1
|
Jeong H, Mendizabal I, Yi SV. Human Brain Aging is Associated with Dysregulation of Cell-Type Epigenetic Identity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.01.596981. [PMID: 38895434 PMCID: PMC11185522 DOI: 10.1101/2024.06.01.596981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Significant links between aging and DNA methylation are emerging from recent studies. On the one hand, DNA methylation undergoes changes with age, a process termed as epigenetic drift. On the other hand, DNA methylation serves as a readily accessible and accurate biomarker for aging. A key missing piece of information, however, is the molecular mechanisms underlying these processes, and how they are related, if any. Addressing the limitations of previous research due to the limited number of investigated CpGs and the heterogeneous nature of tissue samples, here we have examined DNA methylation of over 20 million CpGs across a broad age span in neurons and non-neuronal cells, primarily oligodendrocytes. We show that aging is a primary predictor of DNA methylation variation, surpassing the influence of factors such as sex and schizophrenia diagnosis, among others. On the genome-wide scale, epigenetic drift manifests as significant yet subtle trends that are influenced by the methylation level of individual CpGs. We reveal that CpGs that are highly differentiated between cell types are especially prone to age-associated DNA methylation alterations, leading to the divergence of epigenetic cell type identities as individuals age. On the other hand, CpGs that are included in commonly used epigenetic clocks tend to be those sites that are not highly cell type differentiated. Therefore, dysregulation of epigenetic cell-type identities and current DNA epigenetic clocks represent distinct features of age-associated DNA methylation alterations.
Collapse
Affiliation(s)
- Hyeonsoo Jeong
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Current Address: Altos Labs, San Diego, CA, USA
| | - Isabel Mendizabal
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- Translational prostate cancer Research lab, CIC bioGUNE-Basurto, Biocruces Bizkaia Health Research Institute, Derio, Spain
| | - Soojin V Yi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Department of Ecology, Evolution, and Marine Biology, Department of Molecular, Cellular, and Cell Biology, Neuroscience Research Institute, University of California, Santa Barbara, California 93106, USA
| |
Collapse
|
2
|
Morgan R, Loh E, Singh D, Mendizabal I, Yi SV. DNA methylation differences between the female and male X chromosomes in human brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.16.589778. [PMID: 38659923 PMCID: PMC11042362 DOI: 10.1101/2024.04.16.589778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The mechanisms of X chromosome inactivation suggest fundamental epigenetic differences between the female and male X chromosomes. However, DNA methylation studies often exclude the X chromosomes. In addition, many previous studies relied on techniques that examine non-randomly selected subsets of positions such as array-based methods, rather than assessing the whole X chromosome. Consequently, our understanding of X chromosome DNA methylation lags behind that of autosomes. Here we addressed this gap of knowledge by studying X chromosome DNA methylation using 89 whole genome bisulfite sequencing (WGBS) maps from neurons and oligodendrocytes. Using this unbiased and comprehensive data, we show that DNA methylation of the female X chromosomes is globally reduced (hypomethylated) across the entire chromosome compared to the male X chromosomes and autosomes. On the other hand, the majority of X-linked promoters were more highly methylated (hypermethylated) in females compared to males, consistent with the role of DNA methylation in X chromosome inactivation and dosage compensation. Remarkably, hypermethylation of female X promoters was limited to a group of previously lowly methylated promoters. The other group of highly methylated promoters were both hyper- and hypo-methylated in females with no obvious association with gene expression. Therefore, X chromosome inactivation by DNA methylation was exclusive to a subset of promoters with distinctive epigenetic feature. Apart from this group of promoters, differentially methylated regions in the female and male X chromosomes were dominated by female hypomethylation. Our study furthers the understanding of X-chromosome dosage regulation by DNA methylation on the chromosomal level as well as on individual gene level.
Collapse
Affiliation(s)
- Robert Morgan
- College of Computing, Georgia Institute of Technology, Atlanta, GA 30332
- School of Biological Sciences, Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332
- Current address: Arbor Biotechnologies, Cambridge, MA, 02140
| | - Eddie Loh
- Department of Ecology and Evolution and Marine Biology, Department of Molecular, Cellular and Developmental Biology, Neuroscience Research Institute, University of California, Santa Barbara
| | - Devika Singh
- School of Biological Sciences, Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332
- Current address: Foundation Medicine, Inc., Boston, MA, 02210
| | - Isabel Mendizabal
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- Translational prostate cancer Research lab, CIC bioGUNE-Basurto, Biocruces Bizkaia Health Research Institute, Derio, Spain
| | - Soojin V Yi
- Department of Ecology and Evolution and Marine Biology, Department of Molecular, Cellular and Developmental Biology, Neuroscience Research Institute, University of California, Santa Barbara
| |
Collapse
|
3
|
Lefkowitz RB, Miller CM, Martinez-Caballero JD, Ramos I. Epigenetic Control of Innate Immunity: Consequences of Acute Respiratory Virus Infection. Viruses 2024; 16:197. [PMID: 38399974 PMCID: PMC10893272 DOI: 10.3390/v16020197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024] Open
Abstract
Infections caused by acute respiratory viruses induce a systemic innate immune response, which can be measured by the increased levels of expression of inflammatory genes in immune cells. There is growing evidence that these acute viral infections, alongside transient transcriptomic responses, induce epigenetic remodeling as part of the immune response, such as DNA methylation and histone modifications, which might persist after the infection is cleared. In this article, we first review the primary mechanisms of epigenetic remodeling in the context of innate immunity and inflammation, which are crucial for the regulation of the immune response to viral infections. Next, we delve into the existing knowledge concerning the impact of respiratory virus infections on the epigenome, focusing on Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), Influenza A Virus (IAV), and Respiratory Syncytial Virus (RSV). Finally, we offer perspectives on the potential consequences of virus-induced epigenetic remodeling and open questions in the field that are currently under investigation.
Collapse
Affiliation(s)
- Rivka Bella Lefkowitz
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (R.B.L.); (C.M.M.)
| | - Clare M. Miller
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (R.B.L.); (C.M.M.)
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Juan David Martinez-Caballero
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (R.B.L.); (C.M.M.)
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Irene Ramos
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (R.B.L.); (C.M.M.)
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| |
Collapse
|
4
|
Wang Q, Xiong F, Wu G, Liu W, Chen J, Wang B, Chen Y. Gene body methylation in cancer: molecular mechanisms and clinical applications. Clin Epigenetics 2022; 14:154. [PMID: 36443876 PMCID: PMC9706891 DOI: 10.1186/s13148-022-01382-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 11/18/2022] [Indexed: 11/29/2022] Open
Abstract
DNA methylation is an important epigenetic mechanism that regulates gene expression. To date, most DNA methylation studies have focussed on CpG islands in the gene promoter region, and the mechanism of methylation and the regulation of gene expression after methylation have been clearly elucidated. However, genome-wide methylation studies have shown that DNA methylation is widespread not only in promoters but also in gene bodies. Gene body methylation is widely involved in the expression regulation of many genes and is closely related to the occurrence and progression of malignant tumours. This review focusses on the formation of gene body methylation patterns, its regulation of transcription, and its relationship with tumours, providing clues to explore the mechanism of gene body methylation in regulating gene transcription and its significance and application in the field of oncology.
Collapse
Affiliation(s)
- Qi Wang
- grid.33199.310000 0004 0368 7223Department of Biliary-Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Road, Wuhan, 430074 Hubei Province China
| | - Fei Xiong
- grid.33199.310000 0004 0368 7223Department of Biliary-Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Road, Wuhan, 430074 Hubei Province China
| | - Guanhua Wu
- grid.33199.310000 0004 0368 7223Department of Biliary-Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Road, Wuhan, 430074 Hubei Province China
| | - Wenzheng Liu
- grid.33199.310000 0004 0368 7223Department of Biliary-Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Road, Wuhan, 430074 Hubei Province China
| | - Junsheng Chen
- grid.33199.310000 0004 0368 7223Department of Biliary-Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Road, Wuhan, 430074 Hubei Province China
| | - Bing Wang
- grid.33199.310000 0004 0368 7223Department of Biliary-Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Road, Wuhan, 430074 Hubei Province China
| | - Yongjun Chen
- grid.33199.310000 0004 0368 7223Department of Biliary-Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Road, Wuhan, 430074 Hubei Province China
| |
Collapse
|
5
|
Abstract
DNA methylation is an epigenetic modification that has consistently been shown to be linked with a variety of human traits and diseases. Because DNA methylation is dynamic and potentially reversible in nature and can reflect environmental exposures and predict the onset of diseases, it has piqued interest as a potential disease biomarker. DNA methylation patterns are more stable than transcriptomic or proteomic patterns, and they are relatively easy to measure to track exposure to different environments and risk factors. Importantly, technologies for DNA methylation quantification have become increasingly cost effective-accelerating new research in the field-and have enabled the development of novel DNA methylation biomarkers. Quite a few DNA methylation-based predictors for a number of traits and diseases already exist. Such predictors show potential for being more accurate than self-reported or measured phenotypes (such as smoking behavior and body mass index) and may even hold potential for applications in clinics. In this review, we will first discuss the advantages and challenges of DNA methylation biomarkers in general. We will then review the current state and future potential of DNA methylation biomarkers in two human traits that show rather consistent alterations in methylome-obesity and smoking. Lastly, we will briefly speculate about the future prospects of DNA methylation biomarkers, and possible ways to achieve them.
Collapse
Affiliation(s)
- Aino Heikkinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Sailalitha Bollepalli
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| |
Collapse
|
6
|
Singh Rawat B, Venkataraman R, Budhwar R, Tailor P. Methionine- and Choline-Deficient Diet Identifies an Essential Role for DNA Methylation in Plasmacytoid Dendritic Cell Biology. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:881-897. [PMID: 35101891 DOI: 10.4049/jimmunol.2100763] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 12/02/2021] [Indexed: 06/14/2023]
Abstract
Diet plays an important role in lifestyle disorders associated with the disturbed immune system. During the study of methionine- and choline-deficient diet-induced nonalcoholic fatty liver disease, we observed a specific decrease in the plasmacytoid dendritic cell (pDC) fraction from murine spleens. While delineating the role for individual components, we identified that l-methionine supplementation correlates with representation of the pDC fraction. S-adenosylmethionine (SAM) is a key methyl donor, and we demonstrate that supplementation of methionine-deficient medium with SAM but not homocysteine reverses the defect in pDC development. l-Methionine has been implicated in maintenance of methylation status in the cell. Based on our observed effect of SAM and zebularine on DC subset development, we sought to clarify the role of DNA methylation in pDC biology. Whole-genome bisulfite sequencing analysis from the splenic DC subsets identified that pDCs display differentially hypermethylated regions in comparison with classical DC (cDC) subsets, whereas cDC1 and cDC2 exhibited comparable methylated regions, serving as a control in our study. We validated differentially methylated regions in the sorted pDC, CD8α+ cDC1, and CD4+ cDC2 subsets from spleens as well as FL-BMDC cultures. Upon analysis of genes linked with differentially methylated regions, we identified that differential DNA methylation is associated with the MAPK pathway such that its inhibition guides DC development toward the pDC subtype. Overall, our study identifies an important role for methionine in pDC biology.
Collapse
Affiliation(s)
| | - Ramya Venkataraman
- Laboratory of Innate Immunity, National Institute of Immunology, New Delhi, India
| | - Roli Budhwar
- Bionivid Technology Private Ltd., Bengaluru, Karnataka, India; and
| | - Prafullakumar Tailor
- Laboratory of Innate Immunity, National Institute of Immunology, New Delhi, India;
- Special Centre for Systems Medicine, Jawaharlal Nehru University, New Delhi, India
| |
Collapse
|
7
|
Nuclear Organization during Hepatogenesis in Zebrafish Requires Uhrf1. Genes (Basel) 2021; 12:genes12071081. [PMID: 34356097 PMCID: PMC8304062 DOI: 10.3390/genes12071081] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 01/07/2023] Open
Abstract
Acquisition of cellular fate during development is initiated and maintained by well-coordinated patterns of gene expression that are dictated by the epigenetic landscape and genome organization in the nucleus. While the epigenetic marks that mediate developmental gene expression patterns during organogenesis have been well studied, less is known about how epigenetic marks influence nuclear organization during development. This study examines the relationship between nuclear structure, chromatin accessibility, DNA methylation, and gene expression during hepatic outgrowth in zebrafish larvae. We investigate the relationship between these features using mutants that lack DNA methylation. Hepatocyte nuclear morphology was established coincident with hepatocyte differentiation at 80 h post-fertilization (hpf), and nuclear shape and size continued to change until the conclusion of outgrowth and morphogenesis at 120 hpf. Integrating ATAC-Seq analysis with DNA methylation profiling of zebrafish livers at 120 hpf showed that closed and highly methylated chromatin occupies most transposable elements and that open chromatin correlated with gene expression. DNA hypomethylation, due to mutation of genes encoding ubiquitin-like, containing PHD and RING Finger Domains 1 (uhrf1) and DNA methyltransferase (dnmt1), did not block hepatocyte differentiation, but had dramatic effects on nuclear organization. Hepatocytes in uhrf1 mutants have large, deformed nuclei with multiple nucleoli, downregulation of nucleolar genes, and a complete lack of the nuclear lamina. Loss of lamin B2 staining was phenocopied by dnmt1 mutation. Together, these data show that hepatocyte nuclear morphogenesis coincides with organ morphogenesis and outgrowth, and that DNA methylation directs chromatin organization, and, in turn, hepatocyte nuclear shape and size during liver development.
Collapse
|
8
|
Abstract
Substance use disorders (SUDs) are chronic brain diseases characterized by transitions from recreational to compulsive drug use and aberrant drug craving that persists for months to years after abstinence is achieved. The transition to compulsive drug use implies that plasticity is occurring, altering the physiology of the brain to precipitate addicted states. Epigenetic phenomena represent a varied orchestra of transcriptional tuning mechanisms that, in response to environmental stimuli, create and maintain gene expression-mediated physiological outcomes. Therefore, epigenetic mechanisms represent a convergent regulatory framework through which the plasticity required to achieve an addicted state can arise and then persist long after drug use has ended. In the first section, we will introduce basic concepts in epigenetics, such as chromatin architecture, histones and their posttranslational modifications, DNA methylation, noncoding RNAs, and transcription factors, along with methods for their investigation. We will then examine the implications of these mechanisms in SUDs, with a particular focus on cocaine-mediated neuroepigenetic plasticity across multiple behavioral models of addiction.
Collapse
Affiliation(s)
- Andrew F Stewart
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Sasha L Fulton
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Ian Maze
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| |
Collapse
|
9
|
Åsenius F, Danson AF, Marzi SJ. DNA methylation in human sperm: a systematic review. Hum Reprod Update 2021; 26:841-873. [PMID: 32790874 DOI: 10.1093/humupd/dmaa025] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 05/25/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Studies in non-human mammals suggest that environmental factors can influence spermatozoal DNA methylation, and some research suggests that spermatozoal DNA methylation is also implicated in conditions such as subfertility and imprinting disorders in the offspring. Together with an increased availability of cost-effective methods of interrogating DNA methylation, this premise has led to an increasing number of studies investigating the DNA methylation landscape of human spermatozoa. However, how the human spermatozoal DNA methylome is influenced by environmental factors is still unclear, as is the role of human spermatozoal DNA methylation in subfertility and in influencing offspring health. OBJECTIVE AND RATIONALE The aim of this systematic review was to critically appraise the quality of the current body of literature on DNA methylation in human spermatozoa, summarize current knowledge and generate recommendations for future research. SEARCH METHODS A comprehensive literature search of the PubMed, Web of Science and Cochrane Library databases was conducted using the search terms 'semen' OR 'sperm' AND 'DNA methylation'. Publications from 1 January 2003 to 2 March 2020 that studied human sperm and were written in English were included. Studies that used sperm DNA methylation to develop methodologies or forensically identify semen were excluded, as were reviews, commentaries, meta-analyses or editorial texts. The Grading of Recommendations, Assessment, Development and Evaluations (GRADE) criteria were used to objectively evaluate quality of evidence in each included publication. OUTCOMES The search identified 446 records, of which 135 were included in the systematic review. These 135 studies were divided into three groups according to area of research; 56 studies investigated the influence of spermatozoal DNA methylation on male fertility and abnormal semen parameters, 20 studies investigated spermatozoal DNA methylation in pregnancy outcomes including offspring health and 59 studies assessed the influence of environmental factors on spermatozoal DNA methylation. Findings from studies that scored as 'high' and 'moderate' quality of evidence according to GRADE criteria were summarized. We found that male subfertility and abnormal semen parameters, in particular oligozoospermia, appear to be associated with abnormal spermatozoal DNA methylation of imprinted regions. However, no specific DNA methylation signature of either subfertility or abnormal semen parameters has been convincingly replicated in genome-scale, unbiased analyses. Furthermore, although findings require independent replication, current evidence suggests that the spermatozoal DNA methylome is influenced by cigarette smoking, advanced age and environmental pollutants. Importantly however, from a clinical point of view, there is no convincing evidence that changes in spermatozoal DNA methylation influence pregnancy outcomes or offspring health. WIDER IMPLICATIONS Although it appears that the human sperm DNA methylome can be influenced by certain environmental and physiological traits, no findings have been robustly replicated between studies. We have generated a set of recommendations that would enhance the reliability and robustness of findings of future analyses of the human sperm methylome. Such studies will likely require multicentre collaborations to reach appropriate sample sizes, and should incorporate phenotype data in more complex statistical models.
Collapse
Affiliation(s)
| | - Amy F Danson
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Sarah J Marzi
- UK Dementia Research Institute, Imperial College London, London W12 0NN, UK.,Department of Brain Sciences, Imperial College London, London, UK
| |
Collapse
|
10
|
Bazov I, Sarkisyan D, Kononenko O, Watanabe H, Taqi MM, Stålhandske L, Verbeek DS, Mulder J, Rajkowska G, Sheedy D, Kril J, Sun X, Syvänen AC, Yakovleva T, Bakalkin G. Neuronal Expression of Opioid Gene is Controlled by Dual Epigenetic and Transcriptional Mechanism in Human Brain. Cereb Cortex 2019; 28:3129-3142. [PMID: 28968778 DOI: 10.1093/cercor/bhx181] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Indexed: 12/13/2022] Open
Abstract
Molecular mechanisms that define patterns of neuropeptide expression are essential for the formation and rewiring of neural circuits. The prodynorphin gene (PDYN) gives rise to dynorphin opioid peptides mediating depression and substance dependence. We here demonstrated that PDYN is expressed in neurons in human dorsolateral prefrontal cortex (dlPFC), and identified neuronal differentially methylated region in PDYN locus framed by CCCTC-binding factor binding sites. A short, nucleosome size human-specific promoter CpG island (CGI), a core of this region may serve as a regulatory module, which is hypomethylated in neurons, enriched in 5-hydroxymethylcytosine, and targeted by USF2, a methylation-sensitive E-box transcription factor (TF). USF2 activates PDYN transcription in model systems, and binds to nonmethylated CGI in dlPFC. USF2 and PDYN expression is correlated, and USF2 and PDYN proteins are co-localized in dlPFC. Segregation of activatory TF and repressive CGI methylation may ensure contrasting PDYN expression in neurons and glia in human brain.
Collapse
Affiliation(s)
- Igor Bazov
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Daniil Sarkisyan
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Olga Kononenko
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Hiroyuki Watanabe
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Mumtaz Malik Taqi
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden.,Faculty of Medicine, NORMENT, University of Oslo, Oslo, Norway
| | - Lada Stålhandske
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Dineke S Verbeek
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
| | - Jan Mulder
- Department of Neuroscience, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Grazyna Rajkowska
- Department of Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, MS, USA
| | - Donna Sheedy
- Discipline of Pathology, Sydney Medical School, University of Sydney, Sydney NSW, Australia
| | - Jillian Kril
- Discipline of Pathology, Sydney Medical School, University of Sydney, Sydney NSW, Australia
| | - Xueguang Sun
- Zymo Research Corporation, 17062 Murphy Avenue, Irvine, CA, USA.,Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Ann-Christine Syvänen
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Tatiana Yakovleva
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Georgy Bakalkin
- Division of Biological Research on Drug Dependence, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| |
Collapse
|
11
|
Yi SV. Insights into Epigenome Evolution from Animal and Plant Methylomes. Genome Biol Evol 2018; 9:3189-3201. [PMID: 29036466 PMCID: PMC5721340 DOI: 10.1093/gbe/evx203] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2017] [Indexed: 12/14/2022] Open
Abstract
Evolutionary studies of DNA methylation offer insights into the mechanisms governing the variation of genomic DNA methylation across different species. Comparisons of gross levels of DNA methylation between distantly related species indicate that the size of the genome and the level of genomic DNA methylation are positively correlated. In plant genomes, this can be reliably explained by the genomic contents of repetitive sequences. In animal genomes, the role of repetitive sequences on genomic DNA methylation is less clear. On a shorter timescale, population-level comparisons demonstrate that genetic variation can explain the observed variability of DNA methylation to some degree. The amount of DNA methylation variation that has been attributed to genetic variation in the human population studies so far is substantially lower than that from Arabidopsis population studies, but this disparity might reflect the differences in the computational and experimental techniques used. The effect of genetic variation on DNA methylation has been directly examined in mammalian systems, revealing several causative factors that govern DNA methylation. On the other hand, studies from Arabidopsis have furthered our understanding of spontaneous mutations of DNA methylation, termed “epimutations.” Arabidopsis has an extremely high rate of spontaneous epimutations, which may play a major role in shaping the global DNA methylation landscape in this genome. Key missing information includes the frequencies of spontaneous epimutations in other lineages, in particular animal genomes, and how population-level variation of DNA methylation leads to species-level differences.
Collapse
Affiliation(s)
- Soojin V Yi
- School of Biological Sciences, Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia
| |
Collapse
|
12
|
Jia Y, Li H, Wang J, Meng H, Yang Z. Spectrum structures and biological functions of 8-mers in the human genome. Genomics 2018. [PMID: 29522801 DOI: 10.1016/j.ygeno.2018.03.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The spectra of k-mer frequencies can reveal the structures and evolution of genome sequences. We confirmed that the trimodal spectrum of 8-mers in human genome sequences is distinguished only by CG2, CG1 and CG0 8-mer sets, containing 2,1 or 0 CpG, respectively. This phenomenon is called independent selection law. The three types of CG 8-mers were considered as different functional elements. We conjectured that (1) nucleosome binding motifs are mainly characterized by CG1 8-mers and (2) the core structural units of CpG island sequences are predominantly characterized by CG2 8-mers. To validate our conjectures, nucleosome occupied sequences and CGI sequences were extracted, then the sequence parameters were constructed through the information of the three CG 8-mer sets respectively. ROC analysis showed that CG1 8-mers are more preference in nucleosome occupied segments (AUC > 0.7) and CG2 8-mers are more preference in CGI sequences (AUC > 0.99). This validates our conjecture in principle.
Collapse
Affiliation(s)
- Yun Jia
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China; College of Science, Inner Mongolia University of Technology, Hohhot 010051, China
| | - Hong Li
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China.
| | - Jingfeng Wang
- College of Science, Inner Mongolia University of Technology, Hohhot 010051, China
| | - Hu Meng
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Zhenhua Yang
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| |
Collapse
|
13
|
Mendizabal I, Zeng J, Keller TE, Yi SV. Body-hypomethylated human genes harbor extensive intragenic transcriptional activity and are prone to cancer-associated dysregulation. Nucleic Acids Res 2017; 45:4390-4400. [PMID: 28115635 PMCID: PMC5416765 DOI: 10.1093/nar/gkx020] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 01/05/2017] [Indexed: 01/08/2023] Open
Abstract
Genomic DNA methylation maps (methylomes) encode genetic and environmental effects as stable chemical modifications of DNA. Variations in DNA methylation, especially in regulatory regions such as promoters and enhancers, are known to affect numerous downstream processes. In contrast, most transcription units (gene bodies) in the human genome are thought to be heavily methylated. However, epigenetic reprogramming in cancer often involves gene body hypomethylation with consequences on gene expression. In this study, we focus on the relatively unexplored phenomenon that some gene bodies are devoid of DNA methylation under normal conditions. Utilizing nucleotide-resolution methylomes of diverse samples, we show that nearly 2000 human genes are commonly hypomethylated. Remarkably, these genes occupy highly specialized genomic, epigenomic, evolutionary and functional niches in our genomes. For example, hypomethylated genes tend to be short yet encode significantly more transcripts than expected based upon their lengths, include many genes involved in nucleosome and chromatin formation, and are extensively and significantly enriched for histone-tail modifications and transcription factor binding with particular relevance for cis-regulation. Furthermore, they are significantly more prone to cancer-associated hypomethylation and mutation. Consequently, gene body hypomethylation represents an additional layer of epigenetic regulatory complexity, with implications on cancer-associated epigenetic reprogramming.
Collapse
Affiliation(s)
- Isabel Mendizabal
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.,Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Jia Zeng
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Thomas E Keller
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Soojin V Yi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| |
Collapse
|
14
|
Jeziorska DM, Murray RJS, De Gobbi M, Gaentzsch R, Garrick D, Ayyub H, Chen T, Li E, Telenius J, Lynch M, Graham B, Smith AJH, Lund JN, Hughes JR, Higgs DR, Tufarelli C. DNA methylation of intragenic CpG islands depends on their transcriptional activity during differentiation and disease. Proc Natl Acad Sci U S A 2017; 114:E7526-E7535. [PMID: 28827334 PMCID: PMC5594649 DOI: 10.1073/pnas.1703087114] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The human genome contains ∼30,000 CpG islands (CGIs). While CGIs associated with promoters nearly always remain unmethylated, many of the ∼9,000 CGIs lying within gene bodies become methylated during development and differentiation. Both promoter and intragenic CGIs may also become abnormally methylated as a result of genome rearrangements and in malignancy. The epigenetic mechanisms by which some CGIs become methylated but others, in the same cell, remain unmethylated in these situations are poorly understood. Analyzing specific loci and using a genome-wide analysis, we show that transcription running across CGIs, associated with specific chromatin modifications, is required for DNA methyltransferase 3B (DNMT3B)-mediated DNA methylation of many naturally occurring intragenic CGIs. Importantly, we also show that a subgroup of intragenic CGIs is not sensitive to this process of transcription-mediated methylation and that this correlates with their individual intrinsic capacity to initiate transcription in vivo. We propose a general model of how transcription could act as a primary determinant of the patterns of CGI methylation in normal development and differentiation, and in human disease.
Collapse
Affiliation(s)
- Danuta M Jeziorska
- Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, United Kingdom
| | - Robert J S Murray
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom
- Division of Medical Sciences and Graduate Entry Medicine, School of Medicine, University of Nottingham, Royal Derby Hospital, Derby DE22 3DT, United Kingdom
| | - Marco De Gobbi
- Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, United Kingdom
| | - Ricarda Gaentzsch
- Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, United Kingdom
| | - David Garrick
- Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, United Kingdom
| | - Helena Ayyub
- Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, United Kingdom
| | - Taiping Chen
- Department of Epigenetics and Molecular Carcinogenesis, Division of Basic Science Research, The University of Texas M. D. Anderson Cancer Center, Smithville, TX 78957
| | - En Li
- China Novartis Institutes for BioMedical Research, Shanghai 201203, China
| | - Jelena Telenius
- Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, United Kingdom
| | - Magnus Lynch
- Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, United Kingdom
| | - Bryony Graham
- Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, United Kingdom
| | - Andrew J H Smith
- Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, United Kingdom
- Medical Research Council Centre for Regenerative Medicine, The University of Edinburgh, Edinburgh EH16 4UU, United Kingdom
| | - Jonathan N Lund
- Division of Medical Sciences and Graduate Entry Medicine, School of Medicine, University of Nottingham, Royal Derby Hospital, Derby DE22 3DT, United Kingdom
| | - Jim R Hughes
- Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, United Kingdom
| | - Douglas R Higgs
- Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, United Kingdom;
| | - Cristina Tufarelli
- Division of Medical Sciences and Graduate Entry Medicine, School of Medicine, University of Nottingham, Royal Derby Hospital, Derby DE22 3DT, United Kingdom;
| |
Collapse
|
15
|
Samanta S, Rajasingh S, Cao T, Dawn B, Rajasingh J. Epigenetic dysfunctional diseases and therapy for infection and inflammation. Biochim Biophys Acta Mol Basis Dis 2016; 1863:518-528. [PMID: 27919711 DOI: 10.1016/j.bbadis.2016.11.030] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 11/23/2016] [Accepted: 11/29/2016] [Indexed: 12/20/2022]
Abstract
Even though the discovery of the term 'epigenetics' was in the 1940s, it has recently become one of the most promising and expanding fields to unravel the gene expression pattern in several diseases. The most well studied example is cancer, but other diseases like metabolic disorders, autism, or inflammation-associated diseases such as lung injury, autoimmune disease, asthma, and type-2 diabetes display aberrant gene expression and epigenetic regulation during their occurrence. The change in the epigenetic pattern of a gene may also alter gene function because of a change in the DNA status. Constant environmental pressure, lifestyle, as well as food habits are the other important parameters responsible for transgenerational inheritance of epigenetic traits. Discovery of epigenetic modifiers targeting DNA methylation and histone deacetylation enzymes could be an alternative source to treat or manipulate the pathogenesis of diseases. Particularly, the combination of epigenetic drugs such as 5-aza-2-deoxycytidine (Aza) and trichostatin A (TSA) are well studied to reduce inflammation in an acute lung injury model. It is important to understand the epigenetic machinery and the function of its components in specific diseases to develop targeted epigenetic therapy. Moreover, it is equally critical to know the specific inhibitors other than the widely used pan inhibitors in clinical trials and explore their roles in regulating specific genes in a more defined way during infection.
Collapse
Affiliation(s)
- Saheli Samanta
- Department of Internal Medicine, Cardiovascular Research Institute, University of Kansas Medical Center, Kansas City, KS, USA
| | - Sheeja Rajasingh
- Department of Internal Medicine, Cardiovascular Research Institute, University of Kansas Medical Center, Kansas City, KS, USA
| | - Thuy Cao
- Department of Internal Medicine, Cardiovascular Research Institute, University of Kansas Medical Center, Kansas City, KS, USA
| | - Buddhadeb Dawn
- Department of Internal Medicine, Cardiovascular Research Institute, University of Kansas Medical Center, Kansas City, KS, USA
| | - Johnson Rajasingh
- Department of Internal Medicine, Cardiovascular Research Institute, University of Kansas Medical Center, Kansas City, KS, USA; Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA.
| |
Collapse
|
16
|
Mendizabal I, Shi L, Keller TE, Konopka G, Preuss TM, Hsieh TF, Hu E, Zhang Z, Su B, Yi SV. Comparative Methylome Analyses Identify Epigenetic Regulatory Loci of Human Brain Evolution. Mol Biol Evol 2016; 33:2947-2959. [PMID: 27563052 PMCID: PMC5062329 DOI: 10.1093/molbev/msw176] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
How do epigenetic modifications change across species and how do these modifications affect evolution? These are fundamental questions at the forefront of our evolutionary epigenomic understanding. Our previous work investigated human and chimpanzee brain methylomes, but it was limited by the lack of outgroup data which is critical for comparative (epi)genomic studies. Here, we compared whole genome DNA methylation maps from brains of humans, chimpanzees and also rhesus macaques (outgroup) to elucidate DNA methylation changes during human brain evolution. Moreover, we validated that our approach is highly robust by further examining 38 human-specific DMRs using targeted deep genomic and bisulfite sequencing in an independent panel of 37 individuals from five primate species. Our unbiased genome-scan identified human brain differentially methylated regions (DMRs), irrespective of their associations with annotated genes. Remarkably, over half of the newly identified DMRs locate in intergenic regions or gene bodies. Nevertheless, their regulatory potential is on par with those of promoter DMRs. An intriguing observation is that DMRs are enriched in active chromatin loops, suggesting human-specific evolutionary remodeling at a higher-order chromatin structure. These findings indicate that there is substantial reprogramming of epigenomic landscapes during human brain evolution involving noncoding regions.
Collapse
Affiliation(s)
- Isabel Mendizabal
- School of Biological Sciences, Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, Leioa, Spain
| | - Lei Shi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China The Molecular & Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, MI
| | - Thomas E Keller
- School of Biological Sciences, Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA
| | - Genevieve Konopka
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX
| | - Todd M Preuss
- Division of Neuropharmacology and Neurologic Diseases & Center for Translational Social Neuroscience, Department of Pathology and Laboratory Medicine, Yerkes National Primate Research Center, Emory University School of Medicine, Emory University, Atlanta, GA
| | - Tzung-Fu Hsieh
- Department of Plant and Microbial Biology and Plants for Human Health Institute, North Carolina State University, Raleigh, NC
| | - Enzhi Hu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Zhe Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Soojin V Yi
- School of Biological Sciences, Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA
| |
Collapse
|
17
|
Pagliaroli L, Vető B, Arányi T, Barta C. From Genetics to Epigenetics: New Perspectives in Tourette Syndrome Research. Front Neurosci 2016; 10:277. [PMID: 27462201 PMCID: PMC4940402 DOI: 10.3389/fnins.2016.00277] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/06/2016] [Indexed: 11/13/2022] Open
Abstract
Gilles de la Tourette Syndrome (TS) is a neurodevelopmental disorder marked by the appearance of multiple involuntary motor and vocal tics. TS presents high comorbidity rates with other disorders such as attention deficit hyperactivity disorder (ADHD) and obsessive compulsive disorder (OCD). TS is highly heritable and has a complex polygenic background. However, environmental factors also play a role in the manifestation of symptoms. Different epigenetic mechanisms may represent the link between these two causalities. Epigenetic regulation has been shown to have an impact in the development of many neuropsychiatric disorders, however very little is known about its effects on Tourette Syndrome. This review provides a summary of the recent findings in genetic background of TS, followed by an overview on different epigenetic mechanisms, such as DNA methylation, histone modifications, and non-coding RNAs in the regulation of gene expression. Epigenetic studies in other neurological and psychiatric disorders are discussed along with the TS-related epigenetic findings available in the literature to date. Moreover, we are proposing that some general epigenetic mechanisms seen in other neuropsychiatric disorders may also play a role in the pathogenesis of TS.
Collapse
Affiliation(s)
- Luca Pagliaroli
- Institute of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis UniversityBudapest, Hungary; Research Centre for Natural Sciences, Institute of Enzymology, Hungarian Academy of SciencesBudapest, Hungary
| | - Borbála Vető
- Research Centre for Natural Sciences, Institute of Enzymology, Hungarian Academy of Sciences Budapest, Hungary
| | - Tamás Arányi
- Research Centre for Natural Sciences, Institute of Enzymology, Hungarian Academy of SciencesBudapest, Hungary; Centre National de la Recherche Scientifique UMR 6214, Institut National de la Santé et de la Recherche Médicale U1083, University of AngersAngers, France
| | - Csaba Barta
- Institute of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University Budapest, Hungary
| |
Collapse
|
18
|
Keller TE, Han P, Yi SV. Evolutionary Transition of Promoter and Gene Body DNA Methylation across Invertebrate-Vertebrate Boundary. Mol Biol Evol 2015; 33:1019-28. [PMID: 26715626 PMCID: PMC4776710 DOI: 10.1093/molbev/msv345] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Genomes of invertebrates and vertebrates exhibit highly divergent patterns of DNA methylation. Invertebrate genomes tend to be sparsely methylated, and DNA methylation is mostly targeted to a subset of transcription units (gene bodies). In a drastic contrast, vertebrate genomes are generally globally and heavily methylated, punctuated by the limited local hypo-methylation of putative regulatory regions such as promoters. These genomic differences also translate into functional differences in DNA methylation and gene regulation. Although promoter DNA methylation is an important regulatory component of vertebrate gene expression, its role in invertebrate gene regulation has been little explored. Instead, gene body DNA methylation is associated with expression of invertebrate genes. However, the evolutionary steps leading to the differentiation of invertebrate and vertebrate genomic DNA methylation remain unresolved. Here we analyzed experimentally determined DNA methylation maps of several species across the invertebrate–vertebrate boundary, to elucidate how vertebrate gene methylation has evolved. We show that, in contrast to the prevailing idea, a substantial number of promoters in an invertebrate basal chordate Ciona intestinalis are methylated. Moreover, gene expression data indicate significant, epigenomic context-dependent associations between promoter methylation and expression in C. intestinalis. However, there is no evidence that promoter methylation in invertebrate chordate has been evolutionarily maintained across the invertebrate–vertebrate boundary. Rather, body-methylated invertebrate genes preferentially obtain hypo-methylated promoters among vertebrates. Conversely, promoter methylation is preferentially found in lineage- and tissue-specific vertebrate genes. These results provide important insights into the evolutionary origin of epigenetic regulation of vertebrate gene expression.
Collapse
Affiliation(s)
| | | | - Soojin V Yi
- School of Biology, Georgia Institute of Technology
| |
Collapse
|
19
|
Mendizabal I, Yi SV. Whole-genome bisulfite sequencing maps from multiple human tissues reveal novel CpG islands associated with tissue-specific regulation. Hum Mol Genet 2015; 25:69-82. [PMID: 26512062 PMCID: PMC4690492 DOI: 10.1093/hmg/ddv449] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 10/21/2015] [Indexed: 01/25/2023] Open
Abstract
CpG islands (CGIs) are one of the most widely studied regulatory features of the human genome, with critical roles in development and disease. Despite such significance and the original epigenetic definition, currently used CGI sets are typically predicted from DNA sequence characteristics. Although CGIs are deeply implicated in practical analyses of DNA methylation, recent studies have shown that such computational annotations suffer from inaccuracies. Here we used whole-genome bisulfite sequencing from 10 diverse human tissues to identify a comprehensive, experimentally obtained, single-base resolution CGI catalog. In addition to the unparalleled annotation precision, our method is free from potential bias due to arbitrary sequence features or probe affinity differences. In addition to clarifying substantial false positives in the widely used University of California Santa Cruz (UCSC) annotations, our study identifies numerous novel epigenetic loci. In particular, we reveal significant impact of transposable elements on the epigenetic regulatory landscape of the human genome and demonstrate ubiquitous presence of transcription initiation at CGIs, including alternative promoters in gene bodies and non-coding RNAs in intergenic regions. Moreover, coordinated DNA methylation and chromatin modifications mark tissue-specific enhancers at novel CGIs. Enrichment of specific transcription factor binding from ChIP-seq supports mechanistic roles of CGIs on the regulation of tissue-specific transcription. The new CGI catalog provides a comprehensive and integrated list of genomic hotspots of epigenetic regulation.
Collapse
Affiliation(s)
- Isabel Mendizabal
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA and Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Soojin V Yi
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA and
| |
Collapse
|
20
|
Integrated analysis of epigenomic and genomic changes by DNA methylation dependent mechanisms provides potential novel biomarkers for prostate cancer. Oncotarget 2015; 5:7858-69. [PMID: 25277202 PMCID: PMC4202166 DOI: 10.18632/oncotarget.2313] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Epigenetic silencing mediated by CpG methylation is a common feature of many cancers. Characterizing aberrant DNA methylation changes associated with tumor progression may identify potential prognostic markers for prostate cancer (PCa). We treated two PCa cell lines, 22Rv1 and DU-145 with the demethylating agent 5-Aza 2’–deoxycitidine (DAC) and global methylation status was analyzed by performing methylation-sensitive restriction enzyme based differential methylation hybridization strategy followed by genome-wide CpG methylation array profiling. In addition, we examined gene expression changes using a custom microarray. Gene Set Enrichment Analysis (GSEA) identified the most significantly dysregulated pathways. In addition, we assessed methylation status of candidate genes that showed reduced CpG methylation and increased gene expression after DAC treatment, in Gleason score (GS) 8 vs. GS6 patients using three independent cohorts of patients; the publically available The Cancer Genome Atlas (TCGA) dataset, and two separate patient cohorts. Our analysis, by integrating methylation and gene expression in PCa cell lines, combined with patient tumor data, identified novel potential biomarkers for PCa patients. These markers may help elucidate the pathogenesis of PCa and represent potential prognostic markers for PCa patients.
Collapse
|
21
|
Sun D, Yi SV. Impacts of Chromatin States and Long-Range Genomic Segments on Aging and DNA Methylation. PLoS One 2015; 10:e0128517. [PMID: 26091484 PMCID: PMC4475080 DOI: 10.1371/journal.pone.0128517] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 04/28/2015] [Indexed: 01/13/2023] Open
Abstract
Understanding the fundamental dynamics of epigenome variation during normal aging is critical for elucidating key epigenetic alterations that affect development, cell differentiation and diseases. Advances in the field of aging and DNA methylation strongly support the aging epigenetic drift model. Although this model aligns with previous studies, the role of other epigenetic marks, such as histone modification, as well as the impact of sampling specific CpGs, must be evaluated. Ultimately, it is crucial to investigate how all CpGs in the human genome change their methylation with aging in their specific genomic and epigenomic contexts. Here, we analyze whole genome bisulfite sequencing DNA methylation maps of brain frontal cortex from individuals of diverse ages. Comparisons with blood data reveal tissue-specific patterns of epigenetic drift. By integrating chromatin state information, divergent degrees and directions of aging-associated methylation in different genomic regions are revealed. Whole genome bisulfite sequencing data also open a new door to investigate whether adjacent CpG sites exhibit coordinated DNA methylation changes with aging. We identified significant 'aging-segments', which are clusters of nearby CpGs that respond to aging by similar DNA methylation changes. These segments not only capture previously identified aging-CpGs but also include specific functional categories of genes with implications on epigenetic regulation of aging. For example, genes associated with development are highly enriched in positive aging segments, which are gradually hyper-methylated with aging. On the other hand, regions that are gradually hypo-methylated with aging ('negative aging segments') in the brain harbor genes involved in metabolism and protein ubiquitination. Given the importance of protein ubiquitination in proteome homeostasis of aging brains and neurodegenerative disorders, our finding suggests the significance of epigenetic regulation of this posttranslational modification pathway in the aging brain. Utilizing aging segments rather than individual CpGs will provide more comprehensive genomic and epigenomic contexts to understand the intricate associations between genomic neighborhoods and developmental and aging processes. These results complement the aging epigenetic drift model and provide new insights.
Collapse
Affiliation(s)
- Dan Sun
- School of Biology, Georgia Institute of Technology, Atlanta, GA, 30332, United States of America
| | - Soojin V. Yi
- School of Biology, Georgia Institute of Technology, Atlanta, GA, 30332, United States of America
| |
Collapse
|
22
|
Genome-wide screen of DNA methylation identifies novel markers in childhood obesity. Gene 2015; 566:74-83. [PMID: 25871514 DOI: 10.1016/j.gene.2015.04.032] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 03/20/2015] [Accepted: 04/10/2015] [Indexed: 11/21/2022]
Abstract
Epigenetic modifications have been highlighted in chronic non-communicable diseases. The aim of this study was to investigate genome-wide DNA methylation for the identification of methylation markers in obesity. With obese Chinese preschool children, we performed comprehensive DNA methylation profiling of gene promoters and CpG islands to determine the differentially methylated genes using methylated DNA immunoprecipitation followed by hybridization to the NimbleGen Human DNA Methylation 385K Promoter Plus CpG Island Microarray. We found that compared to lean children, 251 promoters and 575 CGIs were demethylated, and 141 promoters and 277 CGIs were hypermethylated in obese children, and their distribution on chromosomes was imbalanced, showing more promoters and CGIs with demethylation on chromosomes 3, 16, 17 and 19 and more differentially methylated promoters and CGIs on chromosome X compared with chromosome Y. Further analysis indicated that aberrant methylations occurred mostly in HCP promoters and promoter CGIs. Among the top 80 promoters and CGIs that had differentiated methylation between obese and lean children, nearly half have been previously studied, and almost all of them are involved in the pathogenesis of cancers that are associated with many organs. Furthermore, four genes (FZD7, PRLHR, EXOSC4, and EIF6) with differential promoter methylation were validated, and their associations with obesity must be clarified. In conclusion, this study represents the first effort to determine methylation markers in obese Chinese children, which has potential relevance for identifying markers that are useful in elucidating the mechanisms of obesity pathogenesis and its complications.
Collapse
|
23
|
Urdinguio RG, Bayón GF, Dmitrijeva M, Toraño EG, Bravo C, Fraga MF, Bassas L, Larriba S, Fernández AF. Aberrant DNA methylation patterns of spermatozoa in men with unexplained infertility. Hum Reprod 2015; 30:1014-28. [PMID: 25753583 DOI: 10.1093/humrep/dev053] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 02/16/2015] [Indexed: 12/17/2022] Open
Abstract
STUDY QUESTION Are there DNA methylation alterations in sperm that could explain the reduced biological fertility of male partners from couples with unexplained infertility? SUMMARY ANSWER DNA methylation patterns, not only at specific loci but also at Alu Yb8 repetitive sequences, are altered in infertile individuals compared with fertile controls. WHAT IS KNOWN ALREADY Aberrant DNA methylation of sperm has been associated with human male infertility in patients demonstrating either deficiencies in the process of spermatogenesis or low semen quality. STUDY DESIGN, SIZE, DURATION Case and control prospective study. This study compares 46 sperm samples obtained from 17 normospermic fertile men and 29 normospermic infertile patients. PARTICIPANTS/MATERIALS, SETTING, METHODS Illumina Infinium HD Human Methylation 450K arrays were used to identify genomic regions showing differences in sperm DNA methylation patterns between five fertile and seven infertile individuals. Additionally, global DNA methylation of sperm was measured using the Methylamp Global DNA Methylation Quantification Ultra kit (Epigentek) in 14 samples, and DNA methylation at several repetitive sequences (LINE-1, Alu Yb8, NBL2, D4Z4) measured by bisulfite pyrosequencing in 44 sperm samples. A sperm-specific DNA methylation pattern was obtained by comparing the sperm methylomes with the DNA methylomes of differentiated somatic cells using data obtained from methylation arrays (Illumina 450 K) of blood, neural and glial cells deposited in public databases. MAIN RESULTS AND THE ROLE OF CHANCE In this study we conduct, for the first time, a genome-wide study to identify alterations of sperm DNA methylation in individuals with unexplained infertility that may account for the differences in their biological fertility compared with fertile individuals. We have identified 2752 CpGs showing aberrant DNA methylation patterns, and more importantly, these differentially methylated CpGs were significantly associated with CpG sites which are specifically methylated in sperm when compared with somatic cells. We also found statistically significant (P < 0.001) associations between DNA hypomethylation and regions corresponding to those which, in somatic cells, are enriched in the repressive histone mark H3K9me3, and between DNA hypermethylation and regions enriched in H3K4me1 and CTCF, suggesting that the relationship between chromatin context and aberrant DNA methylation of sperm in infertile men could be locus-dependent. Finally, we also show that DNA methylation patterns, not only at specific loci but also at several repetitive sequences (LINE-1, Alu Yb8, NBL2, D4Z4), were lower in sperm than in somatic cells. Interestingly, sperm samples at Alu Yb8 repetitive sequences of infertile patients showed significantly lower DNA methylation levels than controls. LIMITATIONS, REASONS FOR CAUTION Our results are descriptive and further studies would be needed to elucidate the functional effects of aberrant DNA methylation on male fertility. WIDER IMPLICATIONS OF THE FINDINGS Overall, our data suggest that aberrant sperm DNA methylation might contribute to fertility impairment in couples with unexplained infertility and they provide a promising basis for future research. STUDY FUNDING/COMPETING INTERESTS This work has been financially supported by Fundación Cientifica de la AECC (to R.G.U.); IUOPA (to G.F.B.); FICYT (to E.G.T.); the Spanish National Research Council (CSIC; 200820I172 to M.F.F.); Fundación Ramón Areces (to M.F.F); the Plan Nacional de I+D+I 2008-2011/2013-2016/FEDER (PI11/01728 to AF.F., PI12/01080 to M.F.F. and PI12/00361 to S.L.); the PN de I+D+I 2008-20011 and the Generalitat de Catalunya (2009SGR01490). A.F.F. is sponsored by ISCIII-Subdirección General de Evaluación y Fomento de la Investigación (CP11/00131). S.L. is sponsored by the Researchers Stabilization Program from the Spanish National Health System (CES09/020). The IUOPA is supported by the Obra Social Cajastur, Spain.
Collapse
Affiliation(s)
- Rocío G Urdinguio
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo 33006, Spain
| | - Gustavo F Bayón
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo 33006, Spain
| | - Marija Dmitrijeva
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo 33006, Spain
| | - Estela G Toraño
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo 33006, Spain
| | - Cristina Bravo
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo 33006, Spain
| | - Mario F Fraga
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo 33006, Spain Department of Immunology and Oncology, National Center for Biotechnology, CNB-CSIC, Cantoblanco, Madrid 28049, Spain
| | - Lluís Bassas
- Laboratory of Seminology and Embryology, Andrology Service-Fundació Puigvert, Barcelona 08025, Spain
| | - Sara Larriba
- Human Molecular Genetics Group-IDIBELL, L'Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Agustín F Fernández
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo 33006, Spain
| |
Collapse
|
24
|
Huh I, Yang X, Park T, Yi SV. Bis-class: a new classification tool of methylation status using bayes classifier and local methylation information. BMC Genomics 2014; 15:608. [PMID: 25037738 PMCID: PMC4117951 DOI: 10.1186/1471-2164-15-608] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Accepted: 07/07/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Whole genome sequencing of bisulfite converted DNA ('methylC-seq') method provides comprehensive information of DNA methylation. An important application of these whole genome methylation maps is classifying each position as a methylated versus non-methylated nucleotide. A widely used current method for this purpose, the so-called binomial method, is intuitive and straightforward, but lacks power when the sequence coverage and the genome-wide methylation level are low. These problems present a particular challenge when analyzing sparsely methylated genomes, such as those of many invertebrates and plants. RESULTS We demonstrate that the number of sequence reads per position from methylC-seq data displays a large variance and can be modeled as a shifted negative binomial distribution. We also show that DNA methylation levels of adjacent CpG sites are correlated, and this similarity in local DNA methylation levels extends several kilobases. Taking these observations into account, we propose a new method based on Bayesian classification to infer DNA methylation status while considering the neighborhood DNA methylation levels of a specific site. We show that our approach has higher sensitivity and better classification performance than the binomial method via multiple analyses, including computational simulations, Area Under Curve (AUC) analyses, and improved consistencies across biological replicates. This method is especially advantageous in the analyses of sparsely methylated genomes with low coverage. CONCLUSIONS Our method improves the existing binomial method for binary methylation calls by utilizing a posterior odds framework and incorporating local methylation information. This method should be widely applicable to the analyses of methylC-seq data from diverse sparsely methylated genomes. Bis-Class and example data are provided at a dedicated website (http://bibs.snu.ac.kr/software/Bisclass).
Collapse
Affiliation(s)
| | | | - Taesung Park
- Department of Statistics, Bioinformatics and Biostatistics Laboratory, Seoul National University, 151-742 Seoul, Korea.
| | | |
Collapse
|
25
|
Abstract
Epigenetic mechanisms traditionally have been studied in the domains of development and disease, but they may also play important roles in ecological and evolutionary processes. In this article, we revisit historical as well as recent studies that indicate significant impacts of epigenetic processes on evolution. Our main focus is DNA methylation, which is a prevalent chemical modification of genomic DNA. First, it has been long known that DNA methylation acts as a major mutational facilitator in animal genomes and influences nucleotide compositions of genomes. More recently, genome-wide analyses have demonstrated that the current levels of DNA methylation can be predicted from the evolutionary signatures of DNA methylation, indicating that these two processes are intimately correlated. Indeed, the recent explosive growth in the knowledge of genomic DNA methylation in wide-ranging taxa has revealed that patterns of DNA methylation are surprisingly conserved across deep phylogenies. Interestingly, comparative analyses of humans and closely related primate species show that genomic regions that do show evolutionary divergence of DNA methylation are enriched for developmental and tissue specializations. A key question is how epigenetic patterns transmit between generations and impact evolutionary dynamics. On the one hand, some studies report direct transmissions of epigenetic features to the next generation. On the other hand, it is becoming clear that genomic sequence variants exist that encode and presumably regulate distinctive epigenetic patterns. For instance, numerous single-nucleotide polymorphisms that affect DNA-methylation patterns have been discovered in human populations. These studies begin to unveil a dynamic interplay between genomic and epigenomic factors across long and short evolutionary timescales.
Collapse
Affiliation(s)
- I Mendizabal
- School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332, USA Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, SpainSchool of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332, USA Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Spain
| | - T E Keller
- School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332, USA Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Spain
| | - J Zeng
- School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332, USA Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Soojin V Yi
- School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332, USA Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Spain
| |
Collapse
|