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Pandey A, Kakani P, Shukla S. CTCF and BORIS-mediated autophagy regulation via alternative splicing of BNIP3L in breast cancer. J Biol Chem 2024; 300:107416. [PMID: 38810696 DOI: 10.1016/j.jbc.2024.107416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 05/09/2024] [Accepted: 05/17/2024] [Indexed: 05/31/2024] Open
Abstract
Autophagy is a pivotal regulatory and catabolic process, induced under various stressful conditions, including hypoxia. However, little is known about alternative splicing of autophagy genes in the hypoxic landscape in breast cancer. Our research unravels the hitherto unreported alternative splicing of BNIP3L, a crucial hypoxia-induced autophagic gene. We showed that BNIP3L, under hypoxic condition, forms two isoforms, a full-length isoform (BNIP3L-F) and a shorter isoform lacking exon 1 (BNIP3L-Δ1). The hypoxia-induced BNIP3L-F promotes autophagy, while under normoxia, the BNIP3L-Δ1 inhibits autophagy. We discovered a novel dimension of hypoxia-mediated epigenetic modification that regulates the alternative splicing of BNIP3L. Here, we showed differential DNA methylation of BNIP3L intron 1, causing reciprocal binding of epigenetic factor CCCTC-binding factor (CTCF) and its paralog BORIS. Additionally, we highlighted the role of CTCF and BORIS impacting autophagy in breast cancer. The differential binding of CTCF and BORIS results in alternative splicing of BNIP3L forming BNIP3L-F and BNIP3L-Δ1, respectively. The binding of CTCF on unmethylated BNIP3L intron 1 under hypoxia results in RNA Pol-II pause and inclusion of exon 1, promoting BNIP3L-F and autophagy. Interestingly, the binding of BORIS on methylated BNIP3L intron 1 under normoxia also results in RNA Pol-II pause but leads to the exclusion of exon 1 from BNIP3L mRNA. Finally, we reported the critical role of BORIS-mediated RNA Pol-II pause, which subsequently recruits SRSF6, redirecting the proximal splice-site selection, promoting BNIP3L-Δ1, and inhibiting autophagy. Our study provides novel insights into the potential avenues for breast cancer therapy by targeting autophagy regulation, specifically under hypoxic condition.
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Affiliation(s)
- Anchala Pandey
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh, India
| | - Parik Kakani
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh, India
| | - Sanjeev Shukla
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh, India.
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2
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Gerra MC, Dallabona C, Cecchi R. Epigenetic analyses in forensic medicine: future and challenges. Int J Legal Med 2024; 138:701-719. [PMID: 38242965 PMCID: PMC11003920 DOI: 10.1007/s00414-024-03165-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 01/09/2024] [Indexed: 01/21/2024]
Abstract
The possibility of using epigenetics in forensic investigation has gradually risen over the last few years. Epigenetic changes with their dynamic nature can either be inherited or accumulated throughout a lifetime and be reversible, prompting investigation of their use across various fields. In forensic sciences, multiple applications have been proposed, such as the discrimination of monozygotic twins, identifying the source of a biological trace left at a crime scene, age prediction, determination of body fluids and tissues, human behavior association, wound healing progression, and determination of the post-mortem interval (PMI). Despite all these applications, not all the studies considered the impact of PMI and post-sampling effects on the epigenetic modifications and the tissue-specificity of the epigenetic marks.This review aims to highlight the substantial forensic significance that epigenetics could support in various forensic investigations. First, basic concepts in epigenetics, describing the main epigenetic modifications and their functions, in particular, DNA methylation, histone modifications, and non-coding RNA, with a particular focus on forensic applications, were covered. For each epigenetic marker, post-mortem stability and tissue-specificity, factors that should be carefully considered in the study of epigenetic biomarkers in the forensic context, have been discussed. The advantages and limitations of using post-mortem tissues have been also addressed, proposing directions for these innovative strategies to analyze forensic specimens.
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Affiliation(s)
- Maria Carla Gerra
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area Delle Scienze 11a, Viale Delle Scienze 11a, 43124, Parma, PR, Italy
| | - Cristina Dallabona
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area Delle Scienze 11a, Viale Delle Scienze 11a, 43124, Parma, PR, Italy.
| | - Rossana Cecchi
- Department of Medicine and Surgery, University of Parma, Via Antonio Gramsci 14, 43126, Parma, PR, Italy
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Maurici N, Phan TM, Henty-Ridilla JL, Kim YC, Mittal J, Bah A. Uncovering the molecular interactions underlying MBD2 and MBD3 phase separation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.29.591564. [PMID: 38746378 PMCID: PMC11092444 DOI: 10.1101/2024.04.29.591564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Chromatin organization controls DNA's accessibility to regulatory factors to influence gene expression. Heterochromatin, or transcriptionally silent chromatin enriched in methylated DNA and methylated histone tails, self-assembles through multivalent interactions with its associated proteins into a condensed, but dynamic state. Liquid-liquid phase separation (LLPS) of key heterochromatin regulators, such as heterochromatin protein 1 (HP1), plays an essential role in heterochromatin assembly and function. Methyl-CpG-binding protein 2 (MeCP2), the most studied member of the methyl-CpG-binding domain (MBD) family of proteins, has been recently shown to undergo LLPS in the absence and presence of methylated DNA. These studies provide a new mechanistic framework for understanding the role of methylated DNA and its readers in heterochromatin formation. However, the details of the molecular interactions by which other MBD family members undergo LLPS to mediate genome organization and transcriptional regulation are not fully understood. Here, we focus on two MBD proteins, MBD2 and MBD3, that have distinct but interdependent roles in gene regulation. Using an integrated computational and experimental approach, we uncover the homotypic and heterotypic interactions governing MBD2 and MBD3 phase separation and DNA's influence on this process. We show that despite sharing the highest sequence identity and structural homology among all the MBD protein family members, MBD2 and MBD3 exhibit differing residue patterns resulting in distinct phase separation mechanisms. Understanding the molecular underpinnings of MBD protein condensation offers insights into the higher-order, LLPS-mediated organization of heterochromatin.
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Effendi WI, Nagano T. Epigenetics Approaches toward Precision Medicine for Idiopathic Pulmonary Fibrosis: Focus on DNA Methylation. Biomedicines 2023; 11:biomedicines11041047. [PMID: 37189665 DOI: 10.3390/biomedicines11041047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 03/31/2023] Open
Abstract
Genetic information is not transmitted solely by DNA but by the epigenetics process. Epigenetics describes molecular missing link pathways that could bridge the gap between the genetic background and environmental risk factors that contribute to the pathogenesis of pulmonary fibrosis. Specific epigenetic patterns, especially DNA methylation, histone modifications, long non-coding, and microRNA (miRNAs), affect the endophenotypes underlying the development of idiopathic pulmonary fibrosis (IPF). Among all the epigenetic marks, DNA methylation modifications have been the most widely studied in IPF. This review summarizes the current knowledge concerning DNA methylation changes in pulmonary fibrosis and demonstrates a promising novel epigenetics-based precision medicine.
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Tang FL, Zhang XG, Ke PY, Liu J, Zhang ZJ, Hu DM, Gu J, Zhang H, Guo HK, Zang QW, Huang R, Ma YL, Kwan P. MBD5 regulates NMDA receptor expression and seizures by inhibiting Stat1 transcription. Neurobiol Dis 2023; 181:106103. [PMID: 36997128 DOI: 10.1016/j.nbd.2023.106103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 02/21/2023] [Accepted: 03/23/2023] [Indexed: 03/31/2023] Open
Abstract
Epilepsy is considered to result from an imbalance between excitation and inhibition of the central nervous system. Pathogenic mutations in the methyl-CpG binding domain protein 5 gene (MBD5) are known to cause epilepsy. However, the function and mechanism of MBD5 in epilepsy remain elusive. Here, we found that MBD5 was mainly localized in the pyramidal cells and granular cells of mouse hippocampus, and its expression was increased in the brain tissues of mouse models of epilepsy. Exogenous overexpression of MBD5 inhibited the transcription of the signal transducer and activator of transcription 1 gene (Stat1), resulting in increased expression of N-methyl-d-aspartate receptor (NMDAR) subunit 1 (GluN1), 2A (GluN2A) and 2B (GluN2B), leading to aggravation of the epileptic behaviour phenotype in mice. The epileptic behavioural phenotype was alleviated by overexpression of STAT1 which reduced the expression of NMDARs, and by the NMDAR antagonist memantine. These results indicate that MBD5 accumulation affects seizures through STAT1-mediated inhibition of NMDAR expression in mice. Collectively, our findings suggest that the MBD5-STAT1-NMDAR pathway may be a new pathway that regulates the epileptic behavioural phenotype and may represent a new treatment target.
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Yazar V, Dawson VL, Dawson TM, Kang SU. DNA Methylation Signature of Aging: Potential Impact on the Pathogenesis of Parkinson's Disease. JOURNAL OF PARKINSON'S DISEASE 2023; 13:145-164. [PMID: 36710687 PMCID: PMC10041453 DOI: 10.3233/jpd-223517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Regulation of gene expression by epigenetic modifications means lasting and heritable changes in the function of genes without alterations in the DNA sequence. Of all epigenetic mechanisms identified thus far, DNA methylation has been of particular interest in both aging and age-related disease research over the last decade given the consistency of site-specific DNA methylation changes during aging that can predict future health and lifespan. An increasing line of evidence has implied the dynamic nature of DNA (de)methylation events that occur throughout the lifespan has a role in the pathophysiology of aging and age-associated neurodegenerative conditions, including Parkinson's disease (PD). In this regard, PD methylome shows, to some extent, similar genome-wide changes observed in the methylome of healthy individuals of matching age. In this review, we start by providing a brief overview of studies outlining global patterns of DNA methylation, then its mechanisms and regulation, within the context of aging and PD. Considering diverging lines of evidence from different experimental and animal models of neurodegeneration and how they combine to shape our current understanding of tissue-specific changes in DNA methylome in health and disease, we report a high-level comparison of the genomic methylation landscapes of brain, with an emphasis on dopaminergic neurons in PD and in natural aging. We believe this will be particularly useful for systematically dissecting overlapping genome-wide alterations in DNA methylation during PD and healthy aging, and for improving our knowledge of PD-specific changes in methylation patterns independent of aging process.
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Affiliation(s)
- Volkan Yazar
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, USA
- Diana Helis Henry Medical Research Foundation, New Orleans, LA, USA
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pharmacology and and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, USA
- Diana Helis Henry Medical Research Foundation, New Orleans, LA, USA
| | - Sung-Ung Kang
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Mechanisms of DNA methylation and histone modifications. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 197:51-92. [PMID: 37019597 DOI: 10.1016/bs.pmbts.2023.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The field of genetics has expanded a lot in the past few decades due to the accessibility of human genome sequences, but still, the regulation of transcription cannot be explicated exclusively by the sequence of DNA of an individual. The coordination and crosstalk between chromatin factors which are conserved is indispensable for all living creatures. The regulation of gene expression has been dependent on the methylation of DNA, post-translational modifications of histones, effector proteins, chromatin remodeler enzymes that affect the chromatin structure and function, and other cellular activities such as DNA replication, DNA repair, proliferation and growth. The mutation and deletion of these factors can lead to human diseases. Various studies are being performed to identify and understand the gene regulatory mechanisms in the diseased state. The information from these high throughput screening studies is able to aid the treatment developments based on the epigenetics regulatory mechanisms. This book chapter will discourse on various modifications and their mechanisms that take place on histones and DNA that regulate the transcription of genes.
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Marchal C, Defossez PA, Miotto B. Context-dependent CpG methylation directs cell-specific binding of transcription factor ZBTB38. Epigenetics 2022; 17:2122-2143. [PMID: 36000449 DOI: 10.1080/15592294.2022.2111135] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
DNA methylation on CpGs regulates transcription in mammals, both by decreasing the binding of methylation-repelled factors and by increasing the binding of methylation-attracted factors. Among the latter, zinc finger proteins have the potential to bind methylated CpGs in a sequence-specific context. The protein ZBTB38 is unique in that it has two independent sets of zinc fingers, which recognize two different methylated consensus sequences in vitro. Here, we identify the binding sites of ZBTB38 in a human cell line, and show that they contain the two methylated consensus sequences identified in vitro. In addition, we show that the distribution of ZBTB38 sites is highly unusual: while 10% of the ZBTB38 sites are also bound by CTCF, the other 90% of sites reside in closed chromatin and are not bound by any of the other factors mapped in our model cell line. Finally, a third of ZBTB38 sites are found upstream of long and active CpG islands. Our work therefore validates ZBTB38 as a methyl-DNA binder in vivo and identifies its unique distribution in the genome.
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Affiliation(s)
- Claire Marchal
- Université Paris Cité, Institut Cochin, INSERM, CNRS, Paris, France
| | | | - Benoit Miotto
- Université Paris Cité, Institut Cochin, INSERM, CNRS, Paris, France
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Abstract
DNA methylation is one of the most important components of epigenetics, which plays essential roles in maintaining genome stability and regulating gene expression. In recent years, DNA methylation measuring methods have been continuously optimized. Combined with next generation sequencing technologies, these approaches have enabled the detection of genome-wide cytosine methylation at single-base resolution. In this paper, we review the development of 5-methylcytosine and its oxidized derivatives measuring methods, and recent advancement of single-cell epigenome sequencing technologies, offering more referable information for the selection and optimization of DNA methylation sequencing technologies and related research.
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10
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Rajeev R, Dwivedi AP, Sinha A, Agarwaal V, Dev RR, Kar A, Khosla S. Epigenetic interaction of microbes with their mammalian hosts. J Biosci 2021. [PMID: 34728591 PMCID: PMC8550911 DOI: 10.1007/s12038-021-00215-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
The interaction of microbiota with its host has the ability to alter the cellular functions of both, through several mechanisms. Recent work, from many laboratories including our own, has shown that epigenetic mechanisms play an important role in the alteration of these cellular functions. Epigenetics broadly refers to change in the phenotype without a corresponding change in the DNA sequence. This change is usually brought by epigenetic modifications of the DNA itself, the histone proteins associated with the DNA in the chromatin, non-coding RNA or the modifications of the transcribed RNA. These modifications, also known as epigenetic code, do not change the DNA sequence but alter the expression level of specific genes. Microorganisms seem to have learned how to modify the host epigenetic code and modulate the host transcriptome in their favour. In this review, we explore the literature that describes the epigenetic interaction of bacteria, fungi and viruses, with their mammalian hosts.
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Kyrgios I, Giza S, Fragou A, Tzimagiorgis G, Galli-Tsinopoulou A. DNA hypermethylation of PTPN22 gene promoter in children and adolescents with Hashimoto thyroiditis. J Endocrinol Invest 2021; 44:2131-2138. [PMID: 33751486 DOI: 10.1007/s40618-020-01463-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 10/30/2020] [Indexed: 01/09/2023]
Abstract
PURPOSE Protein tyrosine phosphatase non-receptor type 22 (PTPN22) is an inhibitor of T-cell activation, regulating intracellular signal transduction and thereby being implicated in the pathogenesis of autoimmune thyroid disease (AITD). The exact molecular mechanisms have not been fully elucidated. The aim of the present study was to quantitate DNA methylation within the PTPN22 gene promoter in children and adolescents with AITD and healthy controls. METHODS 60 Patients with Hashimoto thyroiditis (HT), 25 patients with HT and type 1 diabetes (HT + T1D), 9 patients with Graves' disease (GD) and 55 healthy controls without any individual or family history of autoimmune disease were enrolled. Whole blood DNA extraction, DNA modification using sodium bisulfate and quantification of DNA methylation in the PTPN22 gene promoter, based on melting curve analysis of the selected DNA fragment using a Real-Time PCR assay, were implemented. RESULTS DNA methylation in the PTPN22 gene promoter was found to be significantly higher in HT patients (39.9 ± 3.1%) in comparison with other study groups (20.3 ± 2.4% for HT + T1D, 32.6 ± 7.8% for GD, 27.1 ± 2.4% for controls, p < 0.001). PTPN22 gene promoter DNA methylation was also associated marginally with thyroid autoimmunity in general (p = 0.059), as well as considerably with thyroid volume (p = 0.004) and the presence of goiter (p = 0.001) but not thyroid function tests. CONCLUSIONS This study demonstrates for the first time that a relationship between autoimmune thyroiditis and PTPN22 gene promoter DNA methylation state is present, thus proposing another possible etiological association between thyroiditis and abnormalities of PTPN22 function. Further expression studies are required to confirm these findings.
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Affiliation(s)
- I Kyrgios
- 4th Department of Pediatrics, Papageorgiou General Hospital, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - S Giza
- 4th Department of Pediatrics, Papageorgiou General Hospital, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - A Fragou
- Laboratory of Biological Chemistry, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - G Tzimagiorgis
- Laboratory of Biological Chemistry, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - A Galli-Tsinopoulou
- 2nd Department of Pediatrics, AHEPA General University Hospital, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, St. Kiriakidi 1, Thessaloniki, 54636, Greece.
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Bie LH, Fei JW, Gao J. Molecular mechanism of methyl-dependent and spatial-specific DNA recognition of c-Jun homodimer. J Mol Model 2021; 27:227. [PMID: 34264385 DOI: 10.1007/s00894-021-04840-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 07/01/2021] [Indexed: 10/20/2022]
Abstract
DNA methylation is important in regulation of gene expression and normal development because it alters the interplay between protein and DNA. Experiments have shown that a single 5-methylcytosine at different CpG sites (mCpG) might have different effects on specific recognition, but the atomistic origin and dynamic details are largely unclear. In this work, we investigated the mechanism of monomethylation at different CpG sites in the cognate motif and the cooperativity of full methylation. By constructing four models of c-Jun/Jun protein binding to the 5[Formula: see text]-XGAGTCA-3[Formula: see text] (X represents C or methylated C) motif, we characterized the dynamics of the contact interface using the all-atom molecular dynamics method. Free energy analysis of MM/GBSA suggests that regardless of whether the C12pG13 site of the bottom strand is methylated, the effects from mC25 of the top strand are dominant and can moderately enhance the binding by [Formula: see text] 31 kcal/mol, whereas mC12 showed a relatively small contribution, in agreement with the experimental data. Remarkably, we found that this spatial-specific influence was induced by different regulatory rules. The influence of the mC25 site is mainly mediated by steric hindrance. The additional methyl group leads to the conformational changes in nearby residues and triggers an obvious structural bending in the protein, which results in the formation of a new T-Asn-C triad that enhances the specific recognition of TCA half-sites. The substitution of the methyl group at the mC12 site of the bottom strand breaks the original H-bonds directly. Such changes in electrostatic interactions also lead to the remote allosteric effects of protein by multifaceted interactions but have negligible contributions to binding. Although these two influence modes are different, they can both fine-tune the local environment, which might produce remote allosteric effects through protein-protein interactions. Further analysis reveals that the discrepancies in these two modes are primarily due to their location. Moreover, when both sites are methylated, the major determinant of binding specificity depends on the context and the location of the methylation site, which is the result of crosstalk and cooperativity.
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Affiliation(s)
- Li-Hua Bie
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Jun-Wen Fei
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Jun Gao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
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Fetke JK, Martinson JW, Flick RW, Huang W, Bencic DC, See MJ, Pilgrim EM, Debry RW, Biales AD. DNA methylation and expression of estrogen receptor alpha in fathead minnows exposed to 17α-ethynylestradiol. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2021; 233:105788. [PMID: 33662878 PMCID: PMC8317993 DOI: 10.1016/j.aquatox.2021.105788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/15/2021] [Accepted: 02/19/2021] [Indexed: 05/12/2023]
Abstract
The gene expression response thought to underlie the negative apical effects resulting from estrogen exposure have been thoroughly described in fish. Although epigenetics are believed to play a critical role translating environmental exposures into the development of adverse apical effects, they remain poorly characterized in fish species. This study investigated alterations of DNA methylation of estrogen receptor alpha (esr1) in brain and liver tissues from 8 to 10 month old male fathead minnows (Pimephales promelas) after a 2d exposure to either 2.5 ng/L or 10 ng/L 17α-ethynylestradiol (EE2). Changes in the patterns of methylation were evaluated using targeted deep sequencing of bisulfite treated DNA in the 5' region of esr1. Methylation and gene expression were assessed at 2d of exposure and after a 7 and 14d depuration period. After 2d EE2 exposure, males exhibited significant demethylation in the 5' upstream region of esr1 in liver tissue, which was inversely correlated to gene expression. This methylation pattern reflected what was seen in females. No gene body methylation (GBM) was observed for liver of exposed males. Differential methylation was observed for a single upstream CpG site in the liver after the 14d depuration. A less pronounced methylation response was observed in the upstream region in brain tissue, however, several CpGs were necessarily excluded from the analysis. In contrast to the liver, a significant GBM response was observed across the entire gene body, which was sustained until at least 7d post-exposure. No differential expression was observed in the brain, limiting functional interpretation of methylation changes. The identification of EE2-dependent changes in methylation levels strongly suggests the importance of epigenetic mechanisms as a mediator of the organismal response to environmental exposures and the need for further characterization of the epigenome. Further, differential methylation following depuration indicates estrogenic effects persist well after the active exposure, which has implications for the risk posed by repeated exposures..
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Affiliation(s)
- J K Fetke
- Oak Ridge Institute for Science and Education (ORISE) Research Participant at US Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, 45268, United States; Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States
| | - J W Martinson
- US Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, 45268, United States
| | - R W Flick
- US Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, 45268, United States
| | - W Huang
- US Environmental Protection Agency, Office of Research and Development, Research Triangle Park, NC, 27709, United States
| | - D C Bencic
- US Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, 45268, United States
| | - M J See
- US Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, 45268, United States
| | - E M Pilgrim
- US Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, 45268, United States
| | - R W Debry
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States
| | - A D Biales
- US Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, 45268, United States.
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Pisera-Fuster A, Zwiller J, Bernabeu R. Methionine Supplementation Abolishes Nicotine-Induced Place Preference in Zebrafish: a Behavioral and Molecular Analysis. Mol Neurobiol 2021; 58:2590-2607. [PMID: 33475949 DOI: 10.1007/s12035-020-02260-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/10/2020] [Indexed: 12/26/2022]
Abstract
In zebrafish, nicotine is known to regulate sensitivity to psychostimulants via epigenetic mechanisms. Little however is known about the regulation of addictive-like behavior by DNA methylation processes. To evaluate the influence of DNA methylation on nicotine-induced conditioned place preference (CPP), zebrafish were exposed to methyl supplementation through oral L-methionine (Met) administration. Met was found to reduce dramatically nicotine-induced CPP as well as behaviors associated with drug reward. The reduction was associated with the upregulation of DNA methyltransferases (DNMT1 and 3) as well as with the downregulation of methyl-cytosine dioxygenase-1 (TET1) and of nicotinic receptor subunits. Met also increased the expression of histone methyltransferases in nicotine-induced CPP groups. It reversed the nicotine-induced reduction in the methylation at α7 and NMDAR1 gene promoters. Treatment with the DNMT inhibitor 5-aza-2'-deoxycytidine (AZA) was found to reverse the effects of Met in structures of the reward pathway. Interestingly, Met did not modify the amount of the phospho-form of CREB (pCREB), a key factor establishing nicotine conditioning, whereas AZA increased pCREB levels. Our data suggest that nicotine-seeking behavior is partially dependent on DNA methylation occurring probably at specific gene loci, such as α7 and NMDAR1 receptor gene promoters. Overall, they suggest that Met should be considered as a potential therapeutic drug to treat nicotine addiction.
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Affiliation(s)
- Antonella Pisera-Fuster
- Department of Physiology and Institute of Physiology and Biophysics, School of Medicine, University of Buenos Aires, Paraguay 2155 7thfloor (C1121ABG), Ciudad Autónoma de Buenos Aires, Argentina
| | - Jean Zwiller
- Laboratoire de Neurosciences Cognitives et Adaptatives, Université de Strasbourg, Strasbourg, France
| | - Ramon Bernabeu
- Department of Physiology and Institute of Physiology and Biophysics, School of Medicine, University of Buenos Aires, Paraguay 2155 7thfloor (C1121ABG), Ciudad Autónoma de Buenos Aires, Argentina.
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Rajeev R, Dwivedi AP, Sinha A, Agarwaal V, Dev RR, Kar A, Khosla S. Epigenetic interaction of microbes with their mammalian hosts. J Biosci 2021; 46:94. [PMID: 34728591 PMCID: PMC8550911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The interaction of microbiota with its host has the ability to alter the cellular functions of both, through several mechanisms. Recent work, from many laboratories including our own, has shown that epigenetic mechanisms play an important role in the alteration of these cellular functions. Epigenetics broadly refers to change in the phenotype without a corresponding change in the DNA sequence. This change is usually brought by epigenetic modifications of the DNA itself, the histone proteins associated with the DNA in the chromatin, non-coding RNA or the modifications of the transcribed RNA. These modifications, also known as epigenetic code, do not change the DNA sequence but alter the expression level of specific genes. Microorganisms seem to have learned how to modify the host epigenetic code and modulate the host transcriptome in their favour. In this review, we explore the literature that describes the epigenetic interaction of bacteria, fungi and viruses, with their mammalian hosts.
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Affiliation(s)
- Ramisetti Rajeev
- grid.145749.a0000 0004 1767 2735Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India ,grid.411639.80000 0001 0571 5193Graduate Studies, Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Ambey Prasad Dwivedi
- grid.145749.a0000 0004 1767 2735Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India ,grid.411639.80000 0001 0571 5193Graduate Studies, Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Anunay Sinha
- grid.145749.a0000 0004 1767 2735Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India ,grid.502122.60000 0004 1774 5631Graduate Studies, Regional Centre for Biotechnology (RCB), Faridabad, India
| | - Viplove Agarwaal
- grid.145749.a0000 0004 1767 2735Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
| | - Rachana Roshan Dev
- grid.145749.a0000 0004 1767 2735Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
| | - Anjana Kar
- grid.145749.a0000 0004 1767 2735Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
| | - Sanjeev Khosla
- grid.145749.a0000 0004 1767 2735Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India ,grid.417641.10000 0004 0504 3165Institute of Microbial Technology (IMTech), Chandigarh, India
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Li S, Tollefsbol TO. DNA methylation methods: Global DNA methylation and methylomic analyses. Methods 2020; 187:28-43. [PMID: 33039572 DOI: 10.1016/j.ymeth.2020.10.002] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 10/02/2020] [Accepted: 10/05/2020] [Indexed: 12/13/2022] Open
Abstract
DNA methylation provides a pivotal layer of epigenetic regulation in eukaryotes that has significant involvement for numerous biological processes in health and disease. The function of methylation of cytosine bases in DNA was originally proposed as a "silencing" epigenetic marker and focused on promoter regions of genes for decades. Improved technologies and accumulating studies have been extending our understanding of the roles of DNA methylation to various genomic contexts including gene bodies, repeat sequences and transcriptional start sites. The demand for comprehensively describing DNA methylation patterns spawns a diversity of DNA methylation profiling technologies that target its genomic distribution. These approaches have enabled the measurement of cytosine methylation from specific loci at restricted regions to single-base-pair resolution on a genome-scale level. In this review, we discuss the different DNA methylation analysis technologies primarily based on the initial treatments of DNA samples: bisulfite conversion, endonuclease digestion and affinity enrichment, involving methodology evolution, principles, applications, and their relative merits. This review may offer referable information for the selection of various platforms for genome-wide analysis of DNA methylation.
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Affiliation(s)
- Shizhao Li
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States.
| | - Trygve O Tollefsbol
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States; Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, United States; Nutrition Obesity Research Center, University of Alabama at Birmingham, Birmingham, AL, United States; Comprehensive Center for Healthy Aging, University of Alabama at Birmingham, Birmingham, AL, United States; Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL, United States.
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Nikolova EN, Stanfield RL, Dyson HJ, Wright PE. A Conformational Switch in the Zinc Finger Protein Kaiso Mediates Differential Readout of Specific and Methylated DNA Sequences. Biochemistry 2020; 59:1909-1926. [PMID: 32352758 PMCID: PMC7253346 DOI: 10.1021/acs.biochem.0c00253] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Recognition of the epigenetic mark 5-methylcytosine (mC) at CpG sites in DNA has emerged as a novel function of many eukaryotic transcription factors (TFs). It remains unclear why the sequence specificity of these TFs differs for CpG-methylated motifs and consensus motifs. Here, we dissect the structural and dynamic basis for this differential DNA binding specificity in the human zinc finger TF Kaiso, which exhibits high affinity for two consecutive mCpG sites in variable contexts and also for a longer, sequence-specific Kaiso binding site (KBS). By integrating structural analysis and DNA binding studies with targeted protein mutagenesis and nucleotide substitutions, we identify distinct mechanisms for readout of methylated and KBS motifs by Kaiso. We show that a key glutamate residue (E535), critical for mCpG site recognition, adopts different conformations in complexes with specific and methylated DNA. These conformational differences, together with intrinsic variations in DNA flexibility and/or solvation at TpG versus mCpG sites, contribute to the different DNA affinity and sequence specificity. With methylated DNA, multiple direct contacts between E535 and the 5' mCpG site dominate the binding affinity, allowing for tolerance of different flanking DNA sequences. With KBS, Kaiso employs E535 as part of an indirect screen of the 5' flanking sequence, relying on key tyrosine-DNA interactions to stabilize an optimal DNA conformation and select against noncognate sites. These findings demonstrate how TFs use conformational adaptation and exploit variations in DNA flexibility to achieve distinct DNA readout outcomes and target a greater variety of regulatory and epigenetic sites than previously appreciated.
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Li LT, Wang X, Zhu WT, Qian GW, Pei DS, Zheng JN. Reciprocal Role Of DNA Methylation And Sp1 Binding In Ki-67 Gene Transcription. Cancer Manag Res 2019; 11:9749-9759. [PMID: 31819613 PMCID: PMC6874502 DOI: 10.2147/cmar.s213769] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 10/16/2019] [Indexed: 01/26/2023] Open
Abstract
Purpose DNA methylation plays major regulatory roles in gene transcription. Our previous studies confirmed that Ki-67 promoter is hypomethylated and Sp1 is a transcriptional activator of Ki-67 gene in cancer cells. However, whether Sp1-mediated transcriptional activation of Ki-67 is related to its methylation has not been studied yet. Materials and methods In this study, we confirmed that methylated CpG binding protein 2 (MBD2) binding to methylated DNA hindered the binding of Sp1 to Ki-67 promoter and then repressed Ki-67 transcription through chromatin immunoprecipitation (ChIP) and quantitative real-time PCR (qRT-PCR). Co-immunoprecipitation (Co-IP), ChIP, methylation-specific PCR (MS-PCR) and Western blot were utilized to analyze the effects of Sp1 binding to Ki-67 promoter on its methylation status. Results Less DNA methyltransferase 1 (DNMT1) bound to the Ki-67 promoter in MKN45 cells than in HK-2 cells. Histone acetyltransferase p300 that was recruited by Sp1 to Ki-67 promoter could attenuate the methylation level of Ki-67 promoter. Furthermore, higher expression of Sp1 and Ki-67 was related to the overall survival (OS), first progression (FP) and post-progression survival (PPS) in gastric cancer by scrutinizing bioinformatics datasets. Conclusion Taken together, our findings suggested that hypomethylation of Ki-67 promoter enhanced the binding of Sp1, which in turn maintained hypomethylation of promoter, leading to increase Ki-67 expression in cancer cells. Sp1 and Ki-67 could act promising prognostic biomarkers for clinical diagnosis and treatment of cancer.
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Affiliation(s)
- Lian-Tao Li
- Cancer Institute, Xuzhou Medical University, Xuzhou 221000, People's Republic of China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221000, People's Republic of China.,Department of Radiation Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221000, People's Republic of China
| | - Xun Wang
- Department of Interventional Radiology, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221000, People's Republic of China
| | - Wen-Tao Zhu
- Department of Pathology, Xuzhou Medical University, Xuzhou 221000, People's Republic of China
| | - Guo-Wei Qian
- Department of Medical Oncology, Shanghai Sixth People's Hospital, Shanghai 200000, People's Republic of China
| | - Dong-Sheng Pei
- Cancer Institute, Xuzhou Medical University, Xuzhou 221000, People's Republic of China.,Department of Pathology, Xuzhou Medical University, Xuzhou 221000, People's Republic of China
| | - Jun-Nian Zheng
- Cancer Institute, Xuzhou Medical University, Xuzhou 221000, People's Republic of China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221000, People's Republic of China
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19
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Hodges AJ, Hudson NO, Buck-Koehntop BA. Cys 2His 2 Zinc Finger Methyl-CpG Binding Proteins: Getting a Handle on Methylated DNA. J Mol Biol 2019:S0022-2836(19)30567-4. [PMID: 31628952 DOI: 10.1016/j.jmb.2019.09.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/13/2019] [Accepted: 09/16/2019] [Indexed: 12/12/2022]
Abstract
DNA methylation is an essential epigenetic modification involved in the maintenance of genomic stability, preservation of cellular identity, and regulation of the transcriptional landscape needed to maintain cellular function. In an increasing number of disease conditions, DNA methylation patterns are inappropriately distributed in a manner that supports the disease phenotype. Methyl-CpG binding proteins (MBPs) are specialized transcription factors that read and translate methylated DNA signals into recruitment of protein assemblies that can alter local chromatin architecture and transcription. MBPs thus play a key intermediary role in gene regulation for both normal and diseased cells. Here, we highlight established and potential structure-function relationships for the best characterized members of the zinc finger (ZF) family of MBPs in propagating DNA methylation signals into downstream cellular responses. Current and future investigations aimed toward expanding our understanding of ZF MBP cellular roles will provide needed mechanistic insight into normal and disease state functions, as well as afford evaluation for the potential of these proteins as epigenetic-based therapeutic targets.
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Affiliation(s)
- Amelia J Hodges
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT, 84112, USA
| | - Nicholas O Hudson
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT, 84112, USA
| | - Bethany A Buck-Koehntop
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT, 84112, USA.
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20
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Li S, Chen M, Li Y, Tollefsbol TO. Prenatal epigenetics diets play protective roles against environmental pollution. Clin Epigenetics 2019; 11:82. [PMID: 31097039 PMCID: PMC6524340 DOI: 10.1186/s13148-019-0659-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 03/27/2019] [Indexed: 12/12/2022] Open
Abstract
It is thought that germ cells and preimplantation embryos during development are most susceptible to endogenous and exogenous environmental factors because the epigenome in those cells is undergoing dramatic elimination and reconstruction. Exposure to environmental factors such as nutrition, climate, stress, pathogens, toxins, and even social behavior during gametogenesis and early embryogenesis has been shown to influence disease susceptibility in the offspring. Early-life epigenetic modifications, which determine the expression of genetic information stored in the genome, are viewed as one of the general mechanisms linking prenatal exposure and phenotypic changes later in life. From atmospheric pollution, endocrine-disrupting chemicals to heavy metals, research increasingly suggests that environmental pollutions have already produced significant consequences on human health. Moreover, mounting evidence now links such pollution to relevant modification in the epigenome. The epigenetics diet, referring to a class of bioactive dietary compounds such as isothiocyanates in broccoli, genistein in soybean, resveratrol in grape, epigallocatechin-3-gallate in green tea, and ascorbic acid in fruits, has been shown to modify the epigenome leading to beneficial health outcomes. This review will primarily focus on the causes and consequences of prenatal environment pollution exposure on the epigenome, and the potential protective role of the epigenetics diet, which could play a central role in neutralizing epigenomic aberrations against environmental pollutions.
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Affiliation(s)
- Shizhao Li
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Min Chen
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Yuanyuan Li
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL, USA.
- Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA.
- Nutrition Obesity Research Center, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Trygve O Tollefsbol
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA.
- Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA.
- Nutrition Obesity Research Center, University of Alabama at Birmingham, Birmingham, AL, USA.
- Comprehensive Center for Healthy Aging, University of Alabama at Birmingham, Birmingham, AL, USA.
- Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL, USA.
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21
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Cancer as an Embryological Phenomenon and Its Developmental Pathways: A Hypothesis regarding the Contribution of the Noncanonical Wnt Pathway. ScientificWorldJournal 2019; 2019:4714781. [PMID: 30940992 PMCID: PMC6421044 DOI: 10.1155/2019/4714781] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 12/18/2018] [Accepted: 01/29/2019] [Indexed: 02/07/2023] Open
Abstract
For gastrulation to occur in human embryos, a mechanism that simultaneously regulates many different processes, such as cell differentiation, proliferation, migration, and invasion, is required to consistently and effectively create a human being during embryonic morphogenesis. The striking similarities in the processes of cancer and gastrulation have prompted speculation regarding the developmental pathways involved in their regulation. One of the fundamental requirements for the developmental pathways in gastrulation and cancer is the ability to respond to environmental stimuli, and it has been proposed that the Kaiso and noncanonical Wnt pathways participate in the mechanisms regulating these developmental pathways. In particular, these pathways might also explain the notable differences in invasive capacity between cancers of endodermal and mesodermal origins and cancers of ectodermal origin. Nevertheless, the available information indicates that cancer is an abnormal state of adult human cells in which developmental pathways are reactivated in inappropriate temporal and spatial contexts.
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22
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Hiramatsu S, Watanabe KS, Zeggar S, Asano Y, Miyawaki Y, Yamamura Y, Katsuyama E, Katsuyama T, Watanabe H, Takano-Narazaki M, Matsumoto Y, Kawabata T, Sada KE, Wada J. Regulation of Cathepsin E gene expression by the transcription factor Kaiso in MRL/lpr mice derived CD4+ T cells. Sci Rep 2019; 9:3054. [PMID: 30816218 PMCID: PMC6395770 DOI: 10.1038/s41598-019-38809-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 11/20/2018] [Indexed: 01/18/2023] Open
Abstract
Global DNA hypomethylation in CD4+ cells in systemic lupus erythematosus (SLE) was suggested to play a key role in the pathogenesis. To identify new methylation-sensitive genes, we integrated genome-wide DNA methylation and mRNA profiling data in CD4+ cells of MRL/lpr (MRL) and C57BL6/J (B6) mice. We identified Cathepsin E (Ctse), in which 13 methyl-CpGs within 583 bp region of intron 1 were hypomethylated, and Ctse mRNA upregulated in MRL compared with B6 mice. One of methyl-CpGs, mCGCG was 93.3 ± 2.05% methylated in B6 mice, while 80.0 ± 6.2% methylated and mutated to CGGG in MRL mice. Kaiso is known to bind to mCGCG and we hypothesized that it represses expression of Ctse in B6 mice. The binding of Kaiso to mCGCG site in B6 mice was reduced in MRL mice revealed by ChIP-PCR. EL4 cells treated with 5-azaC and/or Trichostatin A showed the suppression of binding of Kaiso to mCGCG motif by ChIP-PCR and the overexpression of Ctse was demonstrated by qPCR. Ctse gene silencing by siRNA in EL4 cells resulted in reduction of IL-10 secretion. The hypomethylation of mCGCG motif, reduced recruitment of Kaiso, and increased expression of Ctse and Il-10 in CD4+ cells may be involved in the pathogenesis of SLE.
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Affiliation(s)
- Sumie Hiramatsu
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Okayama, 700-8558, Japan
| | - Katsue S Watanabe
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Okayama, 700-8558, Japan
| | - Sonia Zeggar
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Okayama, 700-8558, Japan
| | - Yosuke Asano
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Okayama, 700-8558, Japan
| | - Yoshia Miyawaki
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Okayama, 700-8558, Japan
| | - Yuriko Yamamura
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Okayama, 700-8558, Japan
| | - Eri Katsuyama
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Okayama, 700-8558, Japan
| | - Takayuki Katsuyama
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Okayama, 700-8558, Japan
| | - Haruki Watanabe
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Okayama, 700-8558, Japan
| | - Mariko Takano-Narazaki
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Okayama, 700-8558, Japan
| | - Yoshinori Matsumoto
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Okayama, 700-8558, Japan
| | - Tomoko Kawabata
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Okayama, 700-8558, Japan
| | - Ken-Ei Sada
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Okayama, 700-8558, Japan
| | - Jun Wada
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Okayama, 700-8558, Japan.
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Thompson JJ, Kaur R, Sosa CP, Lee JH, Kashiwagi K, Zhou D, Robertson KD. ZBTB24 is a transcriptional regulator that coordinates with DNMT3B to control DNA methylation. Nucleic Acids Res 2018; 46:10034-10051. [PMID: 30085123 PMCID: PMC6212772 DOI: 10.1093/nar/gky682] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 06/29/2018] [Accepted: 07/17/2018] [Indexed: 12/12/2022] Open
Abstract
The interplay between transcription factors and epigenetic writers like the DNA methyltransferases (DNMTs), and the role of this interplay in gene expression, is being increasingly appreciated. ZBTB24, a poorly characterized zinc-finger protein, or the de novo methyltransferase DNMT3B, when mutated, cause Immunodeficiency, Centromere Instability, and Facial anomalies (ICF) syndrome, suggesting an underlying mechanistic link. Chromatin immunoprecipitation coupled with loss-of-function approaches in model systems revealed common loci bound by ZBTB24 and DNMT3B, where they function to regulate gene body methylation. Genes coordinately regulated by ZBTB24 and DNMT3B are enriched for molecular mechanisms essential for cellular homeostasis, highlighting the importance of the ZBTB24-DNMT3B interplay in maintaining epigenetic patterns required for normal cellular function. We identify a ZBTB24 DNA binding motif, which is contained within the promoters of most of its transcriptional targets, including CDCA7, AXIN2, and OSTC. Direct binding of ZBTB24 at the promoters of these genes targets them for transcriptional activation. ZBTB24 binding at the promoters of RNF169 and CAMKMT, however, targets them for transcriptional repression. The involvement of ZBTB24 targets in diverse cellular programs, including the VDR/RXR and interferon regulatory pathways, suggest that ZBTB24's role as a transcriptional regulator is not restricted to immune cells.
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Affiliation(s)
- Joyce J Thompson
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, 200 First Street SW, Stabile 12-58, Rochester, MN 55905, USA
| | - Rupinder Kaur
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, 200 First Street SW, Stabile 12-58, Rochester, MN 55905, USA
| | - Carlos P Sosa
- Clinical Genome Sequencing Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Stabile12-58, Rochester, MN 55905, USA
| | - Jeong-Heon Lee
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
- Epigenomics Translational Program, Mayo Clinic, Rochester, MN 55905, USA
| | - Katsunobu Kashiwagi
- Department of Physiology II, Nara Medical University, Kashihara, Nara 634-8521, Japan
| | - Dan Zhou
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Keith D Robertson
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, 200 First Street SW, Stabile 12-58, Rochester, MN 55905, USA
- Epigenomics Translational Program, Mayo Clinic, Rochester, MN 55905, USA
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24
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Hudson NO, Whitby FG, Buck-Koehntop BA. Structural insights into methylated DNA recognition by the C-terminal zinc fingers of the DNA reader protein ZBTB38. J Biol Chem 2018; 293:19835-19843. [PMID: 30355731 DOI: 10.1074/jbc.ra118.005147] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 10/16/2018] [Indexed: 02/05/2023] Open
Abstract
Methyl-CpG-binding proteins (MBPs) are selective readers of DNA methylation that play an essential role in mediating cellular transcription processes in both normal and diseased cells. This physiological function of MBPs has generated significant interest in understanding the mechanisms by which these proteins read and interpret DNA methylation signals. Zinc finger and BTB domain-containing 38 (ZBTB38) represents one member of the zinc finger (ZF) family of MBPs. We recently demonstrated that the C-terminal ZFs of ZBTB38 exhibit methyl-selective DNA binding within the ((A/G)TmCG(G/A)(mC/T)(G/A)) context both in vitro and within cells. Here we report the crystal structure of the first four C-terminal ZBTB38 ZFs (ZFs 6-9) in complex with the previously identified methylated consensus sequence at 1.75 Å resolution. From the structure, methyl-selective binding is preferentially localized at the 5' mCpG site of the bound DNA, which is facilitated through a series of base-specific interactions from residues within the α-helices of ZF7 and ZF8. ZF6 and ZF9 primarily stabilize ZF7 and ZF8 to facilitate the core base-specific interactions. Further structural and biochemical analyses, including solution NMR spectroscopy and electrophoretic mobility gel shift assays, revealed that the C-terminal ZFs of ZBTB38 utilize an alternative mode of mCpG recognition from the ZF MBPs structurally evaluated to date. Combined, these findings provide insight into the mechanism by which this ZF domain of ZBTB38 selectively recognizes methylated CpG sites and expands our understanding of how ZF-containing proteins can interpret this essential epigenetic mark.
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Affiliation(s)
| | - Frank G Whitby
- Biochemistry, University of Utah, Salt Lake City, Utah 84112
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25
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HPV16-Related Cervical Cancers and Precancers Have Increased Levels of Host Cell DNA Methylation in Women Living with HIV. Int J Mol Sci 2018; 19:ijms19113297. [PMID: 30360578 PMCID: PMC6274896 DOI: 10.3390/ijms19113297] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 10/19/2018] [Accepted: 10/19/2018] [Indexed: 02/07/2023] Open
Abstract
Data on human papillomavirus (HPV) type-specific cervical cancer risk in women living with human immunodeficiency virus (WLHIV) are needed to understand HPV–HIV interaction and to inform prevention programs for this population. We assessed high-risk HPV type-specific prevalence in cervical samples from 463 WLHIV from South Africa with different underlying, histologically confirmed stages of cervical disease. Secondly, we investigated DNA hypermethylation of host cell genes ASCL1, LHX8, and ST6GALNAC5, as markers of advanced cervical disease, in relation to type-specific HPV infection. Overall, HPV prevalence was 56% and positivity increased with severity of cervical disease: from 28.0% in cervical intraepithelial neoplasia (CIN) grade 1 or less (≤CIN1) to 100% in invasive cervical cancer (ICC). HPV16 was the most prevalent type, accounting for 9.9% of HPV-positive ≤CIN1, 14.3% of CIN2, 31.7% of CIN3, and 45.5% of ICC. HPV16 was significantly more associated with ICC and CIN3 than with ≤CIN1 (adjusted for age, ORMH 7.36 (95% CI 2.33–23.21) and 4.37 (95% CI 1.81–10.58), respectively), as opposed to non-16 high-risk HPV types. Methylation levels of ASCL1, LHX8, and ST6GALNAC5 in cervical scrapes of women with CIN3 or worse (CIN3+) associated with HPV16 were significantly higher compared with methylation levels in cervical scrapes of women with CIN3+ associated with non-16 high-risk HPV types (p-values 0.017, 0.019, and 0.026, respectively). When CIN3 and ICC were analysed separately, the same trend was observed, but the differences were not significant. Our results confirm the key role that HPV16 plays in uterine cervix carcinogenesis, and suggest that the evaluation of host cell gene methylation levels may monitor the progression of cervical neoplasms also in WLHIV.
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26
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Hudson NO, Buck-Koehntop BA. Zinc Finger Readers of Methylated DNA. Molecules 2018; 23:E2555. [PMID: 30301273 PMCID: PMC6222495 DOI: 10.3390/molecules23102555] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/03/2018] [Accepted: 10/05/2018] [Indexed: 01/07/2023] Open
Abstract
DNA methylation is a prevalent epigenetic modification involved in regulating a number of essential cellular processes, including genomic accessibility and transcriptional outcomes. As such, aberrant alterations in global DNA methylation patterns have been associated with a growing number of disease conditions. Nevertheless, the full mechanisms by which DNA methylation information is interpreted and translated into genomic responses is not yet fully understood. Methyl-CpG binding proteins (MBPs) function as important mediators of this essential process by selectively reading DNA methylation signals and translating this information into down-stream cellular outcomes. The Cys₂His₂ zinc finger scaffold is one of the most abundant DNA binding motifs found within human transcription factors, yet only a few zinc finger containing proteins capable of conferring selectivity for mCpG over CpG sites have been characterized. This review summarizes our current structural understanding for the mechanisms by which the zinc finger MBPs evaluated to date read this essential epigenetic mark. Further, some of the biological implications for mCpG readout elicited by this family of MBPs are discussed.
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Affiliation(s)
- Nicholas O Hudson
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112-0850, USA.
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27
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Kremer WW, Van Zummeren M, Novianti PW, Richter KL, Verlaat W, Snijders PJF, Heideman DAM, Steenbergen RDM, Dreyer G, Meijer CJLM. Detection of hypermethylated genes as markers for cervical screening in women living with HIV. J Int AIDS Soc 2018; 21:e25165. [PMID: 30101434 PMCID: PMC6088247 DOI: 10.1002/jia2.25165] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 07/02/2018] [Indexed: 01/01/2023] Open
Abstract
INTRODUCTION To evaluate the performance of hypermethylation analysis of ASCL1, LHX8 and ST6GALNAC5 in physician-taken cervical scrapes for detection of cervical cancer and cervical intraepithelial neoplasia (CIN) grade 3 in women living with HIV (WLHIV) in South Africa. METHODS Samples from a prospective observational cohort study were used for these analyses. Two cohorts were included: a cohort of WLHIV who were invited for cervical screening (n = 321) and a gynaecologic outpatient cohort of women referred for evaluation of abnormal cytology or biopsy proven cervical cancer (n = 108, 60% HIV seropositive). Cervical scrapes collected from all subjects were analysed for hypermethylation of ASCL1, LHX8 and ST6GALNAC5 by multiplex quantitative methylation specific PCR (qMSP). Histology endpoints were available for all study subjects. RESULTS Hypermethylation levels of ASCL1, LHX8 and ST6GALNAC5 increased with severity of cervical disease. The performance for detection of CIN3 or worse (CIN3+ ) as assessed by the area under the receiver operating characteristic (ROC) curves (AUC) was good for ASCL1 and LHX8 (AUC 0.79 and 0.81 respectively), and moderate for ST6GALNAC5 (AUC 0.71). At a threshold corresponding to 75% specificity, CIN3+ sensitivity was 72.1% for ASCL1 and 73.8% for LHX8 and all samples from women with cervical cancer scored positive for these two markers. CONCLUSIONS Hypermethylation analysis of ASCL1 or LHX8 in cervical scrape material of WLHIV detects all cervical carcinomas with an acceptable sensitivity and good specificity for CIN3+ , warranting further exploration of these methylation markers as a stand-alone test for cervical screening in low-resource settings.
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Affiliation(s)
- Wieke W Kremer
- Department of PathologyCancer Center AmsterdamVU University Medical CenterAmsterdamThe Netherlands
| | - Marjolein Van Zummeren
- Department of PathologyCancer Center AmsterdamVU University Medical CenterAmsterdamThe Netherlands
| | - Putri W Novianti
- Department of PathologyCancer Center AmsterdamVU University Medical CenterAmsterdamThe Netherlands
- Department of Epidemiology and BiostatisticsVU University Medical CenterAmsterdamThe Netherlands
| | - Karin L Richter
- Department of Medical VirologyUniversity of Pretoria and National Health Laboratory ServicesPretoriaSouth Africa
| | - Wina Verlaat
- Department of PathologyCancer Center AmsterdamVU University Medical CenterAmsterdamThe Netherlands
| | - Peter JF Snijders
- Department of PathologyCancer Center AmsterdamVU University Medical CenterAmsterdamThe Netherlands
| | - Daniëlle AM Heideman
- Department of PathologyCancer Center AmsterdamVU University Medical CenterAmsterdamThe Netherlands
| | - Renske DM Steenbergen
- Department of PathologyCancer Center AmsterdamVU University Medical CenterAmsterdamThe Netherlands
| | - Greta Dreyer
- Department of Obstetrics and GynaecologyUniversity of PretoriaPretoriaSouth Africa
| | - Chris JLM Meijer
- Department of PathologyCancer Center AmsterdamVU University Medical CenterAmsterdamThe Netherlands
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Nikolova EN, Stanfield RL, Dyson HJ, Wright PE. CH···O Hydrogen Bonds Mediate Highly Specific Recognition of Methylated CpG Sites by the Zinc Finger Protein Kaiso. Biochemistry 2018; 57:2109-2120. [PMID: 29546986 PMCID: PMC5893398 DOI: 10.1021/acs.biochem.8b00065] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Many eukaryotic transcription factors recognize the epigenetic marker 5-methylcytosine (mC) at CpG sites in DNA. Despite their structural diversity, methyl-CpG-binding proteins (MBPs) share a common mode of recognition of mC methyl groups that involves hydrophobic pockets and weak hydrogen bonds of the CH···O type. The zinc finger protein Kaiso possesses a remarkably high specificity for methylated over unmethylated CpG sites. A key contribution to this specificity is provided by glutamate 535 (E535), which is optimally positioned to form multiple interactions with mCpG, including direct CH···O hydrogen bonds. To examine the role of E535 and CH···O hydrogen bonding in the preferential recognition of mCpG sites, we determined the structures of wild type Kaiso (WT) and E535 mutants and characterized their interactions with methylated DNA by nuclear magnetic resonance spectroscopy (NMR), X-ray crystallography, and in vitro protein-DNA binding assays. Our data show that Kaiso favors an mCpG over a CpG site by 2 orders of magnitude in affinity and that an important component of this effect is the presence of hydrophobic and CH···O contacts involving E535. Moreover, we present the first direct evidence for formation of a CH···O hydrogen bond between an MBP and 5-methylcytosine by using experimental (NMR) and quantum mechanical chemical shift analysis of the mC methyl protons. Together, our findings uncover a critical function of methyl-specific interactions, including CH···O hydrogen bonds, that optimize the specificity and affinity of MBPs for methylated DNA and contribute to the precise control of gene expression.
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Naciri I, Roussel-Gervais A, Defossez PA, Kirsh O. [Unexpected roles for a methyl-binding protein in cancer]. Med Sci (Paris) 2017; 33:714-716. [PMID: 28945554 DOI: 10.1051/medsci/20173308009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Ikrame Naciri
- Équipe « Dynamique de la méthylation de l'ADN des génomes eucaryotes », Centre épigénétique et destin cellulaire, UMR7216 CNRS, université Paris Diderot, université Sorbonne Paris Cité (USPC), 35, rue Hélène Brion, 75205 Paris Cedex 13, France
| | - Audrey Roussel-Gervais
- Équipe « Dynamique de la méthylation de l'ADN des génomes eucaryotes », Centre épigénétique et destin cellulaire, UMR7216 CNRS, université Paris Diderot, université Sorbonne Paris Cité (USPC), 35, rue Hélène Brion, 75205 Paris Cedex 13, France - Département de pathologie et immunologie, centre médical universitaire, université de Genève, Genève, Suisse
| | - Pierre-Antoine Defossez
- Équipe « Dynamique de la méthylation de l'ADN des génomes eucaryotes », Centre épigénétique et destin cellulaire, UMR7216 CNRS, université Paris Diderot, université Sorbonne Paris Cité (USPC), 35, rue Hélène Brion, 75205 Paris Cedex 13, France
| | - Olivier Kirsh
- Équipe « Dynamique de la méthylation de l'ADN des génomes eucaryotes », Centre épigénétique et destin cellulaire, UMR7216 CNRS, université Paris Diderot, université Sorbonne Paris Cité (USPC), 35, rue Hélène Brion, 75205 Paris Cedex 13, France
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Methyl-CpG-Binding Protein MBD1 Regulates Neuronal Lineage Commitment through Maintaining Adult Neural Stem Cell Identity. J Neurosci 2017; 37:523-536. [PMID: 28100736 DOI: 10.1523/jneurosci.1075-16.2016] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 10/31/2016] [Accepted: 11/22/2016] [Indexed: 01/09/2023] Open
Abstract
Methyl-CpG-binding domain 1 (MBD1) belongs to a family of methyl-CpG-binding proteins that are epigenetic "readers" linking DNA methylation to transcriptional regulation. MBD1 is expressed in neural stem cells residing in the dentate gyrus of the adult hippocampus (aNSCs) and MBD1 deficiency leads to reduced neuronal differentiation, impaired neurogenesis, learning deficits, and autism-like behaviors in mice; however, the precise function of MBD1 in aNSCs remains unexplored. Here, we show that MBD1 is important for maintaining the integrity and stemness of NSCs, which is critical for their ability to generate neurons. MBD1 deficiency leads to the accumulation of undifferentiated NSCs and impaired transition into the neuronal lineage. Transcriptome analysis of neural stem and progenitor cells isolated directly from the dentate gyrus of MBD1 mutant (KO) and WT mice showed that gene sets related to cell differentiation, particularly astrocyte lineage genes, were upregulated in KO cells. We further demonstrated that, in NSCs, MBD1 binds and represses directly specific genes associated with differentiation. Our results suggest that MBD1 maintains the multipotency of NSCs by restraining the onset of differentiation genes and that untimely expression of these genes in MBD1-deficient stem cells may interfere with normal cell lineage commitment and cause the accumulation of undifferentiated cells. Our data reveal a novel role for MBD1 in stem cell maintenance and provide insight into how epigenetic regulation contributes to adult neurogenesis and the potential impact of its dysregulation. SIGNIFICANCE STATEMENT Adult neural stem cells (aNSCs) in the hippocampus self-renew and generate neurons throughout life. We show that methyl-CpG-binding domain 1 (MBD1), a DNA methylation "reader," is important for maintaining the integrity of NSCs, which is critical for their neurogenic potency. Our data reveal a novel role for MBD1 in stem cell maintenance and provide insight into how epigenetic regulation preserves the multipotency of stem cells for subsequent differentiation.
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Abstract
A growing epidemic of nonalcoholic fatty liver disease (NAFLD) is paralleling the increase in the incidence of obesity and diabetes mellitus in countries that consume a Western diet. As NAFLD can lead to life-threatening conditions such as cirrhosis and hepatocellular carcinoma, an understanding of the factors that trigger its development and pathological progression is needed. Although by definition this disease is not associated with alcohol consumption, exposure to environmental agents that have been linked to other diseases might have a role in the development of NAFLD. Here, we focus on one class of these agents, endocrine-disrupting chemicals (EDCs), and their potential to influence the initiation and progression of a cascade of pathological conditions associated with hepatic steatosis (fatty liver). Experimental studies have revealed several potential mechanisms by which EDC exposure might contribute to disease pathogenesis, including the modulation of nuclear hormone receptor function and the alteration of the epigenome. However, many questions remain to be addressed about the causal link between acute and chronic EDC exposure and the development of NAFLD in humans. Future studies that address these questions hold promise not only for understanding the linkage between EDC exposure and liver disease but also for elucidating the molecular mechanisms that underpin NAFLD, which in turn could facilitate the development of new prevention and treatment opportunities.
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Affiliation(s)
- Charles E Foulds
- Department of Molecular and Cellular Biology, Baylor College of Medicine
- Center for Precision Environmental Health, Baylor College of Medicine
| | - Lindsey S Treviño
- Department of Molecular and Cellular Biology, Baylor College of Medicine
- Center for Precision Environmental Health, Baylor College of Medicine
| | - Brian York
- Department of Molecular and Cellular Biology, Baylor College of Medicine
- Dan L. Duncan Cancer Center, Baylor College of Medicine
| | - Cheryl L Walker
- Department of Molecular and Cellular Biology, Baylor College of Medicine
- Center for Precision Environmental Health, Baylor College of Medicine
- Dan L. Duncan Cancer Center, Baylor College of Medicine
- Department of Medicine, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, USA
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Li D, Palanca AMS, Won SY, Gao L, Feng Y, Vashisht AA, Liu L, Zhao Y, Liu X, Wu X, Li S, Le B, Kim YJ, Yang G, Li S, Liu J, Wohlschlegel JA, Guo H, Mo B, Chen X, Law JA. The MBD7 complex promotes expression of methylated transgenes without significantly altering their methylation status. eLife 2017; 6. [PMID: 28452714 PMCID: PMC5462541 DOI: 10.7554/elife.19893] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 04/24/2017] [Indexed: 12/23/2022] Open
Abstract
DNA methylation is associated with gene silencing in eukaryotic organisms. Although pathways controlling the establishment, maintenance and removal of DNA methylation are known, relatively little is understood about how DNA methylation influences gene expression. Here we identified a METHYL-CpG-BINDING DOMAIN 7 (MBD7) complex in Arabidopsis thaliana that suppresses the transcriptional silencing of two LUCIFERASE (LUC) reporters via a mechanism that is largely downstream of DNA methylation. Although mutations in components of the MBD7 complex resulted in modest increases in DNA methylation concomitant with decreased LUC expression, we found that these hyper-methylation and gene expression phenotypes can be genetically uncoupled. This finding, along with genome-wide profiling experiments showing minimal changes in DNA methylation upon disruption of the MBD7 complex, places the MBD7 complex amongst a small number of factors acting downstream of DNA methylation. This complex, however, is unique as it functions to suppress, rather than enforce, DNA methylation-mediated gene silencing. DOI:http://dx.doi.org/10.7554/eLife.19893.001
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Affiliation(s)
- Dongming Li
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, United States.,School of Life Sciences, Lanzhou University, Lanzhou, China.,State Key Laboratory of Plant Cell and Chromosome Engineering, Hebei Collaboration Innovation Center for Cell Signaling, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Ana Marie S Palanca
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, United States
| | - So Youn Won
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, United States
| | - Lei Gao
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, United States.,College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen University, Shenzhen, China
| | - Ying Feng
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, United States.,State Key Laboratory of Protein and Plant Gene research, College of Life Sciences, Peking University, Beijing, China
| | - Ajay A Vashisht
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, United States
| | - Li Liu
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, United States
| | - Yuanyuan Zhao
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, United States
| | - Xigang Liu
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, United States.,State Key Laboratory of Plant Cell and Chromosome Engineering, Hebei Collaboration Innovation Center for Cell Signaling, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Xiuyun Wu
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, United States.,Laboratory of Molecular Biology and Protein Science, Laboratory of the Ministry of Education, Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing, China
| | - Shaofang Li
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, United States
| | - Brandon Le
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, United States
| | - Yun Ju Kim
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, United States
| | - Guodong Yang
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, United States
| | - Shengben Li
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, United States
| | - Jinyuan Liu
- Laboratory of Molecular Biology and Protein Science, Laboratory of the Ministry of Education, Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing, China
| | - James A Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, United States
| | - Hongwei Guo
- State Key Laboratory of Protein and Plant Gene research, College of Life Sciences, Peking University, Beijing, China
| | - Beixin Mo
- College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen University, Shenzhen, China
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, United States.,Howard Hughes Medical Institute, University of California, Riverside, United States
| | - Julie A Law
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, United States
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Vineis P, Chatziioannou A, Cunliffe VT, Flanagan JM, Hanson M, Kirsch-Volders M, Kyrtopoulos S. Epigenetic memory in response to environmental stressors. FASEB J 2017; 31:2241-2251. [PMID: 28280003 DOI: 10.1096/fj.201601059rr] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 02/21/2017] [Indexed: 12/22/2022]
Abstract
Exposure to environmental stressors, toxicants, and nutrient deficiencies can affect DNA in several ways. Some exposures cause damage and alter the structure of DNA, but there is increasing evidence that the same or other environmental exposures, including those that occur during fetal development in utero, can cause epigenetic effects that modulate DNA function and gene expression. Some epigenetic changes to DNA that affect gene transcription are at least partially reversible (i.e., they can be enzymatically reversed after cessation of exposure to environmental agents), but some epigenetic modifications seem to persist, even for decades. To explain the effects of early life experiences (such as famine and exposures to other stressors) on the long-term persistence of specific patterns of epigenetic modifications, such as DNA methylation, we propose an analogy with immune memory. We propose that an epigenetic memory can be established and maintained in self-renewing stem cell compartments. We suggest that the observations on early life effects on adult diseases and the persistence of methylation changes in smokers support our hypothesis, for which a mechanistic basis, however, needs to be further clarified. We outline a new model based on methylation changes. Although these changes seem to be mainly adaptive, they are also implicated in the pathogenesis and onset of diseases, depending on individual genotypic background and types of subsequent exposures. Elucidating the relationships between the adaptive and maladaptive consequences of the epigenetic modifications that result from complex environmental exposures is a major challenge for current and future research in epigenetics.-Vineis, P., Chatziioannou, A., Cunliffe, V. T., Flanagan, J. M., Hanson, M., Kirsch-Volders, M., Kyrtopoulos, S. Epigenetic memory in response to environmental stressors.
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Affiliation(s)
- Paolo Vineis
- Medical Research Council-Public Health England Center for Environment and Health, Imperial College London, London, United Kingdom;
| | - Aristotelis Chatziioannou
- Institute of Biology, Medicinal Chemistry, and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Vincent T Cunliffe
- Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
| | - James M Flanagan
- Epigenetics Unit, Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Mark Hanson
- Institute of Developmental Sciences, University Hospital Southampton, University of Southampton, United Kingdom
| | | | - Soterios Kyrtopoulos
- Institute of Biology, Medicinal Chemistry, and Biotechnology, National Hellenic Research Foundation, Athens, Greece
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Abstract
Increasing evidence suggests that epigenetic modifications, including changes in DNA methylation, covalent modifications of histone tails, and gene silencing mediated by non-coding RNA molecules, play a substantial role in the pathogenesis of autoimmune disorders and might be seen as the result of environmental insults that trigger these conditions. Studies in cells and tissues of patients with autoimmune thyroid diseases (AITD), and particularly in Graves' disease (GD) and Hashimoto's thyroiditis (HT), are increasingly revealing altered epigenetic marks and resultant deregulation of gene expression levels, but the available data are still limited to be translated into the clinical settings. Particularly, genome-wide methylation and histone tail modification screenings are limited to a few studies in GD patients, and the diagnostic values of the observed epigenetic changes or their potential prognostic utility are still unclear. Similarly, data concerning microRNA expression in AITD patients are largely descriptive and not yet translated into the clinics. In addition, studies relating certain environmental exposures to specific epigenetic changes in AITD and studies evaluating the crosstalk between different epigenetic mechanisms are largely missing. In summary, despite that there is a clear evidence of epigenetic impairment in AITD, further research is required for a better understanding of the epigenetic networks involved in disease pathogenesis, thereby opening the way for potential diagnostic and prognostic tools, as well as for epigenetic interventions in the patients.
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Affiliation(s)
- Fabio Coppedè
- Department of Translational Research and New Technologies in Medicine and Surgery, Section of Medical Genetics, University of Pisa, Pisa, Italy
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36
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Luttmer R, De Strooper LMA, Steenbergen RDM, Berkhof J, Snijders PJF, Heideman DAM, Meijer CJLM. Management of high-risk HPV-positive women for detection of cervical (pre)cancer. Expert Rev Mol Diagn 2016; 16:961-74. [PMID: 27459506 DOI: 10.1080/14737159.2016.1217157] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
INTRODUCTION Primary HPV-testing has been shown to provide a superior detection of women at risk of cervical (pre)cancer compared to cytology-based screening. However, as most high-risk HPV infections are harmless, additional triage testing of HPV-positive women is necessary to identify those with cervical (pre)cancer. In this paper, we compare the performance, advantages and limitations of clinically relevant available triage strategies for HPV-positive women. AREAS COVERED Many different colposcopy triage strategies, comprising both microscopy-based and molecular (virus/host-related) markers, have been suggested: Pap cytology, p16/Ki-67 dual-stained cytology, HPV16/18 genotyping, viral DNA methylation and host cell DNA methylation. Literature search was limited to triage strategies that have achieved at least phase 2 of the five-phase framework for biomarker development and studies including large cohorts (≥100 hrHPV-positive women). Triage markers were stratified by sample type (cervical scrape, self-collected sample) and by study population (screening, non-attendee, referral). Expert commentary: At present, repeat Pap cytology and Pap cytology combined with HPV16/18 genotyping are the only triage strategies that have been robustly shown to be ready for implementation. Other strategies such as p16/Ki-67 dual-stained cytology and host cell DNA methylation analysis, with or without additional HPV16/18 genotyping, are attractive options for the near future.
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Affiliation(s)
- Roosmarijn Luttmer
- a Department of Pathology , VU University Medical Center , Amsterdam , the Netherlands.,b Department of Obstetrics & Gynecology , Diakonessenhuis , Utrecht , the Netherlands
| | - Lise M A De Strooper
- a Department of Pathology , VU University Medical Center , Amsterdam , the Netherlands
| | | | - Johannes Berkhof
- c Department of Epidemiology & Biostatistics , VU University Medical Center , Amsterdam , the Netherlands
| | - Peter J F Snijders
- a Department of Pathology , VU University Medical Center , Amsterdam , the Netherlands
| | - Daniëlle A M Heideman
- a Department of Pathology , VU University Medical Center , Amsterdam , the Netherlands
| | - Chris J L M Meijer
- a Department of Pathology , VU University Medical Center , Amsterdam , the Netherlands
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Garella D, Atlante S, Borretto E, Cocco M, Giorgis M, Costale A, Stevanato L, Miglio G, Cencioni C, Fernández-de Gortari E, Medina-Franco JL, Spallotta F, Gaetano C, Bertinaria M. Design and synthesis of N-benzoyl amino acid derivatives as DNA methylation inhibitors. Chem Biol Drug Des 2016; 88:664-676. [PMID: 27225604 DOI: 10.1111/cbdd.12794] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 05/02/2016] [Accepted: 05/14/2016] [Indexed: 12/11/2022]
Abstract
The inhibition of human DNA Methyl Transferases (DNMT) is a novel promising approach to address the epigenetic dysregulation of gene expression in different diseases. Inspired by the validated virtual screening hit NSC137546, a series of N-benzoyl amino acid analogues was synthesized and obtained compounds were assessed for their ability to inhibit DNMT-dependent DNA methylation in vitro. The biological screening allowed the definition of a set of preliminary structure-activity relationships and the identification of compounds promising for further development. Among the synthesized compounds, L-glutamic acid derivatives 22, 23, and 24 showed the highest ability to prevent DNA methylation in a total cell lysate. Compound 22 inhibited DNMT1 and DNMT3A activity in a concentration-dependent manner in the micromolar range. In addition, compound 22 proved to be stable in human serum and it was thus selected as a starting point for further biological studies.
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Affiliation(s)
- Davide Garella
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Torino, Italy.
| | - Sandra Atlante
- Division of Cardiovascular Epigenetics, Department of Cardiology, Goethe University, Frankfurt am Main, Germany
| | - Emily Borretto
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Torino, Italy
| | - Mattia Cocco
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Torino, Italy
| | - Marta Giorgis
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Torino, Italy
| | - Annalisa Costale
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Torino, Italy
| | - Livio Stevanato
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Torino, Italy
| | - Gianluca Miglio
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Torino, Italy
| | - Chiara Cencioni
- Division of Cardiovascular Epigenetics, Department of Cardiology, Goethe University, Frankfurt am Main, Germany
| | - Eli Fernández-de Gortari
- Facultad de Química , Departamento de Farmacia, Universidad Nacional Autónoma de México, Mexico City, México
| | - José L Medina-Franco
- Facultad de Química , Departamento de Farmacia, Universidad Nacional Autónoma de México, Mexico City, México
| | - Francesco Spallotta
- Division of Cardiovascular Epigenetics, Department of Cardiology, Goethe University, Frankfurt am Main, Germany
| | - Carlo Gaetano
- Division of Cardiovascular Epigenetics, Department of Cardiology, Goethe University, Frankfurt am Main, Germany.
| | - Massimo Bertinaria
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Torino, Italy
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Suelves M, Carrió E, Núñez-Álvarez Y, Peinado MA. DNA methylation dynamics in cellular commitment and differentiation. Brief Funct Genomics 2016; 15:443-453. [PMID: 27416614 DOI: 10.1093/bfgp/elw017] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
DNA methylation is an essential epigenetic modification for mammalian development and is crucial for the establishment and maintenance of cellular identity. Traditionally, DNA methylation has been considered as a permanent repressive epigenetic mark. However, the application of genome-wide approaches has allowed the analysis of DNA methylation in different genomic contexts, revealing a more dynamic regulation than originally thought, as active DNA methylation and demethylation occur during cell fate commitment and terminal differentiation. Recent data provide insights into the contribution of different epigenetic factors, and DNA methylation in particular, to the establishment of cellular memory during embryonic development and the modulation of cell type-specific gene regulation programs to ensure proper differentiation. This review summarizes published data regarding DNA methylation changes along lineage specification and differentiation programs. We also discuss the current knowledge about DNA methylation alterations occurring in physiological and pathological conditions such as aging and cancer.
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39
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Alivand MR, Sabouni F, Soheili ZS. Probable Chemical Hypoxia Effects on Progress of CNV Through Induction of Promoter CpG Demethylation and Overexpression of IL17RC in Human RPE Cells. Curr Eye Res 2016; 41:1245-54. [DOI: 10.3109/02713683.2015.1095933] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Mohammad Reza Alivand
- Molecular Medicine Department, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
- Department of Medical Genetic, Medical Faculty, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Farzaneh Sabouni
- Molecular Medicine Department, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Zahra-Soheila Soheili
- Molecular Medicine Department, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
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Dasmahapatra AK, Khan IA. Modulation of DNA methylation machineries in Japanese rice fish (Oryzias latipes) embryogenesis by ethanol and 5-azacytidine. Comp Biochem Physiol C Toxicol Pharmacol 2016; 179:174-83. [PMID: 26510680 DOI: 10.1016/j.cbpc.2015.10.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 10/09/2015] [Accepted: 10/22/2015] [Indexed: 01/20/2023]
Abstract
As a sequel of our investigations on the impact of epigenome in inducing fetal alcohol spectrum disorder (FASD) phenotypes in Japanese rice fish, we have investigated on several DNA methylation machinery genes including DNA methyl transferase 3ba (dnmt3ba) and methyl binding proteins (MBPs), namely, mbd1b, mbd3a, mbd3b, and mecp2 at the transcription level. Studies were made during normal development, from 0day post fertilization (dpf) to hatching, and also exposing the fertilized eggs to ethanol or a DNMT inhibitor, 5-azacytidine (5-azaC). We observed that during development, all these genes followed distinct expression patterns, generally high mRNA copies in early phases (0-1dpf) and significantly low mRNA copies prior to or after hatching. Ethanol (100-500mM, 0-2dpf) was unable to alter any of these mRNAs in 2dpf; additional four day (2-6dpf) maintenance of these embryos in ethanol-free environment, on 6dpf, was also unable to establish any significant difference in these mRNA levels in comparison with the corresponding controls. However, continuous exposure of fertilized eggs in 300mM ethanol, 0-6dpf, showed significantly high mRNA copies only in MBPs (mbd1b, mbd3a, mbd3b, mecp2). 5-azaC (2mM) on 2dpf was able to enhance only mbd3b mRNA. Removal of 5-azaC and maintenance of these embryos in clean medium, 2-6dpf, showed significantly enhanced mbd3b and mecp2 mRNAs compared to corresponding controls on 6dpf. Our studies showed that in Japanese rice fish embryogenesis both ethanol and 5-azaC have the potential to specifically modulate the developmental rhythm of DNA methylation machineries.
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Affiliation(s)
- Asok K Dasmahapatra
- National Center for Natural Product Research, School of Pharmacy, University of Mississippi, University, MS 38677, USA; Department of BioMolecular Sciences, Division of Pharmacology, School of Pharmacy, University of Mississippi, University, MS 38677, USA.
| | - Ikhlas A Khan
- National Center for Natural Product Research, School of Pharmacy, University of Mississippi, University, MS 38677, USA; Department of BioMolecular Sciences, Division of Pharmacognosy, School of Pharmacy, University of Mississippi, University, MS 38677, USA
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Abstract
β-catenin is widely regarded as the primary transducer of canonical WNT signals to the nucleus. In most vertebrates, there are eight additional catenins that are structurally related to β-catenin, and three α-catenin genes encoding actin-binding proteins that are structurally related to vinculin. Although these catenins were initially identified in association with cadherins at cell-cell junctions, more recent evidence suggests that the majority of catenins also localize to the nucleus and regulate gene expression. Moreover, the number of catenins reported to be responsive to canonical WNT signals is increasing. Here, we posit that multiple catenins form a functional network in the nucleus, possibly engaging in conserved protein-protein interactions that are currently better characterized in the context of actin-based cell junctions.
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Pierre CC, Longo J, Bassey-Archibong BI, Hallett RM, Milosavljevic S, Beatty L, Hassell JA, Daniel JM. Methylation-dependent regulation of hypoxia inducible factor-1 alpha gene expression by the transcription factor Kaiso. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:1432-41. [PMID: 26514431 DOI: 10.1016/j.bbagrm.2015.10.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 10/01/2015] [Accepted: 10/23/2015] [Indexed: 01/19/2023]
Abstract
Low oxygen tension (hypoxia) is a common characteristic of solid tumors and strongly correlates with poor prognosis and resistance to treatment. In response to hypoxia, cells initiate a cascade of transcriptional events regulated by the hypoxia inducible factor-1 (HIF-1) heterodimer. Since the oxygen-sensitive HIF-1α subunit is stabilized during hypoxia, it functions as the regulatory subunit of the protein. To date, while the mechanisms governing HIF-1α protein stabilization and function have been well studied, those governing HIF1A gene expression are not fully understood. However, recent studies have suggested that methylation of a HIF-1 binding site in the HIF1A promoter prevents its autoregulation. Here we report that the POZ-ZF transcription factor Kaiso modulates HIF1A gene expression by binding to the methylated HIF1A promoter in a region proximal to the autoregulatory HIF-1 binding site. Interestingly, Kaiso's regulation of HIF1A occurs primarily during hypoxia, which is consistent with the finding that Kaiso protein levels peak after 4 h of hypoxic incubation and return to normoxic levels after 24 h. Our data thus support a role for Kaiso in fine-tuning HIF1A gene expression after extended periods of hypoxia.
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Affiliation(s)
- Christina C Pierre
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Joseph Longo
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | | | - Robin M Hallett
- Department of Biochemistry & Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
| | | | - Laura Beatty
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - John A Hassell
- Department of Biochemistry & Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Juliet M Daniel
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada.
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Li S, Liu L, Li S, Gao L, Zhao Y, Kim YJ, Chen X. SUVH1, a Su(var)3-9 family member, promotes the expression of genes targeted by DNA methylation. Nucleic Acids Res 2015; 44:608-20. [PMID: 26400170 PMCID: PMC4737185 DOI: 10.1093/nar/gkv958] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Accepted: 09/11/2015] [Indexed: 12/24/2022] Open
Abstract
Transposable elements are found throughout the genomes of all organisms. Repressive marks such as DNA methylation and histone H3 lysine 9 (H3K9) methylation silence these elements and maintain genome integrity. However, how silencing mechanisms are themselves regulated to avoid the silencing of genes remains unclear. Here, an anti-silencing factor was identified using a forward genetic screen on a reporter line that harbors a LUCIFERASE (LUC) gene driven by a promoter that undergoes DNA methylation. SUVH1, a Su(var)3–9 homolog, was identified as a factor promoting the expression of the LUC gene. Treatment with a cytosine methylation inhibitor completely suppressed the LUC expression defects of suvh1, indicating that SUVH1 is dispensable for LUC expression in the absence of DNA methylation. SUVH1 also promotes the expression of several endogenous genes with promoter DNA methylation. However, the suvh1 mutation did not alter DNA methylation levels at the LUC transgene or on a genome-wide scale; thus, SUVH1 functions downstream of DNA methylation. Histone H3 lysine 4 (H3K4) trimethylation was reduced in suvh1; in contrast, H3K9 methylation levels remained unchanged. This work has uncovered a novel, anti-silencing function for a member of the Su(var)3–9 family that has previously been associated with silencing through H3K9 methylation.
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Affiliation(s)
- Shaofang Li
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Lin Liu
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Shengben Li
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Lei Gao
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Yuanyuan Zhao
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Yun Ju Kim
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA Howard Hughes Medical Institute, University of California, Riverside, CA 92521, USA
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Yan XP, Liu HH, Liu JY, Zhang RP, Wang GS, Li QQ, Wang DMC, Li L, Wang JW. Evidence in duck for supporting alteration of incubation temperature may have influence on methylation of genomic DNA. Poult Sci 2015; 94:2537-45. [PMID: 26354761 PMCID: PMC5011409 DOI: 10.3382/ps/pev201] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Accepted: 06/01/2015] [Indexed: 12/24/2022] Open
Abstract
Incubation temperature has an immediate and long-term influence on the embryonic development in birds. DNA methylation as an important environment-induced mechanism could serve as a potential link between embryos’ phenotypic variability and temperature variation, which reprogrammed by DNA (cytosine-5)-methyltransferases (DNMTS) and Methyl-CpG binding domain proteins (MBPS) 3&5 (MBD3&5). Five genes in DNMTS and MBPS gene families were selected as target genes, given their important role in epigenetic modification. In this study, we aimed to test whether raising incubation temperature from 37.8°C to 38.8°C between embryonic days (ED) 1–10, ED10–20 and ED20–27 have effect on DNA methylation and whether DNMTS, MBPS play roles in thermal epigenetic regulation of early development in duck. Real-time quantitative PCR analysis showed that increased incubation temperature by 1°C has remarkably dynamic effect on gene expression levels of DNMTS and MBPS. Slight changes in incubation temperature significantly increased mRNA levels of target genes in breast muscle tissue during ED1–10, especially for DNMT1, DNMT3A and MBD5. In addition, higher temperature significantly increased enzyme activities of DNMT1 in leg muscle during ED10–20, liver tissue during ED1–10, ED20–27 and DNMT3A in leg muscle and breast muscle tissue during ED10–20. These results suggest that incubation temperature has an extended effect on gene expression levels and enzyme activities of DNMTS and MBPS, which provides evidence that incubation temperature may influence DNA methylation in duck during early developmental stages. Our data indicated that DNMTS and MBPS may involved in thermal epigenetice regulation of embryos during the early development in duck. The potential links between embryonic temperature and epigenetic modification need further investigation
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Affiliation(s)
- Xi-Ping Yan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Ya'an, Sichuan 625014, P.R. China
| | - He-He Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Ya'an, Sichuan 625014, P.R. China
| | - Jun-Ying Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Ya'an, Sichuan 625014, P.R. China
| | - Rong-Ping Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Ya'an, Sichuan 625014, P.R. China
| | - Guo-Song Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Ya'an, Sichuan 625014, P.R. China
| | - Qing-Qing Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Ya'an, Sichuan 625014, P.R. China
| | - Ding-Min-Cheng Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Ya'an, Sichuan 625014, P.R. China
| | - Liang Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Ya'an, Sichuan 625014, P.R. China
| | - Ji-Wen Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Ya'an, Sichuan 625014, P.R. China
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Bergougnoux A, Claustres M, De Sario A. Nasal epithelial cells: a tool to study DNA methylation in airway diseases. Epigenomics 2015; 7:119-26. [PMID: 25687471 DOI: 10.2217/epi.14.65] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
A number of chronic airway diseases are characterized by high inflammation and unbalanced activation of the immune response, which lead to tissue damage and progressive reduction of the pulmonary function. Because they are exposed to various environmental stimuli, lung cells are prone to epigenomic changes. Many genes responsible for the immune response and inflammation are tightly regulated by DNA methylation, which suggests that alteration of the epigenome in lung cells may have a considerable impact on the penetrance and/or the severity of airway diseases. A major hurdle in clinical epigenomic studies is to gather appropriate biospecimens. Herein, we show that nasal epithelial cells are suitable to analyze DNA methylation in human diseases primarily affecting the lower airway tract.
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Affiliation(s)
- Anne Bergougnoux
- Laboratory Genetics of Rare Diseases, INSERM U827, Montpellier, France
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Abstract
Epigenetic regulation is facilitated by a battery of proteins that act as 'writers' or 'erasers' to add or remove biochemical modifications to DNA and histone proteins. DNA modifications, histone modifications and long noncoding RNAs function interdependently through reciprocal crosstalk. This review will focus on DNA methylation and DNA methyltransferases with emphasis on how biological and biochemical factors such as histone modifications and noncoding RNAs might play a role in modulating DNA methylation. Other physiological and biochemical factors that can modify DNA methylation marks will also be discussed including chemical exposures and inflammation.
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Affiliation(s)
- Raymond Lo
- Genetics & Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada
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48
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Hoffmann A, Zimmermann CA, Spengler D. Molecular epigenetic switches in neurodevelopment in health and disease. Front Behav Neurosci 2015; 9:120. [PMID: 26029068 PMCID: PMC4429584 DOI: 10.3389/fnbeh.2015.00120] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 04/26/2015] [Indexed: 12/16/2022] Open
Abstract
Epigenetic mechanisms encode information above and beyond DNA sequence and play a critical role in brain development and the long-lived effects of environmental cues on the pre- and postnatal brain. Switch-like, rather than graded changes, illustrate par excellence how epigenetic events perpetuate altered activity states in the absence of the initial cue. They occur from early neural development to maturation and can give rise to distinct diseases upon deregulation. Many neurodevelopmental genes harbor bivalently marked chromatin domains, states of balanced inhibition, which guide dynamic “ON or OFF” decisions once the balance is tilted in response to developmental or environmental cues. Examples discussed in this review include neuronal differentiation of embryonic stem cells (ESC) into progenitors and beyond, activation of Kiss1 at puberty onset, and early experience-dependent programming of Avp, a major stress gene. At the genome-scale, genomic imprinting can be epigenetically switched on or off at select genes in a tightly controlled temporospatial manner and provides a versatile mechanism for dosage regulation of genes with important roles in stem cell quiescence or differentiation. Moreover, retrotransposition in neural progenitors provides an intriguing example of an epigenetic-like switch, which is stimulated by bivalently marked neurodevelopmental genes and possibly results in increased genomic flexibility regarding unprecedented challenge. Overall, we propose that molecular epigenetic switches illuminate the catalyzing function of epigenetic mechanisms in guiding dynamic changes in gene expression underpinning robust transitions in cellular and organismal phenotypes as well as in the mediation between dynamically changing environments and the static genetic blueprint.
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Affiliation(s)
- Anke Hoffmann
- Translational Research, Max Planck Society, Max Planck Institute of Psychiatry Munich, Bavaria, Germany
| | - Christoph A Zimmermann
- Translational Research, Max Planck Society, Max Planck Institute of Psychiatry Munich, Bavaria, Germany
| | - Dietmar Spengler
- Translational Research, Max Planck Society, Max Planck Institute of Psychiatry Munich, Bavaria, Germany
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Dege C, Hagman J. Mi-2/NuRD chromatin remodeling complexes regulate B and T-lymphocyte development and function. Immunol Rev 2015; 261:126-40. [PMID: 25123281 DOI: 10.1111/imr.12209] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Mi-2/nucleosomal remodeling and deacetylase (NuRD) complexes are important epigenetic regulators of chromatin structure and gene expression. Mi-2/NuRD complexes are an assemblage of proteins that combine key epigenetic regulators necessary for (i) histone deacetylation and demethylation, (ii) binding to methylated DNA, (iii) mobilization of nucleosomes, and (iv) recruitment of additional regulatory proteins. Depending on their context in chromatin, Mi-2/NuRD complexes either activate or repress gene transcription. In this regard, they are important regulators of hematopoiesis and lymphopoiesis. Mi-2/NuRD complexes maintain pools of hematopoietic stem cells. Specifically, components of these complexes control multiple stages of B-cell development by regulating B-cell specific transcription. With one set of components, they inhibit terminal differentiation of germinal center B cells into plasma B cells. They also mediate gene repression together with Blimp-1 during plasma cell differentiation. In cooperation with Ikaros, Mi-2/NuRD complexes also play important roles in T-cell development, including CD4 versus CD8 fate decisions and peripheral T-cell responses. Dysregulation of NuRD during lymphopoiesis promotes leukemogenesis. Here, we review general properties of Mi-2/NuRD complexes and focus on their functions in gene regulation and development of lymphocytes.
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Affiliation(s)
- Carissa Dege
- Integrated Department of Immunology, National Jewish Health and School of Medicine, University of Colorado, Denver, Aurora, CO, USA
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50
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Wang C, Dong X, Jin D, Zhao Y, Xie S, Li X, He X, Lang Z, Lai J, Zhu JK, Gong Z. Methyl-CpG-binding domain protein MBD7 is required for active DNA demethylation in Arabidopsis. PLANT PHYSIOLOGY 2015; 167:905-14. [PMID: 25593350 PMCID: PMC4348759 DOI: 10.1104/pp.114.252106] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 01/14/2015] [Indexed: 05/20/2023]
Abstract
Although researchers have established that DNA methylation and active demethylation are dynamically regulated in plant cells, the molecular mechanism for the regulation of active DNA demethylation is not well understood. By using an Arabidopsis (Arabidopsis thaliana) line expressing the Promoter RESPONSIVE TO DEHYDRATION 29A:LUCIFERASE (ProRD29A:LUC) and Promoter cauliflower mosaic virus 35S:NEOMYCIN PHOSPHOTRANSFERASE II (Pro35S:NPTII) transgenes, we isolated an mbd7 (for methyl-CpG-binding domain protein7) mutant. The mbd7 mutation causes an inactivation of the Pro35S:NPTII transgene but does not affect the expression of the ProRD29A:LUC transgene. The silencing of the Pro35S:NPTII reporter gene is associated with DNA hypermethylation of the reporter gene. MBD7 interacts physically with REPRESSOR OF SILENCING5/INCREASED DNA METHYLATION2, a protein in the small heat shock protein family. MBD7 prefers to target the genomic loci with high densities of DNA methylation around chromocenters. The Gypsy-type long terminal repeat retrotransposons mainly distributed around chromocenters are most affected by mbd7 in all transposons. Our results suggest that MBD7 is required for active DNA demethylation and antisilencing of the genomic loci with high densities of DNA methylation in Arabidopsis.
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Affiliation(s)
- Chunlei Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences (C.W., D.J., Y.Z., X.L., Z.G.), State Key Laboratory of Agrobiotechnology (X.D., J.L.), and China National Maize Improvement Center, Department of Plant Genetics and Breeding (X.D., J.L.), China Agricultural University, Beijing 100193, China;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47906 (S.X., Z.L., J.-K.Z.);National Institute of Biological Sciences, Beijing 102206, China (X.H.); andShanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (J.-K.Z.)
| | - Xiaomei Dong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences (C.W., D.J., Y.Z., X.L., Z.G.), State Key Laboratory of Agrobiotechnology (X.D., J.L.), and China National Maize Improvement Center, Department of Plant Genetics and Breeding (X.D., J.L.), China Agricultural University, Beijing 100193, China;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47906 (S.X., Z.L., J.-K.Z.);National Institute of Biological Sciences, Beijing 102206, China (X.H.); andShanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (J.-K.Z.)
| | - Dan Jin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences (C.W., D.J., Y.Z., X.L., Z.G.), State Key Laboratory of Agrobiotechnology (X.D., J.L.), and China National Maize Improvement Center, Department of Plant Genetics and Breeding (X.D., J.L.), China Agricultural University, Beijing 100193, China;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47906 (S.X., Z.L., J.-K.Z.);National Institute of Biological Sciences, Beijing 102206, China (X.H.); andShanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (J.-K.Z.)
| | - Yusheng Zhao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences (C.W., D.J., Y.Z., X.L., Z.G.), State Key Laboratory of Agrobiotechnology (X.D., J.L.), and China National Maize Improvement Center, Department of Plant Genetics and Breeding (X.D., J.L.), China Agricultural University, Beijing 100193, China;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47906 (S.X., Z.L., J.-K.Z.);National Institute of Biological Sciences, Beijing 102206, China (X.H.); andShanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (J.-K.Z.)
| | - Shaojun Xie
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences (C.W., D.J., Y.Z., X.L., Z.G.), State Key Laboratory of Agrobiotechnology (X.D., J.L.), and China National Maize Improvement Center, Department of Plant Genetics and Breeding (X.D., J.L.), China Agricultural University, Beijing 100193, China;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47906 (S.X., Z.L., J.-K.Z.);National Institute of Biological Sciences, Beijing 102206, China (X.H.); andShanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (J.-K.Z.)
| | - Xiaojie Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences (C.W., D.J., Y.Z., X.L., Z.G.), State Key Laboratory of Agrobiotechnology (X.D., J.L.), and China National Maize Improvement Center, Department of Plant Genetics and Breeding (X.D., J.L.), China Agricultural University, Beijing 100193, China;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47906 (S.X., Z.L., J.-K.Z.);National Institute of Biological Sciences, Beijing 102206, China (X.H.); andShanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (J.-K.Z.)
| | - Xinjian He
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences (C.W., D.J., Y.Z., X.L., Z.G.), State Key Laboratory of Agrobiotechnology (X.D., J.L.), and China National Maize Improvement Center, Department of Plant Genetics and Breeding (X.D., J.L.), China Agricultural University, Beijing 100193, China;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47906 (S.X., Z.L., J.-K.Z.);National Institute of Biological Sciences, Beijing 102206, China (X.H.); andShanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (J.-K.Z.)
| | - Zhaobo Lang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences (C.W., D.J., Y.Z., X.L., Z.G.), State Key Laboratory of Agrobiotechnology (X.D., J.L.), and China National Maize Improvement Center, Department of Plant Genetics and Breeding (X.D., J.L.), China Agricultural University, Beijing 100193, China;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47906 (S.X., Z.L., J.-K.Z.);National Institute of Biological Sciences, Beijing 102206, China (X.H.); andShanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (J.-K.Z.)
| | - Jinsheng Lai
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences (C.W., D.J., Y.Z., X.L., Z.G.), State Key Laboratory of Agrobiotechnology (X.D., J.L.), and China National Maize Improvement Center, Department of Plant Genetics and Breeding (X.D., J.L.), China Agricultural University, Beijing 100193, China;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47906 (S.X., Z.L., J.-K.Z.);National Institute of Biological Sciences, Beijing 102206, China (X.H.); andShanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (J.-K.Z.)
| | - Jian-Kang Zhu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences (C.W., D.J., Y.Z., X.L., Z.G.), State Key Laboratory of Agrobiotechnology (X.D., J.L.), and China National Maize Improvement Center, Department of Plant Genetics and Breeding (X.D., J.L.), China Agricultural University, Beijing 100193, China;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47906 (S.X., Z.L., J.-K.Z.);National Institute of Biological Sciences, Beijing 102206, China (X.H.); andShanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (J.-K.Z.)
| | - Zhizhong Gong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences (C.W., D.J., Y.Z., X.L., Z.G.), State Key Laboratory of Agrobiotechnology (X.D., J.L.), and China National Maize Improvement Center, Department of Plant Genetics and Breeding (X.D., J.L.), China Agricultural University, Beijing 100193, China;Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47906 (S.X., Z.L., J.-K.Z.);National Institute of Biological Sciences, Beijing 102206, China (X.H.); andShanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China (J.-K.Z.)
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