics approaches demonstrates that 2HG disarranges otherwise well-preserved stable nucleosome positioning and promotes cell-to-cell variability. 2HG induces loss of motif accessibility to the luminal-defining transcriptional factors FOXA1, FOXP1, and GATA3 and a shift from luminal to basal-like gene expression. Breast tumors with high 2HG exhibit enhanced heterogeneity with undifferentiated epigenomic signatures linked to adverse prognosis. Further, ascorbate-2-phosphate (A2P) eradicates heterogeneity and impairs growth of high 2HG-producing breast cancer cells. These findings suggest 2HG as a key determinant of cancer plasticity and provide a rational strategy to counteract tumor cell evolution. Kusi et al. show that the oncometabolite 2-hydroxyglutarate (2HG) initiates cell-level epigenome fluctuations in the chromatin regulatory landscape, accompanied by loss of lineage fidelity. Breast tumors with high 2HG accumulation exhibit enhanced cellular heterogeneity with undifferentiated stem-like epigenomic signatures. The findings suggest metabolic derangement as a molecular origin of breast cancer heterogeneity.
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Affiliation(s)
- Meena Kusi
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Maryam Zand
- Department of Computer Science, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Li-Ling Lin
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Meizhen Chen
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Anthony Lopez
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Chun-Lin Lin
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Chiou-Miin Wang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Nicholas D Lucio
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Nameer B Kirma
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Jianhua Ruan
- Department of Computer Science, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Tim H-M Huang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA.
| | - Kohzoh Mitsuya
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA.
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15
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Structure and Function of TET Enzymes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:239-267. [DOI: 10.1007/978-3-031-11454-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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16
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Horánszky A, Becker JL, Zana M, Ferguson-Smith AC, Dinnyés A. Epigenetic Mechanisms of ART-Related Imprinting Disorders: Lessons From iPSC and Mouse Models. Genes (Basel) 2021; 12:genes12111704. [PMID: 34828310 PMCID: PMC8620286 DOI: 10.3390/genes12111704] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 10/24/2021] [Accepted: 10/25/2021] [Indexed: 12/29/2022] Open
Abstract
The rising frequency of ART-conceived births is accompanied by the need for an improved understanding of the implications of ART on gametes and embryos. Increasing evidence from mouse models and human epidemiological data suggests that ART procedures may play a role in the pathophysiology of certain imprinting disorders (IDs), including Beckwith-Wiedemann syndrome, Silver-Russell syndrome, Prader-Willi syndrome, and Angelman syndrome. The underlying molecular basis of this association, however, requires further elucidation. In this review, we discuss the epigenetic and imprinting alterations of in vivo mouse models and human iPSC models of ART. Mouse models have demonstrated aberrant regulation of imprinted genes involved with ART-related IDs. In the past decade, iPSC technology has provided a platform for patient-specific cellular models of culture-associated perturbed imprinting. However, despite ongoing efforts, a deeper understanding of the susceptibility of iPSCs to epigenetic perturbation is required if they are to be reliably used for modelling ART-associated IDs. Comparing the patterns of susceptibility of imprinted genes in mouse models and IPSCs in culture improves the current understanding of the underlying mechanisms of ART-linked IDs with implications for our understanding of the influence of environmental factors such as culture and hormone treatments on epigenetically important regions of the genome such as imprints.
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Affiliation(s)
- Alex Horánszky
- BioTalentum Ltd., H-2100 Gödöllő, Hungary; (A.H.); (M.Z.)
- Department of Physiology and Animal Health, Institute of Physiology and Animal Health, Hungarian University of Agriculture and Life Sciences, H-2100 Gödöllő, Hungary
| | - Jessica L. Becker
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK; (J.L.B.); (A.C.F.-S.)
| | - Melinda Zana
- BioTalentum Ltd., H-2100 Gödöllő, Hungary; (A.H.); (M.Z.)
| | - Anne C. Ferguson-Smith
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK; (J.L.B.); (A.C.F.-S.)
| | - András Dinnyés
- BioTalentum Ltd., H-2100 Gödöllő, Hungary; (A.H.); (M.Z.)
- Department of Physiology and Animal Health, Institute of Physiology and Animal Health, Hungarian University of Agriculture and Life Sciences, H-2100 Gödöllő, Hungary
- HCEMM-USZ Stem Cell Research Group, Hungarian Centre of Excellence for Molecular Medicine, H-6723 Szeged, Hungary
- Department of Cell Biology and Molecular Medicine, University of Szeged, H-6720 Szeged, Hungary
- Correspondence: ; Tel.: +36-20-510-9632; Fax: +36-28-526-151
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17
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Enhancer-associated H3K4 methylation safeguards in vitro germline competence. Nat Commun 2021; 12:5771. [PMID: 34599190 PMCID: PMC8486853 DOI: 10.1038/s41467-021-26065-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/16/2021] [Indexed: 01/27/2023] Open
Abstract
Germline specification in mammals occurs through an inductive process whereby competent cells in the post-implantation epiblast differentiate into primordial germ cells (PGC). The intrinsic factors that endow epiblast cells with the competence to respond to germline inductive signals remain unknown. Single-cell RNA sequencing across multiple stages of an in vitro PGC-like cells (PGCLC) differentiation system shows that PGCLC genes initially expressed in the naïve pluripotent stage become homogeneously dismantled in germline competent epiblast like-cells (EpiLC). In contrast, the decommissioning of enhancers associated with these germline genes is incomplete. Namely, a subset of these enhancers partly retain H3K4me1, accumulate less heterochromatic marks and remain accessible and responsive to transcriptional activators. Subsequently, as in vitro germline competence is lost, these enhancers get further decommissioned and lose their responsiveness to transcriptional activators. Importantly, using H3K4me1-deficient cells, we show that the loss of this histone modification reduces the germline competence of EpiLC and decreases PGCLC differentiation efficiency. Our work suggests that, although H3K4me1 might not be essential for enhancer function, it can facilitate the (re)activation of enhancers and the establishment of gene expression programs during specific developmental transitions.
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18
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Mellis IA, Edelstein HI, Truitt R, Goyal Y, Beck LE, Symmons O, Dunagin MC, Linares Saldana RA, Shah PP, Pérez-Bermejo JA, Padmanabhan A, Yang W, Jain R, Raj A. Responsiveness to perturbations is a hallmark of transcription factors that maintain cell identity in vitro. Cell Syst 2021; 12:885-899.e8. [PMID: 34352221 PMCID: PMC8522198 DOI: 10.1016/j.cels.2021.07.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/27/2020] [Accepted: 07/09/2021] [Indexed: 02/07/2023]
Abstract
Identifying the particular transcription factors that maintain cell type in vitro is important for manipulating cell type. Identifying such transcription factors by their cell-type-specific expression or their involvement in developmental regulation has had limited success. We hypothesized that because cell type is often resilient to perturbations, the transcriptional response to perturbations would reveal identity-maintaining transcription factors. We developed perturbation panel profiling (P3) as a framework for perturbing cells across many conditions and measuring gene expression responsiveness transcriptome-wide. In human iPSC-derived cardiac myocytes, P3 showed that transcription factors important for cardiac myocyte differentiation and maintenance were among the most frequently upregulated (most responsive). We reasoned that one function of responsive genes may be to maintain cellular identity. We identified responsive transcription factors in fibroblasts using P3 and found that suppressing their expression led to enhanced reprogramming. We propose that responsiveness to perturbations is a property of transcription factors that help maintain cellular identity in vitro. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Ian A Mellis
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Genomics and Computational Biology Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hailey I Edelstein
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rachel Truitt
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yogesh Goyal
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lauren E Beck
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Orsolya Symmons
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Margaret C Dunagin
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Ricardo A Linares Saldana
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Parisha P Shah
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Arun Padmanabhan
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA, USA; Division of Cardiology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Wenli Yang
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rajan Jain
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Arjun Raj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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19
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Kinoshita M, Li MA, Barber M, Mansfield W, Dietmann S, Smith A. Disabling de novo DNA methylation in embryonic stem cells allows an illegitimate fate trajectory. Proc Natl Acad Sci U S A 2021; 118:e2109475118. [PMID: 34518230 PMCID: PMC8463881 DOI: 10.1073/pnas.2109475118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2021] [Indexed: 12/13/2022] Open
Abstract
Genome remethylation is essential for mammalian development but specific reasons are unclear. Here we examined embryonic stem (ES) cell fate in the absence of de novo DNA methyltransferases. We observed that ES cells deficient for both Dnmt3a and Dnmt3b are rapidly eliminated from chimeras. On further investigation we found that in vivo and in vitro the formative pluripotency transition is derailed toward production of trophoblast. This aberrant trajectory is associated with failure to suppress activation of Ascl2Ascl2 encodes a bHLH transcription factor expressed in the placenta. Misexpression of Ascl2 in ES cells provokes transdifferentiation to trophoblast-like cells. Conversely, Ascl2 deletion rescues formative transition of Dnmt3a/b mutants and improves contribution to chimeric epiblast. Thus, de novo DNA methylation safeguards against ectopic activation of Ascl2 However, Dnmt3a/b-deficient cells remain defective in ongoing embryogenesis. We surmise that multiple developmental transitions may be secured by DNA methylation silencing potentially disruptive genes.
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Affiliation(s)
- Masaki Kinoshita
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, United Kingdom
| | - Meng Amy Li
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, United Kingdom
| | - Michael Barber
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, United Kingdom
| | - William Mansfield
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, United Kingdom
| | - Sabine Dietmann
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, United Kingdom
| | - Austin Smith
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, United Kingdom;
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
- Living Systems Institute, University of Exeter, Exeter EX4 4QD, United Kingdom
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20
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Abstract
Epigenetics has enriched human disease studies by adding new interpretations to disease features that cannot be explained by genetic and environmental factors. However, identifying causal mechanisms of epigenetic origin has been challenging. New opportunities have risen from recent findings in intra-individual and cyclical epigenetic variation, which includes circadian epigenetic oscillations. Cytosine modifications display deterministic temporal rhythms, which may drive ageing and complex disease. Temporality in the epigenome, or the 'chrono' dimension, may help the integration of epigenetic, environmental and genetic disease studies, and reconcile several disparities stemming from the arbitrarily delimited research fields. The ultimate goal of chrono-epigenetics is to predict disease risk, age of onset and disease dynamics from within individual-specific temporal dynamics of epigenomes.
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21
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Teschendorff AE, Feinberg AP. Statistical mechanics meets single-cell biology. Nat Rev Genet 2021; 22:459-476. [PMID: 33875884 PMCID: PMC10152720 DOI: 10.1038/s41576-021-00341-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2021] [Indexed: 02/07/2023]
Abstract
Single-cell omics is transforming our understanding of cell biology and disease, yet the systems-level analysis and interpretation of single-cell data faces many challenges. In this Perspective, we describe the impact that fundamental concepts from statistical mechanics, notably entropy, stochastic processes and critical phenomena, are having on single-cell data analysis. We further advocate the need for more bottom-up modelling of single-cell data and to embrace a statistical mechanics analysis paradigm to help attain a deeper understanding of single-cell systems biology.
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Affiliation(s)
- Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China. .,UCL Cancer Institute, University College London, London, UK.
| | - Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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22
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Ming X, Zhu B, Li Y. Mitotic inheritance of DNA methylation: more than just copy and paste. J Genet Genomics 2021; 48:1-13. [PMID: 33771455 DOI: 10.1016/j.jgg.2021.01.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/13/2021] [Accepted: 01/22/2021] [Indexed: 12/14/2022]
Abstract
Decades of investigation on DNA methylation have led to deeper insights into its metabolic mechanisms and biological functions. This understanding was fueled by the recent development of genome editing tools and our improved capacity for analyzing the global DNA methylome in mammalian cells. This review focuses on the maintenance of DNA methylation patterns during mitotic cell division. We discuss the latest discoveries of the mechanisms for the inheritance of DNA methylation as a stable epigenetic memory. We also highlight recent evidence showing the rapid turnover of DNA methylation as a dynamic gene regulatory mechanism. A body of work has shown that altered DNA methylomes are common features in aging and disease. We discuss the potential links between methylation maintenance mechanisms and disease-associated methylation changes.
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Affiliation(s)
- Xuan Ming
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Bing Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yingfeng Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
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23
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Spada F, Schiffers S, Kirchner A, Zhang Y, Arista G, Kosmatchev O, Korytiakova E, Rahimoff R, Ebert C, Carell T. Active turnover of genomic methylcytosine in pluripotent cells. Nat Chem Biol 2020; 16:1411-1419. [PMID: 32778844 DOI: 10.1038/s41589-020-0621-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 07/08/2020] [Indexed: 12/20/2022]
Abstract
Epigenetic plasticity underpins cell potency, but the extent to which active turnover of DNA methylation contributes to such plasticity is not known, and the underlying pathways are poorly understood. Here we use metabolic labeling with stable isotopes and mass spectrometry to quantitatively address the global turnover of genomic 5-methyl-2'-deoxycytidine (mdC), 5-hydroxymethyl-2'-deoxycytidine (hmdC) and 5-formyl-2'-deoxycytidine (fdC) across mouse pluripotent cell states. High rates of mdC/hmdC oxidation and fdC turnover characterize a formative-like pluripotent state. In primed pluripotent cells, the global mdC turnover rate is about 3-6% faster than can be explained by passive dilution through DNA synthesis. While this active component is largely dependent on ten-eleven translocation (Tet)-mediated mdC oxidation, we unveil additional oxidation-independent mdC turnover, possibly through DNA repair. This process accelerates upon acquisition of primed pluripotency and returns to low levels in lineage-committed cells. Thus, in pluripotent cells, active mdC turnover involves both mdC oxidation-dependent and oxidation-independent processes.
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Affiliation(s)
- Fabio Spada
- Department of Chemistry, Ludwig Maximilians University Munich and Center for Integrated Protein Science Munich (CIPSM), Munich, Germany.
| | - Sarah Schiffers
- Department of Chemistry, Ludwig Maximilians University Munich and Center for Integrated Protein Science Munich (CIPSM), Munich, Germany
- National Cancer Institute, Center for Cancer Research, Bethesda, MD, USA
| | - Angie Kirchner
- Department of Chemistry, Ludwig Maximilians University Munich and Center for Integrated Protein Science Munich (CIPSM), Munich, Germany
- Cancer Research UK Cambridge Institute, Cambridge, UK
| | - Yingqian Zhang
- Department of Chemistry, Ludwig Maximilians University Munich and Center for Integrated Protein Science Munich (CIPSM), Munich, Germany
- State Key Laboratory of Elemento-organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin, China
| | - Gautier Arista
- Department of Chemistry, Ludwig Maximilians University Munich and Center for Integrated Protein Science Munich (CIPSM), Munich, Germany
| | - Olesea Kosmatchev
- Department of Chemistry, Ludwig Maximilians University Munich and Center for Integrated Protein Science Munich (CIPSM), Munich, Germany
| | - Eva Korytiakova
- Department of Chemistry, Ludwig Maximilians University Munich and Center for Integrated Protein Science Munich (CIPSM), Munich, Germany
| | - René Rahimoff
- Department of Chemistry, Ludwig Maximilians University Munich and Center for Integrated Protein Science Munich (CIPSM), Munich, Germany
- Department of Chemistry, University of California, Los Angeles, Berkeley, CA, USA
| | - Charlotte Ebert
- Department of Chemistry, Ludwig Maximilians University Munich and Center for Integrated Protein Science Munich (CIPSM), Munich, Germany
| | - Thomas Carell
- Department of Chemistry, Ludwig Maximilians University Munich and Center for Integrated Protein Science Munich (CIPSM), Munich, Germany.
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24
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TET1 Interacts Directly with NANOG via Independent Domains Containing Hydrophobic and Aromatic Residues. J Mol Biol 2020; 432:6075-6091. [PMID: 33058869 PMCID: PMC7763487 DOI: 10.1016/j.jmb.2020.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/27/2020] [Accepted: 10/07/2020] [Indexed: 11/29/2022]
Abstract
TET1 and NANOG interact via multiple independent binding regions. TET1 and NANOG interactions are mediated by aromatic and hydrophobic residues. TET1 residues that bind NANOG are highly conserved in mammals. Co-localisation of TET1 and NANOG on chromatin is enriched at NANOG target genes. NANOG and TET1 have regulatory roles in maintaining and reprogramming pluripotency.
The DNA demethylase TET1 is highly expressed in embryonic stem cells and is important both for lineage commitment, and reprogramming to naïve pluripotency. TET1 interacts with the pluripotency transcription factor NANOG which may contribute to its biological activity in pluripotent cells. However, how TET1 interacts with other proteins is largely unknown. Here, we characterise the physical interaction between TET1 and NANOG using embryonic stem cells and bacterial expression systems. TET1 and NANOG interact through multiple binding sites that act independently. Critically, mutating conserved hydrophobic and aromatic residues within TET1 and NANOG abolishes the interaction. On chromatin, NANOG is predominantly localised at ESC enhancers. While TET1 binds to CpG dinucleotides in promoters using its CXXC domain, TET1 also binds to enhancers, though the mechanism involved is unknown. Comparative ChIP-seq analysis identifies genomic loci bound by both TET1 and NANOG, that correspond predominantly to pluripotency enhancers. Importantly, around half of NANOG transcriptional target genes are associated with TET1-NANOG co-bound sites. These results indicate a mechanism by which TET1 protein may be targeted to specific sites of action at enhancers by direct interaction with a transcription factor.
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25
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Abstract
DNA methylation is a key layer of epigenetic regulation. The deposition of methylation marks relies on the catalytic activity of DNA methyltransferases (DNMTs), and their active removal relies on the activity of ten-eleven translocation (TET) enzymes. Paradoxically, in important biological contexts these antagonistic factors are co-expressed and target overlapping genomic regions. The ensuing cyclic biochemistry of cytosine modifications gives rise to a continuous, out-of-thermal equilibrium transition through different methylation states. But what is the purpose of this intriguing turnover of DNA methylation? Recent evidence demonstrates that methylation turnover is enriched at gene distal regulatory elements, including enhancers, and can give rise to large-scale oscillatory dynamics. We discuss this phenomenon and propose that DNA methylation turnover might facilitate key lineage decisions.
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26
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Modeling DNA Methylation Profiles through a Dynamic Equilibrium between Methylation and Demethylation. Biomolecules 2020; 10:biom10091271. [PMID: 32899254 PMCID: PMC7564540 DOI: 10.3390/biom10091271] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 12/30/2022] Open
Abstract
DNA methylation is a heritable epigenetic mark that plays a key role in regulating gene expression. Mathematical modeling has been extensively applied to unravel the regulatory mechanisms of this process. In this study, we aimed to investigate DNA methylation by performing a high-depth analysis of particular loci, and by subsequent modeling of the experimental results. In particular, we performed an in-deep DNA methylation profiling of two genomic loci surrounding the transcription start site of the D-Aspartate Oxidase and the D-Serine Oxidase genes in different samples (n = 51). We found evidence of cell-to-cell differences in DNA methylation status. However, these cell differences were maintained between different individuals, which indeed showed very similar DNA methylation profiles. Therefore, we hypothesized that the observed pattern of DNA methylation was the result of a dynamic balance between DNA methylation and demethylation, and that this balance was identical between individuals. We hence developed a simple mathematical model to test this hypothesis. Our model reliably captured the characteristics of the experimental data, suggesting that DNA methylation and demethylation work together in determining the methylation state of a locus. Furthermore, our model suggested that the methylation status of neighboring cytosines plays an important role in this balance.
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27
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Williams BP, Gehring M. Principles of Epigenetic Homeostasis Shared Between Flowering Plants and Mammals. Trends Genet 2020; 36:751-763. [PMID: 32711945 DOI: 10.1016/j.tig.2020.06.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/30/2020] [Accepted: 06/30/2020] [Indexed: 12/18/2022]
Abstract
In diverse eukaryotes, epigenetic information such as DNA methylation is stably propagated over many cell divisions and generations, and can remain the same over thousands or millions of years. However, this stability is the product of dynamic processes that add and remove DNA methylation by specialized enzymatic pathways. The activities of these dynamic pathways must therefore be finely orchestrated in order to ensure that the DNA methylation landscape is maintained with high fidelity - a concept we term epigenetic homeostasis. In this review, we summarize recent insights into epigenetic homeostasis mechanisms in flowering plants and mammals, highlighting analogous mechanisms that have independently evolved to achieve the same goal of stabilizing the epigenetic landscape.
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Affiliation(s)
- Ben P Williams
- Whitehead Institute for Biomedical Research, 455 Main St, Cambridge, MA 02142, USA.
| | - Mary Gehring
- Whitehead Institute for Biomedical Research, 455 Main St, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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28
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Abstract
Mammalian fertilization begins with the fusion of two specialized gametes, followed by major epigenetic remodeling leading to the formation of a totipotent embryo. During the development of the pre-implantation embryo, precise reprogramming progress is a prerequisite for avoiding developmental defects or embryonic lethality, but the underlying molecular mechanisms remain elusive. For the past few years, unprecedented breakthroughs have been made in mapping the regulatory network of dynamic epigenomes during mammalian early embryo development, taking advantage of multiple advances and innovations in low-input genome-wide chromatin analysis technologies. The aim of this review is to highlight the most recent progress in understanding the mechanisms of epigenetic remodeling during early embryogenesis in mammals, including DNA methylation, histone modifications, chromatin accessibility and 3D chromatin organization.
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29
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Alda-Catalinas C, Bredikhin D, Hernando-Herraez I, Santos F, Kubinyecz O, Eckersley-Maslin MA, Stegle O, Reik W. A Single-Cell Transcriptomics CRISPR-Activation Screen Identifies Epigenetic Regulators of the Zygotic Genome Activation Program. Cell Syst 2020; 11:25-41.e9. [PMID: 32634384 PMCID: PMC7383230 DOI: 10.1016/j.cels.2020.06.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 04/17/2020] [Accepted: 06/05/2020] [Indexed: 01/09/2023]
Abstract
Zygotic genome activation (ZGA) is an essential transcriptional event in embryonic development that coincides with extensive epigenetic reprogramming. Complex manipulation techniques and maternal stores of proteins preclude large-scale functional screens for ZGA regulators within early embryos. Here, we combined pooled CRISPR activation (CRISPRa) with single-cell transcriptomics to identify regulators of ZGA-like transcription in mouse embryonic stem cells, which serve as a tractable, in vitro proxy of early mouse embryos. Using multi-omics factor analysis (MOFA+) applied to ∼200,000 single-cell transcriptomes comprising 230 CRISPRa perturbations, we characterized molecular signatures of ZGA and uncovered 24 factors that promote a ZGA-like response. Follow-up assays validated top screen hits, including the DNA-binding protein Dppa2, the chromatin remodeler Smarca5, and the transcription factor Patz1, and functional experiments revealed that Smarca5’s regulation of ZGA-like transcription is dependent on Dppa2. Together, our single-cell transcriptomic profiling of CRISPRa-perturbed cells provides both system-level and molecular insights into the mechanisms that orchestrate ZGA. Large-scale pooled CRISPR-activation screen with single-cell RNA-seq for 230 genes MOFA+ identified 24 screen hits that induced a ZGA-like signature Nine genes were independently validated as regulators of ZGA-like transcription Smarca5 regulates ZGA-like transcription in a Dppa2-dependent manner
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Affiliation(s)
- Celia Alda-Catalinas
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Danila Bredikhin
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg 69117, Germany
| | | | - Fátima Santos
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Oana Kubinyecz
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | | | - Oliver Stegle
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg 69117, Germany; Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SA, UK; Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
| | - Wolf Reik
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK; Centre for Trophoblast Research University of Cambridge, Cambridge CB2 3EG, UK.
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30
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Charlton J, Jung EJ, Mattei AL, Bailly N, Liao J, Martin EJ, Giesselmann P, Brändl B, Stamenova EK, Müller FJ, Kiskinis E, Gnirke A, Smith ZD, Meissner A. TETs compete with DNMT3 activity in pluripotent cells at thousands of methylated somatic enhancers. Nat Genet 2020; 52:819-827. [PMID: 32514123 PMCID: PMC7415576 DOI: 10.1038/s41588-020-0639-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 04/30/2020] [Indexed: 12/17/2022]
Abstract
Mammalian cells stably maintain high levels of DNA methylation despite expressing both positive (DNMT3A/B) and negative (TET1-3) regulators. Here, we analyzed the independent and combined effects of these regulators on the DNA methylation landscape using a panel of knockout human embryonic stem cell (ESC) lines. The greatest impact on global methylation levels was observed in DNMT3-deficient cells, including reproducible focal demethylation at thousands of normally methylated loci. Demethylation depends on TET expression and occurs only when both DNMT3s are absent. Dynamic loci are enriched for hydroxymethylcytosine and overlap with subsets of putative somatic enhancers that are methylated in ESCs and can be activated upon differentiation. We observe similar dynamics in mouse ESCs that were less frequent in epiblast stem cells (EpiSCs) and scarce in somatic tissues, suggesting a conserved pluripotency-linked mechanism. Taken together, our data reveal tightly regulated competition between DNMT3s and TETs at thousands of somatic regulatory sequences within pluripotent cells.
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Affiliation(s)
- Jocelyn Charlton
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Eunmi J Jung
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Alexandra L Mattei
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Nina Bailly
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Jing Liao
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Eric J Martin
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Pay Giesselmann
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Björn Brändl
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - Franz-Josef Müller
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Zentrum für Integrative Psychiatrie gGmbH, Universitätsklinikum Schleswig-Holstein, Kiel, Germany
| | - Evangelos Kiskinis
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | | | - Zachary D Smith
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alexander Meissner
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany. .,Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany.
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31
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DNA methylation in the vertebrate germline: balancing memory and erasure. Essays Biochem 2020; 63:649-661. [PMID: 31755927 DOI: 10.1042/ebc20190038] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/02/2019] [Accepted: 10/03/2019] [Indexed: 02/07/2023]
Abstract
Cytosine methylation is a DNA modification that is critical for vertebrate development and provides a plastic yet stable information module in addition to the DNA code. DNA methylation memory establishment, maintenance and erasure is carefully balanced by molecular machinery highly conserved among vertebrates. In mammals, extensive erasure of epigenetic marks, including 5-methylcytosine (5mC), is a hallmark of early embryo and germline development. Conversely, global cytosine methylation patterns are preserved in at least some non-mammalian vertebrates over comparable developmental windows. The evolutionary mechanisms which drove this divergence are unknown, nevertheless a direct consequence of retaining epigenetic memory in the form of 5mC is the enhanced potential for transgenerational epigenetic inheritance (TEI). Given that DNA methylation dynamics remains underexplored in most vertebrate lineages, the extent of information transferred to offspring by epigenetic modification might be underestimated.
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32
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Scherer M, Nebel A, Franke A, Walter J, Lengauer T, Bock C, Müller F, List M. Quantitative comparison of within-sample heterogeneity scores for DNA methylation data. Nucleic Acids Res 2020; 48:e46. [PMID: 32103242 PMCID: PMC7192612 DOI: 10.1093/nar/gkaa120] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 02/14/2020] [Indexed: 12/13/2022] Open
Abstract
DNA methylation is an epigenetic mark with important regulatory roles in cellular identity and can be quantified at base resolution using bisulfite sequencing. Most studies are limited to the average DNA methylation levels of individual CpGs and thus neglect heterogeneity within the profiled cell populations. To assess this within-sample heterogeneity (WSH) several window-based scores that quantify variability in DNA methylation in sequencing reads have been proposed. We performed the first systematic comparison of four published WSH scores based on simulated and publicly available datasets. Moreover, we propose two new scores and provide guidelines for selecting appropriate scores to address cell-type heterogeneity, cellular contamination and allele-specific methylation. Most of the measures were sensitive in detecting DNA methylation heterogeneity in these scenarios, while we detected differences in susceptibility to technical bias. Using recently published DNA methylation profiles of Ewing sarcoma samples, we show that DNA methylation heterogeneity provides information complementary to the DNA methylation level. WSH scores are powerful tools for estimating variance in DNA methylation patterns and have the potential for detecting novel disease-associated genomic loci not captured by established statistics. We provide an R-package implementing the WSH scores for integration into analysis workflows.
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Affiliation(s)
- Michael Scherer
- Computational Biology, Max Planck Institute for Informatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Graduate School of Computer Science, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Department of Genetics/Epigenetics, Saarland University, 66123 Saarbrücken, Germany
| | - Almut Nebel
- Institute of Clinical Molecular Biology, Kiel University, 24105 Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, 24105 Kiel, Germany
| | - Jörn Walter
- Department of Genetics/Epigenetics, Saarland University, 66123 Saarbrücken, Germany
| | - Thomas Lengauer
- Computational Biology, Max Planck Institute for Informatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Fabian Müller
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Markus List
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
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33
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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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34
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Wang Y, Wang F, Hong DK, Gao SJ, Wang R, Wang JD. Molecular characterization of DNA methyltransferase 1 and its role in temperature change of armyworm Mythimna separata Walker. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2020; 103:e21651. [PMID: 31943343 DOI: 10.1002/arch.21651] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/10/2019] [Accepted: 11/21/2019] [Indexed: 06/10/2023]
Abstract
DNA methylation refers to the addition of cytosine residues in a CpG context (5'-cytosine-phosphate-guanine-3'). As one of the most common mechanisms of epigenetic modification, it plays a crucial role in regulating gene expression and in a diverse range of biological processes across all multicellular organisms. The relationship between temperature and DNA methylation and how it acts on the adaptability of migratory insects remain unknown. In the present work, a 5,496 bp full-length complementary DNA encoding 1,436 amino acids (named MsDnmt1) was cloned from the devastating migratory pest oriental armyworm, Mythimna separata Walker. The protein shares 36.8-84.4% identity with other insect Dnmt1 isoforms. Spatial and temporal expression analysis revealed that MsDnmt1 was highly expressed in adult stages and head tissue. The changing temperature decreased the expression of MsDnmt1 in both high and low temperature condition. Besides, we found that M. separata exhibited the shortest duration time from the last instar to pupae under 36°C environment when injected with DNA methylation inhibitor. Therefore, our data highlight a potential role for DNA methylation in thermal resistance, which help us to understand the biological role adaptability and colonization of migratory pest in various environments.
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Affiliation(s)
- Yaru Wang
- National Engineering Research Center of Sugarcane, Fujian Agricultural University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agricultural and Forestry University, Fuzhou, China
| | - Falv Wang
- National Engineering Research Center of Sugarcane, Fujian Agricultural University, Fuzhou, China
| | - Ding-Kai Hong
- National Engineering Research Center of Sugarcane, Fujian Agricultural University, Fuzhou, China
| | - San-Ji Gao
- National Engineering Research Center of Sugarcane, Fujian Agricultural University, Fuzhou, China
| | - Ran Wang
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jin-da Wang
- National Engineering Research Center of Sugarcane, Fujian Agricultural University, Fuzhou, China
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35
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Dynamic CpG methylation delineates subregions within super-enhancers selectively decommissioned at the exit from naive pluripotency. Nat Commun 2020; 11:1112. [PMID: 32111830 PMCID: PMC7048827 DOI: 10.1038/s41467-020-14916-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 02/08/2020] [Indexed: 12/29/2022] Open
Abstract
Clusters of enhancers, referred as to super-enhancers (SEs), control the expression of cell identity genes. The organisation of these clusters, and how they are remodelled upon developmental transitions remain poorly understood. Here, we report the existence of two types of enhancer units within SEs typified by distinctive CpG methylation dynamics in embryonic stem cells (ESCs). We find that these units are either prone for decommissioning or remain constitutively active in epiblast stem cells (EpiSCs), as further established in the peri-implantation epiblast in vivo. Mechanistically, we show a pivotal role for ESRRB in regulating the activity of ESC-specific enhancer units and propose that the developmentally regulated silencing of ESRRB triggers the selective inactivation of these units within SEs. Our study provides insights into the molecular events that follow the loss of ESRRB binding, and offers a mechanism by which the naive pluripotency transcriptional programme can be partially reset upon embryo implantation.
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36
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Abstract
Epigenetic regulatory mechanisms, encompassing diverse molecular processes including DNA methylation, histone post-translational modifications, and noncoding RNAs, are essential to numerous processes such as cell differentiation, growth and development, environmental adaptation, aging, and disease states. In many cases, epigenetic changes occur in response to environmental cues and lifestyle factors, resulting in persistent changes in gene expression that affect vascular disease risk during the lifetime of the individual. Biological aging-a powerful cardiovascular risk factor-is partly genetically determined yet strongly influenced by traditional risk factors, reflecting epigenetic modulation. Quantification of specific DNA methylation patterns may serve as an accurate predictor of biological age-a concept known as the epigenetic clock, which could help to refine cardiovascular risk assessment. Epigenetic reprogramming of monocytes rewires cellular immune signaling and induces a metabolic shift toward aerobic glycolysis, thereby increasing innate immune responses. This form of trained epigenetic memory can be maladaptive, thus augmenting vascular inflammation. Somatic mutations in epigenetic regulatory enzymes lead to clonal hematopoiesis of indeterminate potential, a precursor of hematologic malignancies and a recently recognized cardiovascular risk factor; moreover, epigenetic regulators are increasingly being targeted in cancer therapeutics. Thus, understanding epigenetic regulatory mechanisms lies at the intersection between cancer and cardiovascular disease and is of paramount importance to the burgeoning field of cardio-oncology (Graphic Abstract).
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Affiliation(s)
- Abdalrahman Zarzour
- From the Department of Medicine, Vascular Biology Center, Medical College of Georgia at Augusta University
| | - Ha Won Kim
- From the Department of Medicine, Vascular Biology Center, Medical College of Georgia at Augusta University
| | - Neal L Weintraub
- From the Department of Medicine, Vascular Biology Center, Medical College of Georgia at Augusta University
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37
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Bleckwehl T, Rada-Iglesias A. Transcriptional and epigenetic control of germline competence and specification. Curr Opin Cell Biol 2019; 61:1-8. [DOI: 10.1016/j.ceb.2019.05.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/17/2019] [Accepted: 05/23/2019] [Indexed: 12/11/2022]
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38
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Bell CG, Lowe R, Adams PD, Baccarelli AA, Beck S, Bell JT, Christensen BC, Gladyshev VN, Heijmans BT, Horvath S, Ideker T, Issa JPJ, Kelsey KT, Marioni RE, Reik W, Relton CL, Schalkwyk LC, Teschendorff AE, Wagner W, Zhang K, Rakyan VK. DNA methylation aging clocks: challenges and recommendations. Genome Biol 2019; 20:249. [PMID: 31767039 PMCID: PMC6876109 DOI: 10.1186/s13059-019-1824-y] [Citation(s) in RCA: 437] [Impact Index Per Article: 87.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 09/16/2019] [Indexed: 12/15/2022] Open
Abstract
Epigenetic clocks comprise a set of CpG sites whose DNA methylation levels measure subject age. These clocks are acknowledged as a highly accurate molecular correlate of chronological age in humans and other vertebrates. Also, extensive research is aimed at their potential to quantify biological aging rates and test longevity or rejuvenating interventions. Here, we discuss key challenges to understand clock mechanisms and biomarker utility. This requires dissecting the drivers and regulators of age-related changes in single-cell, tissue- and disease-specific models, as well as exploring other epigenomic marks, longitudinal and diverse population studies, and non-human models. We also highlight important ethical issues in forensic age determination and predicting the trajectory of biological aging in an individual.
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Affiliation(s)
- Christopher G Bell
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
| | - Robert Lowe
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
| | - Peter D Adams
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
- Beatson Institute for Cancer Research and University of Glasgow, Glasgow, UK.
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA.
| | - Stephan Beck
- Medical Genomics, Paul O'Gorman Building, UCL Cancer Institute, University College London, London, UK.
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA.
- Department of Molecular and Systems Biology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA.
- Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA.
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Bastiaan T Heijmans
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands.
| | - Steve Horvath
- Department of Human Genetics, Gonda Research Center, David Geffen School of Medicine, Los Angeles, CA, USA.
- Department of Biostatistics, School of Public Health, University of California-Los Angeles, Los Angeles, CA, USA.
| | - Trey Ideker
- San Diego Center for Systems Biology, University of California-San Diego, San Diego, CA, USA.
| | - Jean-Pierre J Issa
- Fels Institute for Cancer Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA.
| | - Karl T Kelsey
- Department of Epidemiology, Brown University, Providence, RI, USA.
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA.
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK.
| | - Wolf Reik
- Epigenetics Programme, The Babraham Institute, Cambridge, UK.
- The Wellcome Trust Sanger Institute, Cambridge, UK.
| | - Caroline L Relton
- Medical Research Council Integrative Epidemiology Unit (MRC IEU), School of Social and Community Medicine, University of Bristol, Bristol, UK.
| | | | - Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China.
- UCL Cancer Institute, Paul O'Gorman Building, University College London, 72 Huntley Street, London, WC1E 6BT, UK.
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen Faculty of Medicine, Aachen, Germany.
| | - Kang Zhang
- Faculty of Medicine, Macau University of Science and Technology, Taipa, Macau.
| | - Vardhman K Rakyan
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
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Colì D, Orlandini E, Michieletto D, Marenduzzo D. Magnetic polymer models for epigenetics-driven chromosome folding. Phys Rev E 2019; 100:052410. [PMID: 31869901 DOI: 10.1103/physreve.100.052410] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Indexed: 05/12/2023]
Abstract
Epigenetics is a driving force of important and ubiquitous phenomena in nature such as cell differentiation or even metamorphosis. Opposite to its widespread role, understanding the biophysical principles that allow epigenetics to control and rewire gene regulatory networks remains an open challenge. In this work we study the effects of epigenetic modifications on the spatial folding of chromosomes-and hence on the expression of the underlying genes-by mapping the problem to a class of models known as magnetic polymers. In this work we show that a first order phase transition underlies the simultaneous spreading of certain epigenetic marks and the conformational collapse of a chromosome. Further, we describe Brownian dynamics simulations of the model in which the topology of the polymer and thermal fluctuations are fully taken into account and that confirm our mean field predictions. Extending our models to allow for nonequilibrium terms yields new stable phases which qualitatively agrees with observations in vivo. Our results show that statistical mechanics techniques applied to models of magnetic polymers can be successfully exploited to rationalize the outcomes of experiments designed to probe the interplay between a dynamic epigenetic landscape and chromatin organization.
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Affiliation(s)
- Davide Colì
- Dipartimento di Fisica and Sezione INFN, Università degli Studi di Padova, I-35131 Padova, Italy
| | - Enzo Orlandini
- Dipartimento di Fisica and Sezione INFN, Università degli Studi di Padova, I-35131 Padova, Italy
| | - Davide Michieletto
- SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3FD, United Kingdom; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom; and Centre for Mathematical Biology, and Department of Mathematical Sciences, University of Bath, North Rd, Bath BA2 7AY, United Kingdom
| | - Davide Marenduzzo
- SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
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40
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Selective demethylation of two CpG sites causes postnatal activation of the Dao gene and consequent removal of D-serine within the mouse cerebellum. Clin Epigenetics 2019; 11:149. [PMID: 31661019 PMCID: PMC6819446 DOI: 10.1186/s13148-019-0732-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 08/29/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Programmed epigenetic modifications occurring at early postnatal brain developmental stages may have a long-lasting impact on brain function and complex behavior throughout life. Notably, it is now emerging that several genes that undergo perinatal changes in DNA methylation are associated with neuropsychiatric disorders. In this context, we envisaged that epigenetic modifications during the perinatal period may potentially drive essential changes in the genes regulating brain levels of critical neuromodulators such as D-serine and D-aspartate. Dysfunction of this fine regulation may contribute to the genesis of schizophrenia or other mental disorders, in which altered levels of D-amino acids are found. We recently demonstrated that Ddo, the D-aspartate degradation gene, is actively demethylated to ultimately reduce D-aspartate levels. However, the role of epigenetics as a mechanism driving the regulation of appropriate D-ser levels during brain development has been poorly investigated to date. METHODS We performed comprehensive ultradeep DNA methylation and hydroxymethylation profiling along with mRNA expression and HPLC-based D-amino acids level analyses of genes controlling the mammalian brain levels of D-serine and D-aspartate. DNA methylation changes occurring in specific cerebellar cell types were also investigated. We conducted high coverage targeted bisulfite sequencing by next-generation sequencing and single-molecule bioinformatic analysis. RESULTS We report consistent spatiotemporal modifications occurring at the Dao gene during neonatal development in a specific brain region (the cerebellum) and within specific cell types (astrocytes) for the first time. Dynamic demethylation at two specific CpG sites located just downstream of the transcription start site was sufficient to strongly activate the Dao gene, ultimately promoting the complete physiological degradation of cerebellar D-serine a few days after mouse birth. High amount of 5'-hydroxymethylcytosine, exclusively detected at relevant CpG sites, strongly evoked the occurrence of an active demethylation process. CONCLUSION The present investigation demonstrates that robust and selective demethylation of two CpG sites is associated with postnatal activation of the Dao gene and consequent removal of D-serine within the mouse cerebellum. A single-molecule methylation approach applied at the Dao locus promises to identify different cell-type compositions and functions in different brain areas and developmental stages.
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Ageing affects DNA methylation drift and transcriptional cell-to-cell variability in mouse muscle stem cells. Nat Commun 2019; 10:4361. [PMID: 31554804 PMCID: PMC6761124 DOI: 10.1038/s41467-019-12293-4] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 09/03/2019] [Indexed: 12/29/2022] Open
Abstract
Age-related tissue alterations have been associated with a decline in stem cell number and function. Although increased cell-to-cell variability in transcription or epigenetic marks has been proposed to be a major hallmark of ageing, little is known about the molecular diversity of stem cells during ageing. Here we present a single cell multi-omics study of mouse muscle stem cells, combining single-cell transcriptome and DNA methylome profiling. Aged cells show a global increase of uncoordinated transcriptional heterogeneity biased towards genes regulating cell-niche interactions. We find context-dependent alterations of DNA methylation in aged stem cells. Importantly, promoters with increased methylation heterogeneity are associated with increased transcriptional heterogeneity of the genes they drive. These results indicate that epigenetic drift, by accumulation of stochastic DNA methylation changes in promoters, is associated with the degradation of coherent transcriptional networks during stem cell ageing. Furthermore, our observations also shed light on the mechanisms underlying the DNA methylation clock. Age-related tissue alterations have been associated with a decline in stem cell number and function. Here the authors report a single cell multi-omics study of mouse muscle stem cells, combining single cell transcriptome and DNA methylome profiling and find that aged cells have a global increase of uncoordinated transcriptional heterogeneity biased towards genes regulating cell-niche interactions.
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42
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Hemberger M, Hanna CW, Dean W. Mechanisms of early placental development in mouse and humans. Nat Rev Genet 2019; 21:27-43. [PMID: 31534202 DOI: 10.1038/s41576-019-0169-4] [Citation(s) in RCA: 241] [Impact Index Per Article: 48.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2019] [Indexed: 02/08/2023]
Abstract
The importance of the placenta in supporting mammalian development has long been recognized, but our knowledge of the molecular, genetic and epigenetic requirements that underpin normal placentation has remained remarkably under-appreciated. Both the in vivo mouse model and in vitro-derived murine trophoblast stem cells have been invaluable research tools for gaining insights into these aspects of placental development and function, with recent studies starting to reshape our view of how a unique epigenetic environment contributes to trophoblast differentiation and placenta formation. These advances, together with recent successes in deriving human trophoblast stem cells, open up new and exciting prospects in basic and clinical settings that will help deepen our understanding of placental development and associated disorders of pregnancy.
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Affiliation(s)
- Myriam Hemberger
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada. .,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada. .,Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada. .,Epigenetics Programme, The Babraham Institute, Babraham Research Campus, Cambridge, UK. .,Centre for Trophoblast Research, University of Cambridge, Cambridge, UK.
| | - Courtney W Hanna
- Epigenetics Programme, The Babraham Institute, Babraham Research Campus, Cambridge, UK.,Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | - Wendy Dean
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada. .,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada. .,Epigenetics Programme, The Babraham Institute, Babraham Research Campus, Cambridge, UK. .,Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, Calgary, Canada.
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43
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Song Y, van den Berg PR, Markoulaki S, Soldner F, Dall'Agnese A, Henninger JE, Drotar J, Rosenau N, Cohen MA, Young RA, Semrau S, Stelzer Y, Jaenisch R. Dynamic Enhancer DNA Methylation as Basis for Transcriptional and Cellular Heterogeneity of ESCs. Mol Cell 2019; 75:905-920.e6. [PMID: 31422875 DOI: 10.1016/j.molcel.2019.06.045] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 05/06/2019] [Accepted: 06/26/2019] [Indexed: 12/18/2022]
Abstract
Variable levels of DNA methylation have been reported at tissue-specific differential methylation regions (DMRs) overlapping enhancers, including super-enhancers (SEs) associated with key cell identity genes, but the mechanisms responsible for this intriguing behavior are not well understood. We used allele-specific reporters at the endogenous Sox2 and Mir290 SEs in embryonic stem cells and found that the allelic DNA methylation state is dynamically switching, resulting in cell-to-cell heterogeneity. Dynamic DNA methylation is driven by the balance between DNA methyltransferases and transcription factor binding on one side and co-regulated with the Mediator complex recruitment and H3K27ac level changes at regulatory elements on the other side. DNA methylation at the Sox2 and the Mir290 SEs is independently regulated and has distinct consequences on the cellular differentiation state. Dynamic allele-specific DNA methylation at the two SEs was also seen at different stages in preimplantation embryos, revealing that methylation heterogeneity occurs in vivo.
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Affiliation(s)
- Yuelin Song
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Biology Department, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | | | | | - Frank Soldner
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | | | | | - Jesse Drotar
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Nicholas Rosenau
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Malkiel A Cohen
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Biology Department, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
| | - Stefan Semrau
- Leiden Institute of Physics, Leiden University, 2300 RA Leiden, the Netherlands.
| | - Yonatan Stelzer
- Department of Molecular Cell Biology, Weizmann Institute of Science, 76100 Rehovot, Israel.
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Biology Department, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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Bar S, Benvenisty N. Epigenetic aberrations in human pluripotent stem cells. EMBO J 2019; 38:embj.2018101033. [PMID: 31088843 DOI: 10.15252/embj.2018101033] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 03/13/2019] [Accepted: 03/15/2019] [Indexed: 12/14/2022] Open
Abstract
Human pluripotent stem cells (hPSCs) are being increasingly utilized worldwide in investigating human development, and modeling and discovering therapies for a wide range of diseases as well as a source for cellular therapy. Yet, since the first isolation of human embryonic stem cells (hESCs) 20 years ago, followed by the successful reprogramming of human-induced pluripotent stem cells (hiPSCs) 10 years later, various studies shed light on abnormalities that sometimes accumulate in these cells in vitro Whereas genetic aberrations are well documented, epigenetic alterations are not as thoroughly discussed. In this review, we highlight frequent epigenetic aberrations found in hPSCs, including alterations in DNA methylation patterns, parental imprinting, and X chromosome inactivation. We discuss the potential origins of these abnormalities in hESCs and hiPSCs, survey the different methods for detecting them, and elaborate on their potential consequences for the different utilities of hPSCs.
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Affiliation(s)
- Shiran Bar
- Department of Genetics, The Azrieli Center for Stem Cells and Genetic Research, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Nissim Benvenisty
- Department of Genetics, The Azrieli Center for Stem Cells and Genetic Research, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
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Abstract
Germ cells undergo epigenome reprogramming for proper development of the next generation. The achievement of in vitro germ cell derivation from human and mouse pluripotent stem cells and further differentiation in a plane culture and in aggregation with gonadal somatic cells offers unprecedented opportunities for investigation of the germ cell development. Moreover, advances in low-input/single-cell genomics have enabled detailed investigation of epigenome dynamics during germ cell development. These technologies have advanced our knowledge of epigenome reprogramming during the specification and development of primordial germ cells, their sex differentiation, and gametogenesis. Key findings include details of chromatin remodeling and transcriptional regulation, progressive and comprehensive DNA demethylation, and tight links between DNA demethylation and histone marks during the development of primordial germ cells, acquisition of unique totipotent epigenome during oogenesis (e.g., broad H3K4me3 domains and low-level three-dimensional genomic organization), and unexpected organization of the sperm genome. Moreover, these studies suggest the importance of epigenome analyses for in-depth evaluations of in vitro gametogenesis.
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Affiliation(s)
- Kazuki Kurimoto
- Department of Embryology, Nara Medical University, Nara, Japan.
| | - Mitinori Saitou
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan; Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan; Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
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Jouneau A. Heterogeneity in Epiblast Stem Cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1123:5-17. [PMID: 31016592 DOI: 10.1007/978-3-030-11096-3_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Epiblast stem cells (EpiSCs) are pluripotent cells that are derived from mouse embryos at gastrulation stages. They represent the primed state of pluripotency, in which cells are on the verge of differentiation and already express markers of the three primary lineages (mesoderm, endoderm, neurectoderm). EpiSCs display some heterogeneity intra- and inter-cell lines in the expression of some of these lineage markers. We relate this heterogeneity to signalling pathways that are active in EpiSCs, either due to addition of growth factors (FGF2 and activin) in the culture medium, or endogenously active (FGF, Nodal, and Wnt). By modulating Wnt or activin/nodal pathways, cell lines close to EpiSCs but with different properties can be obtained. These signalling pathways are all at work in vivo to pattern the pluripotent epiblast and specify cellular fates.
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Affiliation(s)
- Alice Jouneau
- UMR BDR, INRA, ENVA, Université Paris Saclay, Jouy en Josas, France.
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47
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DNA Methylation Clocks in Aging: Categories, Causes, and Consequences. Mol Cell 2019; 71:882-895. [PMID: 30241605 DOI: 10.1016/j.molcel.2018.08.008] [Citation(s) in RCA: 312] [Impact Index Per Article: 62.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/03/2018] [Accepted: 08/06/2018] [Indexed: 02/07/2023]
Abstract
Age-associated changes to the mammalian DNA methylome are well documented and thought to promote diseases of aging, such as cancer. Recent studies have identified collections of individual methylation sites whose aggregate methylation status measures chronological age, referred to as the DNA methylation clock. DNA methylation may also have value as a biomarker of healthy versus unhealthy aging and disease risk; in other words, a biological clock. Here we consider the relationship between the chronological and biological clocks, their underlying mechanisms, potential consequences, and their utility as biomarkers and as targets for intervention to promote healthy aging and longevity.
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48
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An S, Ma L, Wan L. TSEE: an elastic embedding method to visualize the dynamic gene expression patterns of time series single-cell RNA sequencing data. BMC Genomics 2019; 20:224. [PMID: 30967106 PMCID: PMC6456934 DOI: 10.1186/s12864-019-5477-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Time series single-cell RNA sequencing (scRNA-seq) data are emerging. However, the analysis of time series scRNA-seq data could be compromised by 1) distortion created by assorted sources of data collection and generation across time samples and 2) inheritance of cell-to-cell variations by stochastic dynamic patterns of gene expression. This calls for the development of an algorithm able to visualize time series scRNA-seq data in order to reveal latent structures and uncover dynamic transition processes. RESULTS In this study, we propose an algorithm, termed time series elastic embedding (TSEE), by incorporating experimental temporal information into the elastic embedding (EE) method, in order to visualize time series scRNA-seq data. TSEE extends the EE algorithm by penalizing the proximal placement of latent points that correspond to data points otherwise separated by experimental time intervals. TSEE is herein used to visualize time series scRNA-seq datasets of embryonic developmental processed in human and zebrafish. We demonstrate that TSEE outperforms existing methods (e.g. PCA, tSNE and EE) in preserving local and global structures as well as enhancing the temporal resolution of samples. Meanwhile, TSEE reveals the dynamic oscillation patterns of gene expression waves during zebrafish embryogenesis. CONCLUSIONS TSEE can efficiently visualize time series scRNA-seq data by diluting the distortions of assorted sources of data variation across time stages and achieve the temporal resolution enhancement by preserving temporal order and structure. TSEE uncovers the subtle dynamic structures of gene expression patterns, facilitating further downstream dynamic modeling and analysis of gene expression processes. The computational framework of TSEE is generalizable by allowing the incorporation of other sources of information.
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Affiliation(s)
- Shaokun An
- Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Liang Ma
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Lin Wan
- Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
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Schlesinger S, Meshorer E. Open Chromatin, Epigenetic Plasticity, and Nuclear Organization in Pluripotency. Dev Cell 2019; 48:135-150. [DOI: 10.1016/j.devcel.2019.01.003] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 10/30/2018] [Accepted: 12/31/2018] [Indexed: 12/27/2022]
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Abstract
The classical model of cytosine DNA methylation (the presence of 5-methylcytosine, 5mC) regulation depicts this covalent modification as a stable repressive regulator of promoter activity. However, whole-genome analysis of 5mC reveals widespread tissue- and cell type-specific patterns and pervasive dynamics during mammalian development. Here we review recent findings that delineate 5mC functions in developmental stages and diverse genomic compartments as well as discuss the molecular mechanisms that connect transcriptional regulation and 5mC. Beyond the newly appreciated dynamics, regulatory roles for 5mC have been suggested in new biological contexts, such as learning and memory or aging. The use of new single-cell measurement techniques and precise editing tools will enable functional analyses of 5mC in gene expression, clarifying its role in various biological processes.
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Affiliation(s)
- Chongyuan Luo
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Petra Hajkova
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, W12 0NN London, UK.
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, W12 0NN London, UK
| | - Joseph R Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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