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Zang X, Huang Q, Gan J, Jiang L, Meng F, Gu T, Cai G, Li Z, Wu Z, Hong L. Protein Dynamic Landscape of Pig Embryos during Peri-Implantation Development. J Proteome Res 2024; 23:775-785. [PMID: 38227546 DOI: 10.1021/acs.jproteome.3c00656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
Properly developed embryos are critical for successful embryo implantation. The dynamic landscape of proteins as executors of biological processes in pig peri-implantation embryos has not been reported so far. In this study, we collected pig embryos from days 9, 12, and 15 of pregnancy during the peri-implantation stage for a PASEF-based quantitative proteomic analysis. In total, approximately 8000 proteins were identified. These proteins were classified as stage-exclusive proteins and stage-specific proteins, respectively, based on their presence and dynamic abundance changes at each stage. Functional analysis showed that their roles are consistent with the physiological processes of corresponding stages, such as the biosynthesis of amino acids and peptides at P09, the regulation of actin cytoskeletal organization and complement activation at P12, and the vesicular transport at P15. Correlation analysis between mRNAs and proteins showed a general positive correlation between pig peri-implantation embryonic mRNAs and proteins. Cross-species comparisons with human early embryos identified some conserved proteins that may be important in regulating embryonic development, such as STAT3, AP2A1, and PFAS. Our study provides a comprehensive overview of the pig embryo proteome during implantation, fills gaps in relevant developmental studies, and identifies some important proteins that may serve as potential targets for future research.
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Affiliation(s)
- Xupeng Zang
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Qiuying Huang
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Jianyu Gan
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Lei Jiang
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Fanming Meng
- Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510642, China
| | - Ting Gu
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Yunfu Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu 527300, China
- Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China
| | - Gengyuan Cai
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Yunfu Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu 527300, China
- Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China
| | - Zicong Li
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Yunfu Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu 527300, China
- Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China
| | - Zhenfang Wu
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Yunfu Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu 527300, China
- Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China
| | - Linjun Hong
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Yunfu Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu 527300, China
- Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China
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Popova S, Charness ME, Burd L, Crawford A, Hoyme HE, Mukherjee RAS, Riley EP, Elliott EJ. Fetal alcohol spectrum disorders. Nat Rev Dis Primers 2023; 9:11. [PMID: 36823161 DOI: 10.1038/s41572-023-00420-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/16/2023] [Indexed: 02/25/2023]
Abstract
Alcohol readily crosses the placenta and may disrupt fetal development. Harm from prenatal alcohol exposure (PAE) is determined by the dose, pattern, timing and duration of exposure, fetal and maternal genetics, maternal nutrition, concurrent substance use, and epigenetic responses. A safe dose of alcohol use during pregnancy has not been established. PAE can cause fetal alcohol spectrum disorders (FASD), which are characterized by neurodevelopmental impairment with or without facial dysmorphology, congenital anomalies and poor growth. FASD are a leading preventable cause of birth defects and developmental disability. The prevalence of FASD in 76 countries is >1% and is high in individuals living in out-of-home care or engaged in justice and mental health systems. The social and economic effects of FASD are profound, but the diagnosis is often missed or delayed and receives little public recognition. Future research should be informed by people living with FASD and be guided by cultural context, seek consensus on diagnostic criteria and evidence-based treatments, and describe the pathophysiology and lifelong effects of FASD. Imperatives include reducing stigma, equitable access to services, improved quality of life for people with FASD and FASD prevention in future generations.
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Affiliation(s)
- Svetlana Popova
- Institute for Mental Health Policy Research, Centre for Addiction and Mental Health, University of Toronto, Toronto, Ontario, Canada.
| | - Michael E Charness
- VA Boston Healthcare System, West Roxbury, MA, USA.,Department of Neurology, Harvard Medical School, Boston, MA, USA.,Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA.,Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - Larry Burd
- North Dakota Fetal Alcohol Syndrome Center, Department of Pediatrics, University of North Dakota School of Medicine and Health Sciences, Pediatric Therapy Services, Altru Health System, Grand Forks, ND, USA
| | - Andi Crawford
- Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - H Eugene Hoyme
- Sanford Children's Genomic Medicine Consortium, Sanford Health, and University of South Dakota Sanford School of Medicine, Sioux Falls, SD, USA
| | - Raja A S Mukherjee
- National UK FASD Clinic, Surrey and Borders Partnership NHS Foundation Trust, Redhill, Surrey, UK
| | - Edward P Riley
- Center for Behavioral Teratology, San Diego State University, San Diego, CA, USA
| | - Elizabeth J Elliott
- Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia.,New South Wales FASD Assessment Service, CICADA Centre for Care and Intervention for Children and Adolescents affected by Drugs and Alcohol, Sydney Children's Hospitals Network, Westmead, Sydney, New South Wales, Australia
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Kim M, Delgado E, Ko S. DNA methylation in cell plasticity and malignant transformation in liver diseases. Pharmacol Ther 2023; 241:108334. [PMID: 36535346 PMCID: PMC9841769 DOI: 10.1016/j.pharmthera.2022.108334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/09/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
The liver possesses extraordinary regenerative capacity mainly attributable to the ability of hepatocytes (HCs) and biliary epithelial cells (BECs) to self-replicate. This ability is left over from their bipotent parent cell, the hepatoblast, during development. When this innate regeneration is compromised due to the absence of proliferative parenchymal cells, such as during cirrhosis, HCs and BEC can transdifferentiate; thus, adding another layer of complexity to the process of liver repair. In addition, dysregulated lineage maintenance in these two cell populations has been shown to promote malignant growth in experimental conditions. Here, malignant transformation, driven in part by insufficient maintenance of lineage reprogramming, contributes to end-stage liver disease. Epigenetic changes are key drivers for cell fate decisions as well as transformation by finetuning overall transcription and gene expression. In this review, we address how altered DNA methylation contributes to the initiation and progression of hepatic cell fate conversion and cancer formation. We also discussed the diagnostic and therapeutic potential of targeting DNA methylation in liver cancer, its current limitations, and what future research is necessary to facilitate its contribution to clinical translation.
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Affiliation(s)
- Minwook Kim
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
| | - Evan Delgado
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America; Pittsburgh Liver Research Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
| | - Sungjin Ko
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America; Pittsburgh Liver Research Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America.
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Saini A, Varshney A, Saini A, Mani I. Insight into epigenetics and human diseases. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 197:1-21. [PMID: 37019588 DOI: 10.1016/bs.pmbts.2023.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
The most eminent research of the 21st century whirls around the epigenetic and the variability of DNA sequences in humans. The reciprocity between the epigenetic changes and the exogenous factors drives an influence on the inheritance biology and gene expression both inter-generationally and trans-generationally. Chromatin level modifications like DNA methylation, histone modifications or changes in transcripts functions either at transcription level or translational level pave the way for certain diseases or cancer in humans. The ability of epigenetics to explain the processes of various diseases has been demonstrated by recent epigenetic studies. Multidisciplinary therapeutic strategies were developed in order to analyse how epigenetic elements interact with different disease pathways. In this chapter we summarize how an organism may be predisposed to certain diseases by exposure to environmental variables such as chemicals, medications, stress, or infections during particular, vulnerable phases of life, and the epigenetic component may influence some of the diseases in humans.
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Tachibana K, Kawazoe S, Onoda A, Umezawa M, Takeda K. Effects of Prenatal Exposure to Titanium Dioxide Nanoparticles on DNA Methylation and Gene Expression Profile in the Mouse Brain. FRONTIERS IN TOXICOLOGY 2022; 3:705910. [PMID: 35295148 PMCID: PMC8915839 DOI: 10.3389/ftox.2021.705910] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 09/13/2021] [Indexed: 12/12/2022] Open
Abstract
Background and Objectives: Titanium dioxide nanoparticles (TiO2-NP) are important materials used in commercial practice. Reportedly, TiO2-NP exposure during pregnancy can affect the development of the central nervous system in mouse offspring; however, the underlying mechanism remains unknown. In the present study, we investigated the impact of prenatal TiO2-NP exposure on global DNA methylation and mRNA expression patterns in the brains of neonatal mice. Materials and Methods: Pregnant C57BL/6J mice were intratracheally administered a TiO2-NP suspension (100 μg/mouse) on gestational day 10.5, and brains were collected from male and female offspring at day 1 postpartum. After extraction of methylated DNA by immunoprecipitation, the DNA methylation profile was analyzed using a mouse CpG island microarray. Total RNA was obtained, and mRNA expression profiles were comprehensively assessed using microarray analysis. Results: Among genes in the CpG island microarray, DNA methylation was increased in 614 and 2,924 genes and decreased in 6,220 and 6,477 genes in male and female offspring, respectively. Combined with mRNA microarray analysis, 88 and 89 genes were upregulated (≥1.5-fold) accompanied by demethylation of CpG islands, whereas 13 and 33 genes were downregulated (≤0.67-fold) accompanied by methylation of CpG islands in male and female offspring mice, respectively. Gene Set Enrichment Analysis (GSEA) revealed that these genes were enriched in gene ontology terms related to the regulation of transcription factors, cell proliferation, and organism development. Additionally, MeSH terms related to stem cells and morphogenesis were enriched. Conclusion: Prenatal TiO2-NP exposure induced genome-wide alterations in DNA methylation and mRNA expression in the brains of male and female offspring. Based on GSEA findings, it can be speculated that prenatal TiO2-NP exposure causes adverse effects on brain functions by altering the DNA methylation state of the fetal brain, especially neural stem cells, resulting in the subsequent abnormal regulation of transcription factors that modulate development and differentiation.
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Affiliation(s)
- Ken Tachibana
- Division of Toxicology and Health Science, Faculty of Pharmaceutical Sciences, Sanyo-onoda City University, Sanyo-onoda, Japan.,The Center for Environmental Health Science for the Next Generation, Research Institute for Science and Technology, Organization for Research Advancement, Tokyo University of Science, Noda, Japan.,Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Japan
| | - Shotaro Kawazoe
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Japan
| | - Atsuto Onoda
- Division of Toxicology and Health Science, Faculty of Pharmaceutical Sciences, Sanyo-onoda City University, Sanyo-onoda, Japan.,The Center for Environmental Health Science for the Next Generation, Research Institute for Science and Technology, Organization for Research Advancement, Tokyo University of Science, Noda, Japan.,Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Japan
| | - Masakazu Umezawa
- The Center for Environmental Health Science for the Next Generation, Research Institute for Science and Technology, Organization for Research Advancement, Tokyo University of Science, Noda, Japan.,Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Japan.,Department of Materials Science and Technology, Faculty of Advanced Engineering, Tokyo University of Science, Katsushika, Japan
| | - Ken Takeda
- Division of Toxicology and Health Science, Faculty of Pharmaceutical Sciences, Sanyo-onoda City University, Sanyo-onoda, Japan.,The Center for Environmental Health Science for the Next Generation, Research Institute for Science and Technology, Organization for Research Advancement, Tokyo University of Science, Noda, Japan.,Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Japan
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6
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Li C, Cao M, Zhou X. Role of epigenetics in parturition and preterm birth. Biol Rev Camb Philos Soc 2021; 97:851-873. [PMID: 34939297 DOI: 10.1111/brv.12825] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 11/29/2021] [Accepted: 12/02/2021] [Indexed: 12/19/2022]
Abstract
Preterm birth occurs worldwide and is associated with high morbidity, mortality, and economic cost. Although several risk factors associated with parturition and preterm birth have been identified, mechanisms underlying this syndrome remain unclear, thereby limiting the implementation of interventions for prevention and management. Known triggers of preterm birth include conditions related to inflammatory and immunological pathways, as well as genetics and maternal history. Importantly, epigenetics, which is the study of heritable phenotypic changes that occur without alterations in the DNA sequence, may play a role in linking social and environmental risk factors for preterm birth. Epigenetic approaches to the study of preterm birth, including analyses of the effects of microRNAs, long non-coding RNAs, DNA methylation, and histone modification, have contributed to an improved understanding of the molecular bases of both term and preterm birth. Additionally, epigenetic modifications have been linked to factors already associated with preterm birth, including obesity and smoking. The prevention and management of preterm birth remains a challenge worldwide. Although epigenetic analysis provides valuable insights into the causes and risk factors associated with this syndrome, further studies are necessary to determine whether epigenetic approaches can be used routinely for the diagnosis, prevention, and management of preterm birth.
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Affiliation(s)
- Chunjin Li
- College of Animal Sciences, Jilin University, Changchun, Jilin, 130062, China
| | - Maosheng Cao
- College of Animal Sciences, Jilin University, Changchun, Jilin, 130062, China
| | - Xu Zhou
- College of Animal Sciences, Jilin University, Changchun, Jilin, 130062, China
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7
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Fatima N, Baqri SSR, Bhattacharya A, Koney NKK, Husain K, Abbas A, Ansari RA. Role of Flavonoids as Epigenetic Modulators in Cancer Prevention and Therapy. Front Genet 2021; 12:758733. [PMID: 34858475 PMCID: PMC8630677 DOI: 10.3389/fgene.2021.758733] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 10/26/2021] [Indexed: 12/16/2022] Open
Abstract
Epigenetic regulation involves reversible changes in histones and DNA modifications that can be inherited without any changes in the DNA sequence. Dysregulation of normal epigenetic processes can lead to aberrant gene expression as observed in many diseases, notably cancer. Recent insights into the mechanisms of DNA methylation, histone modifications, and non-coding RNAs involved in altered gene expression profiles of tumor cells have caused a paradigm shift in the diagnostic and therapeutic approaches towards cancer. There has been a surge in search for compounds that could modulate the altered epigenetic landscape of tumor cells, and to exploit their therapeutic potential against cancers. Flavonoids are naturally occurring phenol compounds which are abundantly found among phytochemicals and have potentials to modulate epigenetic processes. Knowledge of the precise flavonoid-mediated epigenetic alterations is needed for the development of epigenetics drugs and combinatorial therapeutic approaches against cancers. This review is aimed to comprehensively explore the epigenetic modulations of flavonoids and their anti-tumor activities.
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Affiliation(s)
- Nishat Fatima
- Department of Chemistry, Shia Postgraduate College, Lucknow, India
| | | | - Atrayee Bhattacharya
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, United States
| | - Nii Koney-Kwaku Koney
- Department of Anatomy, University of Ghana Medical School, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Kazim Husain
- Department of Molecular Medicine, University of South Florida, Tampa, FL, United States
| | - Ata Abbas
- Division of Hematology and Oncology, Department of Medicine, Case Western Reserve University, Cleveland, OH, United States.,Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States
| | - Rais A Ansari
- Department of Pharmaceutical Sciences, Nova Southeastern University, Fort Lauderdale, FL, United States
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H3K4 di-methylation governs smooth muscle lineage identity and promotes vascular homeostasis by restraining plasticity. Dev Cell 2021; 56:2765-2782.e10. [PMID: 34582749 PMCID: PMC8567421 DOI: 10.1016/j.devcel.2021.09.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 07/09/2021] [Accepted: 08/30/2021] [Indexed: 12/15/2022]
Abstract
Epigenetic mechanisms contribute to the regulation of cell differentiation and function. Vascular smooth muscle cells (SMCs) are specialized contractile cells that retain phenotypic plasticity even after differentiation. Here, by performing selective demethylation of histone H3 lysine 4 di-methylation (H3K4me2) at SMC-specific genes, we uncovered that H3K4me2 governs SMC lineage identity. Removal of H3K4me2 via selective editing in cultured vascular SMCs and in murine arterial vasculature led to loss of differentiation and reduced contractility due to impaired recruitment of the DNA methylcytosine dioxygenase TET2. H3K4me2 editing altered SMC adaptative capacities during vascular remodeling due to loss of miR-145 expression. Finally, H3K4me2 editing induced a profound alteration of SMC lineage identity by redistributing H3K4me2 toward genes associated with stemness and developmental programs, thus exacerbating plasticity. Our studies identify the H3K4me2-TET2-miR145 axis as a central epigenetic memory mechanism controlling cell identity and function, whose alteration could contribute to various pathophysiological processes.
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Shakiba N, Jones RD, Weiss R, Del Vecchio D. Context-aware synthetic biology by controller design: Engineering the mammalian cell. Cell Syst 2021; 12:561-592. [PMID: 34139166 PMCID: PMC8261833 DOI: 10.1016/j.cels.2021.05.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 04/19/2021] [Accepted: 05/14/2021] [Indexed: 12/25/2022]
Abstract
The rise of systems biology has ushered a new paradigm: the view of the cell as a system that processes environmental inputs to drive phenotypic outputs. Synthetic biology provides a complementary approach, allowing us to program cell behavior through the addition of synthetic genetic devices into the cellular processor. These devices, and the complex genetic circuits they compose, are engineered using a design-prototype-test cycle, allowing for predictable device performance to be achieved in a context-dependent manner. Within mammalian cells, context effects impact device performance at multiple scales, including the genetic, cellular, and extracellular levels. In order for synthetic genetic devices to achieve predictable behaviors, approaches to overcome context dependence are necessary. Here, we describe control systems approaches for achieving context-aware devices that are robust to context effects. We then consider cell fate programing as a case study to explore the potential impact of context-aware devices for regenerative medicine applications.
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Affiliation(s)
- Nika Shakiba
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Ross D Jones
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Ron Weiss
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Domitilla Del Vecchio
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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10
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Elsherbiny A, Dobreva G. Epigenetic memory of cell fate commitment. Curr Opin Cell Biol 2021; 69:80-87. [PMID: 33535129 DOI: 10.1016/j.ceb.2020.12.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/15/2020] [Accepted: 12/22/2020] [Indexed: 12/23/2022]
Abstract
During development, discrete cell fates are established in precise spatiotemporal order guided by morphogen signals. These signals converge in the nucleus to induce transcriptional and epigenetic programming that determines cell fate. Once cell identity is established, cell programs have to be accurately sustained through multiple rounds of cell division, during which DNA replication serves as a window of opportunity for altering cell fate. In this review, we summarize recent advances in understanding the molecular players that underlie epigenetic memory of cell fate decisions, with a particular focus on histone modifications and mitotic bookmarking factors. We also discuss the different mechanisms of inheritance of repressed and active chromatin states.
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Affiliation(s)
- Adel Elsherbiny
- Department of Anatomy and Developmental Biology, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; German Centre for Cardiovascular Research (DZHK), Germany
| | - Gergana Dobreva
- Department of Anatomy and Developmental Biology, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; German Centre for Cardiovascular Research (DZHK), Germany.
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11
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Radiation-induced H3K9 methylation on E-cadherin promoter mediated by ROS/Snail axis : Role of G9a signaling during lung epithelial-mesenchymal transition. Toxicol In Vitro 2020; 70:105037. [PMID: 33148527 DOI: 10.1016/j.tiv.2020.105037] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 10/05/2020] [Accepted: 10/20/2020] [Indexed: 12/14/2022]
Abstract
Lung cancer patients who have undergone radiotherapy developed severe complications such as pneumonitis and fibrosis. Upon irradiation, epithelial cells acquire mesenchymal phenotype via a process called epithelial to mesenchymal transition (EMT), which plays a vital role in organ fibrosis. Several mechanisms have been studied on EMT, however, the correlation between radiation-induced EMT and epigenetic changes are not well known. In the present study, we investigated the role of histone methyltransferase G9a on radiation-induced EMT signaling. There was an increase in total global histone methylation level in irradiated epithelial cells. Western blot analysis on irradiated cells showed an increased expression of H3K9me2/3. The pre-treatment of G9a inhibitor enhanced E-cadherin expression and decreased the mesenchymal markers like N-cadherin, vimentin in the radiated group. Surprisingly, radiation-induced ROS generation and pERK1/2 levels were also inhibited by G9a inhibitor BIX01294, which is showing its antioxidant potential. The ChIP-qPCR analysis on the E-cadherin promoter suggested that G9a and Snail might have formed complex to enrich suppressive marker H3K9me2/3. On the whole, our present study suggested that 1] ROS could modify H3K9 methylation via G9a and promote radiation-induced lung EMT in Beas2B and A549 cells 2] E-cadherin promoter enrichment with heterochromatin mark H3K9me2 expression upon irradiation could be modified by regulating G9a methyltransferase.
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12
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Zhang L, Shi X, Gu C, Chen B, Wang M, Yu Y, Sun K, Zhang R. Identification of cell-to-cell interactions by ligand-receptor pairs in human fetal heart. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165917. [PMID: 32800943 DOI: 10.1016/j.bbadis.2020.165917] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/24/2020] [Accepted: 08/08/2020] [Indexed: 12/14/2022]
Abstract
The heart is the first organ to form during embryogenesis and its development is a complex process. In this study, we identified 120 ligand-receptor pairs including 65 ligands and 58 receptors specifically expressed in one of the nine cell types. The correlation analysis of the cell proportions revealed that the cell-to-cell contact exhibited spatial patterns in human fetal heart. Specifically, the cardiomyocytes (CMs) proportion might have negative correlation with proportion of endothelial cell in left atrium and ventricle during the heart development. In contrast, fibroblast-like cells and macrophages were jointly increased with the gestation. Furthermore, the ligand in CM, NPPA (Natriuretic Peptide A), and receptor in endothelial cell (EC), NPR3 (Natriuretic Peptide Receptor 3), were specifically expressed in atrial CM and endocardial cells, respectively, indicating that the atrial CM might communicate with endocardial cells via NPPA-NRP3 interaction. Moreover, the interplay between fibroblast-like cell and macrophage was observed in both left and right atriums via the ligand-receptor interactions of COL1A1/COL1A2 (Collagen Type I Alpha 1/2 Chain)-CD36 and CTGF (connective tissue growth factor)-ITGB2 (Integrin Subunit Beta 2). Functional enrichment analysis revealed that the ligand-receptor interactions might be associated with the intracellular activation of cGMP-PKG signaling pathway in ECs, PDGF-beta signaling pathway in fibroblast-like cell, and Toll-like receptor signaling in macrophage, respectively. Collectively, the present study unveiled the potential cell-cell communication and underlying mechanism involved in cardiac development, which broadened our insights into developmental biology of heart.
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Affiliation(s)
- Li Zhang
- Key Laboratory of Advanced Theory and Application in Statistics and Data Science - MOE, School of Statistics, East China Normal University, Shanghai, China
| | - Xin Shi
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, China; Department of Pediatric Cardiology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Chang Gu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Bo Chen
- Department of Pediatric Cardiology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ming Wang
- Department of Cardiology, Huadong Hospital, Fudan University, Shanghai, China
| | - Yu Yu
- Department of Pediatric Cardiology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Institute for Development and Regenerative Cardiovascular Medicine, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Kun Sun
- Department of Pediatric Cardiology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Riquan Zhang
- Key Laboratory of Advanced Theory and Application in Statistics and Data Science - MOE, School of Statistics, East China Normal University, Shanghai, China.
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Abstract
Antiviral drugs have traditionally been developed by directly targeting essential viral components. However, this strategy often fails due to the rapid generation of drug-resistant viruses. Recent genome-wide approaches, such as those employing small interfering RNA (siRNA) or clustered regularly interspaced short palindromic repeats (CRISPR) or those using small molecule chemical inhibitors targeting the cellular "kinome," have been used successfully to identify cellular factors that can support virus replication. Since some of these cellular factors are critical for virus replication, but are dispensable for the host, they can serve as novel targets for antiviral drug development. In addition, potentiation of immune responses, regulation of cytokine storms, and modulation of epigenetic changes upon virus infections are also feasible approaches to control infections. Because it is less likely that viruses will mutate to replace missing cellular functions, the chance of generating drug-resistant mutants with host-targeted inhibitor approaches is minimized. However, drug resistance against some host-directed agents can, in fact, occur under certain circumstances, such as long-term selection pressure of a host-directed antiviral agent that can allow the virus the opportunity to adapt to use an alternate host factor or to alter its affinity toward the target that confers resistance. This review describes novel approaches for antiviral drug development with a focus on host-directed therapies and the potential mechanisms that may account for the acquisition of antiviral drug resistance against host-directed agents.
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14
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Baumbach JL, Zovkic IB. Hormone-epigenome interactions in behavioural regulation. Horm Behav 2020; 118:104680. [PMID: 31927018 DOI: 10.1016/j.yhbeh.2020.104680] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/03/2020] [Accepted: 01/05/2020] [Indexed: 02/06/2023]
Abstract
Interactions between hormones and epigenetic factors are key regulators of behaviour, but the mechanisms that underlie their effects are complex. Epigenetic factors can modify sensitivity to hormones by altering hormone receptor expression, and hormones can regulate epigenetic factors by recruiting epigenetic regulators to DNA. The bidirectional nature of this relationship is becoming increasingly evident and suggests that the ability of hormones to regulate certain forms of behaviour may depend on their ability to induce changes in the epigenome. Moreover, sex differences have been reported for several epigenetic modifications, and epigenetic factors are thought to regulate sexual differentiation of behaviour, although specific mechanisms remain to be understood. Indeed, hormone-epigenome interactions are highly complex and involve both canonical and non-canonical regulatory pathways that may permit for highly specific gene regulation to promote variable forms of behavioural adaptation.
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Affiliation(s)
- Jennet L Baumbach
- Department of Psychology, University of Toronto Mississauga, Mississauga, Canada
| | - Iva B Zovkic
- Department of Psychology, University of Toronto Mississauga, Mississauga, Canada.
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15
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Zhu Z, Cao F, Li X. Epigenetic Programming and Fetal Metabolic Programming. Front Endocrinol (Lausanne) 2019; 10:764. [PMID: 31849831 PMCID: PMC6901800 DOI: 10.3389/fendo.2019.00764] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 10/21/2019] [Indexed: 12/30/2022] Open
Abstract
Fetal metabolic programming caused by the adverse intrauterine environment can induce metabolic syndrome in adult offspring. Adverse intrauterine environment introduces fetal long-term relatively irreversible changes in organs and metabolism, and thus causes fetal metabolic programming leading metabolic syndrome in adult offspring. Fetal metabolic programming of obesity and insulin resistance plays a key role in this process. The mechanism of fetal metabolic programming is still not very clear. It is suggested that epigenetic programming, also induced by the adverse intrauterine environment, is a critical underlying mechanism of fetal metabolic programming. Fetal epigenetic programming affects gene expression changes and cellular function through epigenetic modifications without DNA nucleotide sequence changes. Epigenetic modifications can be relatively stably retained and transmitted through mitosis and generations, and thereby induce the development of metabolic syndrome in adult offspring. This manuscript provides an overview of the critical role of epigenetic programming in fetal metabolic programming.
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Affiliation(s)
- Ziqiang Zhu
- Children's Hospital of Soochow University, Suzhou, China
- Changzhou Maternity and Child Health Care Hospital affiliated to Nanjing Medical University, Changzhou, China
| | - Fang Cao
- Changzhou Maternity and Child Health Care Hospital affiliated to Nanjing Medical University, Changzhou, China
| | - Xiaozhong Li
- Children's Hospital of Soochow University, Suzhou, China
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16
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Saeed WH, Eissa AA, Al-Doski AA. Impact Of TP53 Gene Promoter Methylation On Chronic Lymphocytic Leukemia Pathogenesis And Progression. J Blood Med 2019; 10:399-404. [PMID: 31819692 PMCID: PMC6883927 DOI: 10.2147/jbm.s221707] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 11/05/2019] [Indexed: 01/10/2023] Open
Abstract
Background Chronic lymphocytic leukemia (CLL) is a malignant lymphoid disorder that results from the overgrowth of mature-looking lymphoid cells in the blood and lymphatic tissue. Various clinical presentations have been attributed to the disease as a result of the different underlying genetic and epigenetic alterations. The current study has been initiated to study the role of an epigenetic alteration affecting the promoter of the TP53gene on CLL pathogenesis and progression. Methods The current study involved 54 newly diagnosed patients presenting with CLL as well as 30 normal individuals as controls. After obtaining verbal consent, data collection was done and the blood collected from all enrolled individuals for hematological investigations as well as for molecular categorization of TP53 methylation status. Methylation-specific polymerase chain reaction (MS-PCR) technique was used to define the methylation status of the TP53 gene promoter that encompasses DNA extraction, bisulfite conversion, conventional PCR amplification, running on agarose gel and documentation. Finally, statistical analysis was done to assess any correlation of the TP53 epigenetic alteration to the disease etiology and the progression. Results In the current study, all controls and 42 of 54 patients show unmethylated TP53 gene promoter; on the other hand, the methylated promoter was detected among 12 patients with a p-value of 0.001. TP53 gene promoter methylation significantly linked to reduced platelet count (p-value of 0.047) and advanced stage at presentation (p-value of 0.076). No significant differences were seen among both methylated and unmethylated TP53 promoters in relation to the age of the affected individuals, total white blood cell counts and hemoglobin level of the affected individuals. Conclusion The current study revealed a significant correlation of TP53 gene promoter methylation to chronic lymphocytic leukemia pathogenesis and lower platelet counts.
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Affiliation(s)
- Waleed Haji Saeed
- Department of Nursing, Akre Technical Institute, Duhok Polytechnic University, Duhok, Iraq
| | - Adil Abozaid Eissa
- Department of Pathology, College of Medicine, University of Duhok, Duhok, Iraq
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17
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Petri T, Dankert D, Demond H, Wennemuth G, Horsthemke B, Grümmer R. In vitro postovulatory oocyte aging affects H3K9 trimethylation in two-cell embryos after IVF. Ann Anat 2019; 227:151424. [PMID: 31610252 DOI: 10.1016/j.aanat.2019.151424] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/19/2019] [Accepted: 09/24/2019] [Indexed: 12/15/2022]
Abstract
BACKGROUND The physiological time axis of oocyte maturation comprises highly sensitive processes. A prolonged time span between ovulation and fertilization may impair oocyte developmental competence and subsequent embryo development, possibly due to epigenetic modifications. Since post-translational histone modifications can modify chromatin activity, and trimethylation of H3K9 (H3K9me3) has been shown to increase in the murine oocyte during maturation, here the effect of postovulatory oocyte aging on H3K9me3 was analyzed. METHODS The competence of murine oocytes which were aged for 2, 4, 6 and 8 h in vitro after oocyte retrieval to develop to the two-cell and blastocyst stage was determined. Degree of H3K9me3 was analyzed in the postovulatory aged oocytes as well as in the resulting two-cell embryos after IVF. RESULTS The current study shows that postovulatory aging of oocytes for up to eight hours after oocyte retrieval exhibited no effect on two-cell embryo and blastocyst rate; however, changes in H3K9me3 in the resulting two-cell embryos were observed. CONCLUSION Prolonged postovulatory oocyte aging leads to epigenetic modifications of H3K9. Such modifications may affect the developmental capacity of embryos at post-implantation developmental stages.
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Affiliation(s)
- Theresa Petri
- Institute of Anatomy, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Debora Dankert
- Institute of Anatomy, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Hannah Demond
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Gunther Wennemuth
- Institute of Anatomy, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Bernhard Horsthemke
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Ruth Grümmer
- Institute of Anatomy, University Hospital Essen, University Duisburg-Essen, Essen, Germany.
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18
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Blanc M, Rüegg J, Scherbak N, Keiter SH. Environmental chemicals differentially affect epigenetic-related mechanisms in the zebrafish liver (ZF-L) cell line and in zebrafish embryos. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2019; 215:105272. [PMID: 31442592 DOI: 10.1016/j.aquatox.2019.105272] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 08/07/2019] [Accepted: 08/13/2019] [Indexed: 06/10/2023]
Abstract
A number of chemicals have been shown to affect epigenetic patterning and functions. Since epigenetic mechanisms regulate transcriptional networks, epigenetic changes induced by chemical exposure can represent early molecular events for long-term adverse physiological effects. Epigenetics has thus appeared as a research field of major interest within (eco)toxicological sciences. The present study aimed at measuring effects on epigenetic-related mechanisms of selected environmental chemicals (bisphenols, perfluorinated chemicals, methoxychlor, permethrin, vinclozolin and coumarin 47) in zebrafish embryos and liver cells (ZFL). Transcription of genes related to DNA methylation and histone modifications was measured and global DNA methylation was assessed in ZFL cells using the LUMA assay. The differences in results gathered from both models suggest that chemicals affect different mechanisms related to epigenetics in embryos and cells. In zebrafish embryos, exposure to bisphenol A, coumarin 47, methoxychlor and permethrin lead to significant transcriptional changes in epigenetic factors suggesting that they can impact early epigenome reprogramming related to embryonic development. In ZFL cells, significant transcriptional changes were observed upon exposure to all chemicals but coumarin 47; however, only perfluorooctane sulfonate induced significant effects on global DNA methylation. Notably, in contrast to the other tested chemicals, perfluorooctane sulfonate affected only the expression of the histone demethylase kdm5ba. In addition, kdm5ba appeared as a sensitive gene in zebrafish embryos as well. Taken together, the present results suggest a role for kdm5ba in regulating epigenetic patterns in response to chemical exposure, even though mechanisms remain unclear. To confirm these findings, further evidence is required regarding changes in site-specific histone marks and DNA methylation together with their long-term effects on physiological outcomes.
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Affiliation(s)
- Mélanie Blanc
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Fakultetsgatan 1, S-701 82, Örebro, Sweden.
| | - Joëlle Rüegg
- Institute for Environmental Medicine, Karolinska Institutet, Nobels väg 13, 171 65, Solna, Sweden
| | - Nikolai Scherbak
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Fakultetsgatan 1, S-701 82, Örebro, Sweden; Örebro Life Science Centre, School of Science and Technology, Örebro University, Fakultetsgatan 1, S-701 82, Örebro, Sweden
| | - Steffen H Keiter
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Fakultetsgatan 1, S-701 82, Örebro, Sweden
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19
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Gao R, Liang X, Cheedipudi S, Cordero J, Jiang X, Zhang Q, Caputo L, Günther S, Kuenne C, Ren Y, Bhattacharya S, Yuan X, Barreto G, Chen Y, Braun T, Evans SM, Sun Y, Dobreva G. Pioneering function of Isl1 in the epigenetic control of cardiomyocyte cell fate. Cell Res 2019; 29:486-501. [PMID: 31024170 PMCID: PMC6796926 DOI: 10.1038/s41422-019-0168-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 04/01/2019] [Indexed: 01/25/2023] Open
Abstract
Generation of widely differing and specialized cell types from a single totipotent zygote involves large-scale transcriptional changes and chromatin reorganization. Pioneer transcription factors play key roles in programming the epigenome and facilitating recruitment of additional regulatory factors during successive cell lineage specification and differentiation steps. Here we show that Isl1 acts as a pioneer factor driving cardiomyocyte lineage commitment by shaping the chromatin landscape of cardiac progenitor cells. Using an Isl1 hypomorphic mouse line which shows congenital heart defects, genome-wide profiling of Isl1 binding together with RNA- and ATAC-sequencing of cardiac progenitor cells and their derivatives, we uncover a regulatory network downstream of Isl1 that orchestrates cardiogenesis. Mechanistically, we show that Isl1 binds to compacted chromatin and works in concert with the Brg1-Baf60c-based SWI/SNF complex to promote permissive cardiac lineage-specific alterations in the chromatin landscape not only of genes with critical functions in cardiac progenitor cells, but also of cardiomyocyte structural genes that are highly expressed when Isl1 itself is no longer present. Thus, the Isl1/Brg1-Baf60c complex plays a crucial role in orchestrating proper cardiogenesis and in establishing epigenetic memory of cardiomyocyte fate commitment.
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Affiliation(s)
- Rui Gao
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
- Department of Anatomy and Developmental Biology, CBTM, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Xingqun Liang
- Key Laboratory of Arrhythmia, Ministry of Education, East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | | | - Julio Cordero
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
- Department of Anatomy and Developmental Biology, CBTM, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Xue Jiang
- Key Laboratory of Arrhythmia, Ministry of Education, East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Qingquan Zhang
- Key Laboratory of Arrhythmia, Ministry of Education, East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Luca Caputo
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Stefan Günther
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Carsten Kuenne
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Yonggang Ren
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
- Department of Anatomy and Developmental Biology, CBTM, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | | | - Xuejun Yuan
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Guillermo Barreto
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Yihan Chen
- Key Laboratory of Arrhythmia, Ministry of Education, East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Thomas Braun
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Sylvia M Evans
- Department of Medicine, Skaggs School of Pharmacy, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Yunfu Sun
- Key Laboratory of Arrhythmia, Ministry of Education, East Hospital, Tongji University School of Medicine, Shanghai, 200120, China.
| | - Gergana Dobreva
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany.
- Department of Anatomy and Developmental Biology, CBTM, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
- European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
- Medical Faculty, University of Frankfurt, 60590, Frankfurt am Main, Germany.
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20
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Ebrahimi A, Keske E, Mehdipour A, Ebrahimi-Kalan A, Ghorbani M. Somatic cell reprogramming as a tool for neurodegenerative diseases. Biomed Pharmacother 2019; 112:108663. [DOI: 10.1016/j.biopha.2019.108663] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/23/2019] [Accepted: 02/02/2019] [Indexed: 12/21/2022] Open
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21
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Torday JS. The Singularity of nature. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 142:23-31. [DOI: 10.1016/j.pbiomolbio.2018.07.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 07/18/2018] [Accepted: 07/19/2018] [Indexed: 12/21/2022]
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22
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Tikhodeyev ON. The mechanisms of epigenetic inheritance: how diverse are they? Biol Rev Camb Philos Soc 2018; 93:1987-2005. [PMID: 29790249 DOI: 10.1111/brv.12429] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 04/22/2018] [Accepted: 04/27/2018] [Indexed: 12/18/2022]
Abstract
Although epigenetic inheritance (EI) is a rapidly growing field of modern biology, it still has no clear place in fundamental genetic concepts which are traditionally based on the hereditary role of DNA. Moreover, not all mechanisms of EI attract the same attention, with most studies focused on DNA methylation, histone modification, RNA interference and amyloid prionization, but relatively few considering other mechanisms such as stable inhibition of plastid translation. Herein, we discuss all known and some hypothetical mechanisms that can underlie the stable inheritance of phenotypically distinct hereditary factors that lack differences in DNA sequence. These mechanisms include (i) regulation of transcription by DNA methylation, histone modifications, and transcription factors, (ii) RNA splicing, (iii) RNA-mediated post-transcriptional silencing, (iv) organellar translation, (v) protein processing by truncation, (vi) post-translational chemical modifications, (vii) protein folding, and (viii) homologous and non-homologous protein interactions. The breadth of this list suggests that any or almost any regulatory mechanism that participates in gene expression or gene-product functioning, under certain circumstances, may produce EI. Although the modes of EI are highly variable, in many epigenetic systems, stable allelic variants can be distinguished. Irrespective of their nature, all such alleles have an underlying similarity: each is a bimodular hereditary unit, whose features depend on (i) a certain epigenetic mark (epigenetic determinant) in the DNA sequence or its product, and (ii) the DNA sequence itself (DNA determinant; if this is absent, the epigenetic allele fails to perpetuate). Thus, stable allelic epigenetic inheritance (SAEI) does not contradict the hereditary role of DNA, but involves additional molecular mechanisms with no or almost no limitations to their variety.
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Affiliation(s)
- Oleg N Tikhodeyev
- Department of Genetics & Biotechnology, Saint-Petersburg State University, Saint-Petersburg 199034, Russia
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23
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Identification and functional analysis of long non-coding RNAs in human and mouse early embryos based on single-cell transcriptome data. Oncotarget 2018; 7:61215-61228. [PMID: 27542205 PMCID: PMC5308646 DOI: 10.18632/oncotarget.11304] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 08/08/2016] [Indexed: 11/25/2022] Open
Abstract
Epigenetics regulations have an important role in fertilization and proper embryonic development, and several human diseases are associated with epigenetic modification disorders, such as Rett syndrome, Beckwith-Wiedemann syndrome and Angelman syndrome. However, the dynamics and functions of long non-coding RNAs (lncRNAs), one type of epigenetic regulators, in human pre-implantation development have not yet been demonstrated. In this study, a comprehensive analysis of human and mouse early-stage embryonic lncRNAs was performed based on public single-cell RNA sequencing data. Expression profile analysis revealed that lncRNAs are expressed in a developmental stage-specific manner during human early-stage embryonic development, whereas a more temporal-specific expression pattern was identified in mouse embryos. Weighted gene co-expression network analysis suggested that lncRNAs involved in human early-stage embryonic development are associated with several important functions and processes, such as oocyte maturation, zygotic genome activation and mitochondrial functions. We also found that the network of lncRNAs involved in zygotic genome activation was highly preservative between human and mouse embryos, whereas in other stages no strong correlation between human and mouse embryo was observed. This study provides insight into the molecular mechanism underlying lncRNA involvement in human pre-implantation embryonic development.
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24
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Nishikawa K, Kinjo AR. Mechanism of evolution by genetic assimilation : Equivalence and independence of genetic mutation and epigenetic modulation in phenotypic expression. Biophys Rev 2018; 10:667-676. [PMID: 29468522 DOI: 10.1007/s12551-018-0403-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Accepted: 02/05/2018] [Indexed: 12/21/2022] Open
Abstract
Conrad H. Waddington discovered the phenomenon of genetic assimilation through a series of experiments on fruit flies. In those experiments, artificially exerted environmental stress induced plastic phenotypic changes in the fruit flies, but after some generations, the same phenotypic variant started to appear without the environmental stress. Both the initial state (where the phenotypic changes were environmentally induced and plastic) and the final state (where the phenotypic changes were genetically fixed and constitutive) are experimental facts. However, it remains unclear how the environmentally induced phenotypic change in the first generation becomes genetically fixed in the central process of genetic assimilation itself. We have argued that the key to understanding the mechanism of genetic assimilation lies in epigenetics, and proposed the "cooperative model" in which the evolutionary process depends on both genetic and epigenetic factors. Evolutionary simulations based on the cooperative model reproduced the process of genetic assimilation. Detailed analysis of the trajectories has revealed genetic assimilation is a process in which epigenetically induced phenotypic changes are incrementally and statistically replaced with multiple minor genetic mutations through natural selection. In this scenario, epigenetic and genetic changes may be considered as mutually independent but equivalent in terms of their effects on phenotypic changes. This finding rejects the common (and confused) hypothesis that epigenetically induced phenotypic changes depend on genetic mutations. Furthermore, we argue that transgenerational epigenetic inheritance is not required for evolution by genetic assimilation.
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Affiliation(s)
- Ken Nishikawa
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
| | - Akira R Kinjo
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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25
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Glanzner WG, Wachter A, Coutinho ARS, Albornoz MS, Duggavathi R, GonÇAlves PBD, Bordignon V. Altered expression of BRG1 and histone demethylases, and aberrant H3K4 methylation in less developmentally competent embryos at the time of embryonic genome activation. Mol Reprod Dev 2016; 84:19-29. [PMID: 27879032 DOI: 10.1002/mrd.22762] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 11/18/2016] [Indexed: 12/16/2022]
Abstract
Epigenetics is a fundamental regulator underlying many biological functions, such as development and cell differentiation. Epigenetic modifications affect key chromatin regulation, including transcription and DNA repair, which are critical for normal embryo development. In this study, we profiled the expression of epigenetic modifiers and patterns of epigenetic changes in porcine embryos around the period of embryonic genome activation (EGA). We observed that Brahma-related gene 1 (BRG1) and Lysine demethylase 1A (KDM1A), which can alter the methylation status of lysine 4 in histone 3 (H3K4), localize to the nucleus at Day 3-4 of development. We then compared the abundance of epigenetic modifiers between early- and late-cleaving embryos, which were classified based on the time to the first cell cleavage, to investigate if their nuclear localization contributes to developmental competence. The mRNA abundance of BRG1, KDM1A, as well as other lysine demethylases (KDM1B, KDM5A, KDM5B, and KDM5C), were significantly higher in late- compared to early-cleaving embryos near the EGA period, although these difference disappeared at the blastocyst stage. The abundance of H3K4 mono- (H3K4me) and di-methylation (H3K4me2) during the EGA period was reduced in late-cleaving and less developmentally competent embryos. By contrast, BRG1, KDM1A, and H3K4me2 abundance was greater in embryos with more than eight cells at Day 3-4 of development compared to those with fewer than four cells. These findings suggest that altered epigenetic modifications of H3K4 around the EGA period may affect the developmental capacity of porcine embryos to reach the blastocyst stage. Mol. Reprod. Dev. 84: 19-29, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Werner G Glanzner
- Laboratory of Biotechnology and Animal Reproduction - BioRep, Federal University of Santa Maria (UFSM), Santa Maria, Rio Grande do Sul, Brazil
| | - Audrey Wachter
- Department of Animal Science, McGill University, Sainte Anne de Bellevue, Quebec, Canada
| | - Ana Rita S Coutinho
- Department of Animal Science, McGill University, Sainte Anne de Bellevue, Quebec, Canada
| | - Marcelo S Albornoz
- Department of Animal Science, McGill University, Sainte Anne de Bellevue, Quebec, Canada
| | - Raj Duggavathi
- Department of Animal Science, McGill University, Sainte Anne de Bellevue, Quebec, Canada
| | - Paulo B D GonÇAlves
- Laboratory of Biotechnology and Animal Reproduction - BioRep, Federal University of Santa Maria (UFSM), Santa Maria, Rio Grande do Sul, Brazil
| | - Vilceu Bordignon
- Department of Animal Science, McGill University, Sainte Anne de Bellevue, Quebec, Canada
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26
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Park J, Park JW, Oh H, Maria FS, Kang J, Tian X. Gene-Specific Assessment of Guanine Oxidation as an Epigenetic Modulator for Cardiac Specification of Mouse Embryonic Stem Cells. PLoS One 2016; 11:e0155792. [PMID: 27249188 PMCID: PMC4889044 DOI: 10.1371/journal.pone.0155792] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Accepted: 05/03/2016] [Indexed: 12/11/2022] Open
Abstract
Epigenetics have essential roles in development and human diseases. Compared to the complex histone modifications, epigenetic changes on mammalian DNA are as simple as methylation on cytosine. Guanine, however, can be oxidized as an epigenetic change which can undergo base-pair transversion, causing a genetic difference. Accumulating evidence indicates that reactive oxygen species (ROS) are important signaling molecules for embryonic stem cell (ESC) differentiation, possibly through transient changes on genomic DNA such as 7,8-dihydro-8-oxoguanine (8-oxoG). Technical limitations on detecting such DNA modifications, however, restrict the investigation of the role of 8-oxoG in ESC differentiation. Here, we developed a Hoogsteen base pairing-mediated PCR-sequencing assay to detect 8-oxoG lesions that can subsequently cause G to T transversions during PCR. We then used this assay to assess the epigenetic and transient 8-oxoG formation in the Tbx5 gene of R1 mouse ESCs subjected to oxidative stress by removing 2-mercaptoethanol (2ME) from the culture media. To our surprise, significantly higher numbers of 8-oxoG-mediated G∙C to C∙G transversion, not G∙C to T∙A, were detected at 7th and 9th base position from the transcription start site of exon 1 of Tbx5 in ESCs in the (-)2ME than (+)2ME group (p < 0.05). This was consistent with the decrease in the amount of amplifiable of DNA harboring the 8-oxoG lesions at the Tbx5 promoter region in the oxidative stressed ESCs. The ESCs responded to oxidative stress, possibly through the epigenetic effects of guanine oxidation with decreased proliferation (p < 0.05) and increased formation of beating embryoid bodies (EBs; p < 0.001). Additionally, the epigenetic changes of guanine induced up-regulation of Ogg1 and PolB, two base excision repairing genes for 8-oxoG, in ESCs treated with (-)2ME (p < 0.01). Together, we developed a gene-specific and direct quantification assay for guanine oxidation. Using oxidative stressed mouse ESCs, we validated this assay and assessed the epigenetic effects of 8-oxoG by studying expression of DNA repair genes, ESC proliferation, and EB formation.
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Affiliation(s)
- Joonghoon Park
- Center for Regenerative Biology and Department of Animal Science, University of Connecticut, Storrs, Connecticut, 06269, United States of America
| | - Jong Woo Park
- Research Center for Epigenome Regulation, School of Pharmacy, Sungkyunkwan University, Suwon, 440746, Republic of Korea
| | - Hawmok Oh
- Research Center for Epigenome Regulation, School of Pharmacy, Sungkyunkwan University, Suwon, 440746, Republic of Korea
| | - Fernanda S Maria
- Center for Regenerative Biology and Department of Animal Science, University of Connecticut, Storrs, Connecticut, 06269, United States of America
- Department of Animal Reproduction, College of Veterinary Medicine, University of Sao Paulo, Sao Paulo, 05508, Brazil
| | - Jaeku Kang
- Department of Pharmacology, College of Medicine, Konyang University, Daejeon, 302718, Republic of Korea
| | - Xiuchun Tian
- Center for Regenerative Biology and Department of Animal Science, University of Connecticut, Storrs, Connecticut, 06269, United States of America
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Jha HC, Banerjee S, Robertson ES. The Role of Gammaherpesviruses in Cancer Pathogenesis. Pathogens 2016; 5:pathogens5010018. [PMID: 26861404 PMCID: PMC4810139 DOI: 10.3390/pathogens5010018] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 01/27/2016] [Indexed: 12/15/2022] Open
Abstract
Worldwide, one fifth of cancers in the population are associated with viral infections. Among them, gammaherpesvirus, specifically HHV4 (EBV) and HHV8 (KSHV), are two oncogenic viral agents associated with a large number of human malignancies. In this review, we summarize the current understanding of the molecular mechanisms related to EBV and KSHV infection and their ability to induce cellular transformation. We describe their strategies for manipulating major cellular systems through the utilization of cell cycle, apoptosis, immune modulation, epigenetic modification, and altered signal transduction pathways, including NF-kB, Notch, Wnt, MAPK, TLR, etc. We also discuss the important EBV latent antigens, namely EBNA1, EBNA2, EBNA3’s and LMP’s, which are important for targeting these major cellular pathways. KSHV infection progresses through the engagement of the activities of the major latent proteins LANA, v-FLIP and v-Cyclin, and the lytic replication and transcription activator (RTA). This review is a current, comprehensive approach that describes an in-depth understanding of gammaherpes viral encoded gene manipulation of the host system through targeting important biological processes in viral-associated cancers.
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Affiliation(s)
- Hem Chandra Jha
- Department of Microbiology and Tumor Virology Program, Abramson Comprehensive Cancer Center, Perelman School of Medicine at the University of Pennsylvania, 201E Johnson Pavilion, 3610, Hamilton Walk, Philadelphia, PA 19104, USA.
| | - Shuvomoy Banerjee
- Department of Microbiology and Tumor Virology Program, Abramson Comprehensive Cancer Center, Perelman School of Medicine at the University of Pennsylvania, 201E Johnson Pavilion, 3610, Hamilton Walk, Philadelphia, PA 19104, USA.
| | - Erle S Robertson
- Department of Microbiology and Tumor Virology Program, Abramson Comprehensive Cancer Center, Perelman School of Medicine at the University of Pennsylvania, 201E Johnson Pavilion, 3610, Hamilton Walk, Philadelphia, PA 19104, USA.
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28
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Makova KD, Hardison RC. The effects of chromatin organization on variation in mutation rates in the genome. Nat Rev Genet 2015; 16:213-23. [PMID: 25732611 PMCID: PMC4500049 DOI: 10.1038/nrg3890] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The variation in local rates of mutations can affect both the evolution of genes and their function in normal and cancer cells. Deciphering the molecular determinants of this variation will be aided by the elucidation of distinct types of mutations, as they differ in regional preferences and in associations with genomic features. Chromatin organization contributes to regional variation in mutation rates, but its contribution differs among mutation types. In both germline and somatic mutations, base substitutions are more abundant in regions of closed chromatin, perhaps reflecting error accumulation late in replication. By contrast, a distinctive mutational state with very high levels of insertions and deletions (indels) and substitutions is enriched in regions of open chromatin. These associations indicate an intricate interplay between the nucleotide sequence of DNA and its dynamic packaging into chromatin, and have important implications for current biomedical research. This Review focuses on recent studies showing associations between chromatin state and mutation rates, including pairwise and multivariate investigations of germline and somatic (particularly cancer) mutations.
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Affiliation(s)
- Kateryna D Makova
- Department of Biology, Huck Institute for Genome Sciences, The Pennsylvania State University, University Park, State College, Pennsylvania 16802, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Huck Institute for Genome Sciences, The Pennsylvania State University, University Park, State College, Pennsylvania 16802, USA
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29
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Han J, Wang T, Fu L, Shi LY, Zhu CC, Liu J, Zhang Y, Cui XS, Kim NH, Sun SC. Altered oxidative stress, apoptosis/autophagy, and epigenetic modifications in Zearalenone-treated porcine oocytes. Toxicol Res (Camb) 2015. [DOI: 10.1039/c5tx00070j] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
ZEN affected porcine oocyte maturation and early embryonic development. Oxidative stress, autophagy and apoptosis occurred. Aberrant epigenetic modifications were also observed.
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Affiliation(s)
- Jun Han
- College of Animal Science and Technology
- Nanjing Agricultural University
- Nanjing 210095
- China
| | - Ting Wang
- College of Animal Science and Technology
- Nanjing Agricultural University
- Nanjing 210095
- China
| | - Le Fu
- College of Animal Science and Technology
- Nanjing Agricultural University
- Nanjing 210095
- China
| | - Liang-Yu Shi
- College of Animal Science and Technology
- Nanjing Agricultural University
- Nanjing 210095
- China
| | - Cheng-Cheng Zhu
- College of Animal Science and Technology
- Nanjing Agricultural University
- Nanjing 210095
- China
| | - Jun Liu
- College of Animal Science and Technology
- Nanjing Agricultural University
- Nanjing 210095
- China
| | - Yu Zhang
- College of Animal Science and Technology
- Nanjing Agricultural University
- Nanjing 210095
- China
| | - Xiang-Shun Cui
- Department of Animal Sciences
- Chungbuk National University
- Cheongju
- Korea
| | - Nam-Hyung Kim
- Department of Animal Sciences
- Chungbuk National University
- Cheongju
- Korea
| | - Shao-Chen Sun
- College of Animal Science and Technology
- Nanjing Agricultural University
- Nanjing 210095
- China
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30
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Bornstein C, Winter D, Barnett-Itzhaki Z, David E, Kadri S, Garber M, Amit I. A negative feedback loop of transcription factors specifies alternative dendritic cell chromatin States. Mol Cell 2014; 56:749-62. [PMID: 25453760 DOI: 10.1016/j.molcel.2014.10.014] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 08/13/2014] [Accepted: 10/14/2014] [Indexed: 01/11/2023]
Abstract
During hematopoiesis, cells originating from the same stem cell reservoir differentiate into distinct cell types. The mechanisms enabling common progenitors to differentiate into alternative cell fates are not fully understood. Here, we identify cell-fate-determining transcription factors (TFs) governing dendritic cell (DC) development by annotating the enhancer landscapes of the DC lineage. Combining these analyses with detailed overexpression, knockdown, and ChIP-Seq studies, we show that Irf8 functions as a plasmacytoid DC epigenetic and fate-determining TF, regulating massive, cell-specific chromatin changes in thousands of pDC enhancers. Importantly, Irf8 forms a negative feedback loop with Cebpb, a monocyte-derived DC epigenetic fate-determining TF. We show that using this circuit logic, a pulse of TF expression can stably define epigenetic and transcriptional states, regardless of the microenvironment. More broadly, our study proposes a general paradigm that allows closely related cells with a similar set of signal-dependent factors to generate differential and persistent enhancer landscapes.
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Affiliation(s)
| | - Deborah Winter
- Department of Immunology, Weizmann Institute, Rehovot 76100, Israel
| | | | - Eyal David
- Department of Immunology, Weizmann Institute, Rehovot 76100, Israel
| | - Sabah Kadri
- Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Manuel Garber
- Program in Bioinformatics and Integrative Biology and Program in Molecular Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ido Amit
- Department of Immunology, Weizmann Institute, Rehovot 76100, Israel.
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31
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Yao Y, Des Marais TL, Costa M. Chromatin Memory in the Development of Human Cancers. GENE TECHNOLOGY 2014; 3:114. [PMID: 25606572 PMCID: PMC4297643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Cancer is a complex disease with acquired genomic and epigenomic alterations that affect cell proliferation, viability and invasiveness. Almost all the epigenetic mechanisms including cytosine methylation and hydroxymethylation, chromatin remodeling and non-coding RNAs have been found associate with carcinogenesis and cancer specific expression profile. Altered histone modification as an epigenetic hallmark is frequently found in tumors. Understanding the epigenetic alterations induced by carcinogens or infectious agents may help us understand early epigenetic changes prior to the development of cancer. In this review, we focus on chromatin remodeling and the associated histone modifiers in the development of cancer; the application of these modifiers as a cancer therapy target in different clinical trial phases is also discussed.
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Affiliation(s)
- Yixin Yao
- Department of Environmental Medicine New York University, New York, USA,Corresponding author: Yixin Yao, Department of Environmental Medicine, New York University, New York, USA; Tel: 845-731-3517;
| | | | - Max Costa
- Department of Environmental Medicine New York University, New York, USA,Department of Biochemistry and Molecular Pharmacology, New York University Langone Medical Center, Tuxedo, New York, USA
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