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Kerr L, Kafetzopoulos I, Grima R, Sproul D. Genome-wide single-molecule analysis of long-read DNA methylation reveals heterogeneous patterns at heterochromatin that reflect nucleosome organisation. PLoS Genet 2023; 19:e1010958. [PMID: 37782664 PMCID: PMC10569558 DOI: 10.1371/journal.pgen.1010958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 10/12/2023] [Accepted: 09/04/2023] [Indexed: 10/04/2023] Open
Abstract
High-throughput sequencing technology is central to our current understanding of the human methylome. The vast majority of studies use chemical conversion to analyse bulk-level patterns of DNA methylation across the genome from a population of cells. While this technology has been used to probe single-molecule methylation patterns, such analyses are limited to short reads of a few hundred basepairs. DNA methylation can also be directly detected using Nanopore sequencing which can generate reads measuring megabases in length. However, thus far these analyses have largely focused on bulk-level assessment of DNA methylation. Here, we analyse DNA methylation in single Nanopore reads from human lymphoblastoid cells, to show that bulk-level metrics underestimate large-scale heterogeneity in the methylome. We use the correlation in methylation state between neighbouring sites to quantify single-molecule heterogeneity and find that heterogeneity varies significantly across the human genome, with some regions having heterogeneous methylation patterns at the single-molecule level and others possessing more homogeneous methylation patterns. By comparing the genomic distribution of the correlation to epigenomic annotations, we find that the greatest heterogeneity in single-molecule patterns is observed within heterochromatic partially methylated domains (PMDs). In contrast, reads originating from euchromatic regions and gene bodies have more ordered DNA methylation patterns. By analysing the patterns of single molecules in more detail, we show the existence of a nucleosome-scale periodicity in DNA methylation that accounts for some of the heterogeneity we uncover in long single-molecule DNA methylation patterns. We find that this periodic structure is partially masked in bulk data and correlates with DNA accessibility as measured by nanoNOMe-seq, suggesting that it could be generated by nucleosomes. Our findings demonstrate the power of single-molecule analysis of long-read data to understand the structure of the human methylome.
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Affiliation(s)
- Lyndsay Kerr
- MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Ioannis Kafetzopoulos
- MRC Human Genetics Unit and CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
- Current address: Altos Labs Cambridge Institute, Cambridge, United Kingdom
| | - Ramon Grima
- School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Duncan Sproul
- MRC Human Genetics Unit and CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
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2
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Pederson K, Meints GA, Drobny GP. Base Dynamics in the HhaI Protein Binding Site. J Phys Chem B 2023; 127:7266-7275. [PMID: 37561575 PMCID: PMC10461302 DOI: 10.1021/acs.jpcb.3c03687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/18/2023] [Indexed: 08/12/2023]
Abstract
Protein-DNA interactions play an important role in numerous biological functions within the living cell. In many of these interactions, the DNA helix is significantly distorted upon protein-DNA complex formation. The HhaI restriction-modification system is one such system, where the methylation target is flipped out of the helix when bound to the methyltransferase. However, the base flipping mechanism is not well understood. The dynamics of the binding site of the HhaI methyltransferase and endonuclease (underlined) within the DNA oligomer [d(G1A2T3A4G5C6G7C8T9A10T11C12)]2 are studied using deuterium solid-state NMR (SSNMR). SSNMR spectra obtained from DNAs deuterated on the base of nucleotides within and flanking the [5'-GCGC-3']2 sequence indicate that all of these positions are structurally flexible. Previously, conformational flexibility within the phosphodiester backbone and furanose ring within the target sequence has been observed and hypothesized to play a role in the distortion mechanism. However, whether that distortion was occurring through an active or passive mechanism remained unclear. These NMR data demonstrate that although the [5'-GCGC-3']2 sequence is dynamic, the target cytosine is not passively flipping out of the double-helix on the millisecond-picosecond time scale. Additionally, although previous studies have shown that both the furanose ring and phosphodiester backbone experience a change in dynamics upon methylation, which may play a role in recognition and cleavage by the endonuclease, our observations here indicate that methylation has no effect on the dynamics of the base itself.
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Affiliation(s)
- Kari Pederson
- Department
of Chemistry & Biochemistry, California
State University at Dominguez Hills, Carson, California 90747, United States
| | - Gary A. Meints
- Department
of Chemistry, Missouri State University, Springfield, Missouri 65897, United States
| | - Gary P. Drobny
- Department
of Chemistry, University of Washington, Seattle, Washington 98195-1700, United
States
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3
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Isolation and Comprehensive in Silico Characterisation of a New 3-Hydroxy-3-Methylglutaryl-Coenzyme A Reductase 4 (HMGR4) Gene Promoter from Salvia miltiorrhiza: Comparative Analyses of Plant HMGR Promoters. PLANTS 2022; 11:plants11141861. [PMID: 35890495 PMCID: PMC9318348 DOI: 10.3390/plants11141861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/29/2022] [Accepted: 07/12/2022] [Indexed: 11/17/2022]
Abstract
Salvia miltiorrhiza synthesises tanshinones with multidirectional therapeutic effects. These compounds have a complex biosynthetic pathway, whose first rate limiting enzyme is 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGR). In the present study, a new 1646 bp fragment of the S. miltiorrhiza HMGR4 gene consisting of a promoter, 5′ untranslated region and part of a coding sequence was isolated and characterised in silico using bioinformatics tools. The results indicate the presence of a TATA box, tandem repeat and pyrimidine-rich sequence, and the absence of CpG islands. The sequence was rich in motifs recognised by specific transcription factors sensitive mainly to light, salicylic acid, bacterial infection and auxins; it also demonstrated many binding sites for microRNAs. Moreover, our results suggest that HMGR4 expression is possibly regulated during flowering, embryogenesis, organogenesis and the circadian rhythm. The obtained data were verified by comparison with microarray co-expression results obtained for Arabidopsis thaliana. Alignment of the isolated HMGR4 sequence with other plant HMGRs indicated the presence of many common binding sites for transcription factors, including conserved ones. Our findings provide valuable information for understanding the mechanisms that direct transcription of the S. miltiorrhiza HMGR4 gene.
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Choi J, Lyons DB, Zilberman D. Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. eLife 2021; 10:72676. [PMID: 34850679 PMCID: PMC8828055 DOI: 10.7554/elife.72676] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 11/30/2021] [Indexed: 11/27/2022] Open
Abstract
Flowering plants utilize small RNA (sRNA) molecules to guide DNA methyltransferases to genomic sequences. This RNA-directed DNA methylation (RdDM) pathway preferentially targets euchromatic transposable elements. However, RdDM is thought to be recruited by methylation of histone H3 at lysine 9 (H3K9me), a hallmark of heterochromatin. How RdDM is targeted to euchromatin despite an affinity for H3K9me is unclear. Here, we show that loss of histone H1 enhances heterochromatic RdDM, preferentially at nucleosome linker DNA. Surprisingly, this does not require SHH1, the RdDM component that binds H3K9me. Furthermore, H3K9me is dispensable for RdDM, as is CG DNA methylation. Instead, we find that non-CG methylation is specifically associated with sRNA biogenesis, and without H1 sRNA production quantitatively expands to non-CG-methylated loci. Our results demonstrate that H1 enforces the separation of euchromatic and heterochromatic DNA methylation pathways by excluding the sRNA-generating branch of RdDM from non-CG-methylated heterochromatin. Cells adapt to different roles by turning different groups of genes on and off. One way cells control which genes are on or off is by creating regions of active and inactive DNA, which are created and maintained by different groups of proteins. Genes in active DNA regions can be turned on, while genes in inactive regions are switched off or silenced. Silenced DNA regions also turn off ‘transposable elements’: pieces of DNA that can copy themselves and move to other regions of the genome if they become active. Transposons can be dangerous if they are activated, because they can disrupt genes or regulatory sequences when they move. There are different types of active and inactive DNA, but it is not always clear why these differences exist, or how they are maintained over time. In plants, such as the commonly-studied weed Arabidopsis thaliana, there are two types of inactive DNA, called E and H, that can silence transposons. In both types, DNA has small chemicals called methyl groups attached to it, which help inactivate the DNA. Type E DNA is methylated by a process called RNA-directed DNA methylation (RdDM), but RdDM is rarely seen in type H DNA. Choi, Lyons and Zilberman showed that RdDM is attracted to E and H regions by previously existing methylated DNA. However, in the H regions, a protein called histone H1 blocks RdDM from attaching methyl groups. This helps focus RdDM onto E regions where it is most needed, because E regions contain the types of transposons RdDM is best suited to silence. When Choi, Lyons and Zilberman examined genetically modified A. thaliana plants that do not produce histone H1, they found that RdDM happened in both E and H regions. There are many more H regions than E regions, so stretching RdDM across both made it less effective at silencing DNA. This work shows how different DNA silencing processes are focused onto specific genetic regions, helping explain why there are different types of active and inactive DNA within cells. RdDM has been studied as a way to affect crop growth and yield by altering DNA methylation. These results may help such studies by explaining how RdDM is naturally targeted.
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Affiliation(s)
- Jaemyung Choi
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - David B Lyons
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - Daniel Zilberman
- Department of Cell and Developmental Biology, John Innes Centre, Klosterneuburg, Austria
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Shen CH, Allan J. MNase Digestion Protection Patterns of the Linker DNA in Chromatosomes. Cells 2021; 10:cells10092239. [PMID: 34571888 PMCID: PMC8469290 DOI: 10.3390/cells10092239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 11/16/2022] Open
Abstract
The compact nucleosomal structure limits DNA accessibility and regulates DNA-dependent cellular activities. Linker histones bind to nucleosomes and compact nucleosomal arrays into a higher-order chromatin structure. Recent developments in high throughput technologies and structural computational studies provide nucleosome positioning at a high resolution and contribute to the information of linker histone location within a chromatosome. However, the precise linker histone location within the chromatin fibre remains unclear. Using monomer extension, we mapped core particle and chromatosomal positions over a core histone-reconstituted, 1.5 kb stretch of DNA from the chicken adult β-globin gene, after titration with linker histones and linker histone globular domains. Our results show that, although linker histone globular domains and linker histones display a wide variation in their binding affinity for different positioned nucleosomes, they do not alter nucleosome positions or generate new nucleosome positions. Furthermore, the extra ~20 bp of DNA protected in a chromatosome is usually symmetrically distributed at each end of the core particle, suggesting linker histones or linker histone globular domains are located close to the nucleosomal dyad axis.
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Affiliation(s)
- Chang-Hui Shen
- Biology Department, College of Staten Island, City University of New York, 2800 Victory Boulevard, Staten Island, NY 10314, USA
- Biochemistry and Biology Ph.D. Program, Graduate Center, City University of New York, New York, NY 10016, USA
- Institute for Macromolecular Assemblies, City University of New York, New York, NY 10031, USA
- Correspondence: ; Tel.: +1-718-982-3998; Fax: +1-718-982-3852
| | - James Allan
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK;
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DNA Methylation and Histone H1 Jointly Repress Transposable Elements and Aberrant Intragenic Transcripts. Mol Cell 2020; 77:310-323.e7. [DOI: 10.1016/j.molcel.2019.10.011] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 08/26/2019] [Accepted: 10/10/2019] [Indexed: 12/12/2022]
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Ibáñez MA, Alvarez-Mari A, Rodríguez-Sanz H, Kremer C, González-Benito ME, Martín C. Genetic and epigenetic stability of recovered mint apices after several steps of a cryopreservation protocol by encapsulation-dehydration. A new approach for epigenetic analysis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 143:299-307. [PMID: 31539759 DOI: 10.1016/j.plaphy.2019.08.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/24/2019] [Accepted: 08/29/2019] [Indexed: 06/10/2023]
Abstract
The genetic and epigenetic stability (analysis of DNA methylation using MSAP markers) of mint (Mentha x piperita L.) apices was studied after each step of a cryopreservation protocol, by encapsulation-dehydration. The effect of the addition of an antioxidant (ascorbic acid) during one of the protocol steps was also evaluated. Eight-week old in vitro recovered shoots from apices after each step of the protocol were genetically stable when compared to control in vitro shoots, using RAPD and AFLP markers. The addition of ascorbic acid in the medium with the highest sucrose concentration did not improve recovery and did not have any effect on stability. Apices sampled immediately after each step showed increased epigenetic differences as the protocol advanced, compared to in vitro control apices, in particular related to de novo methylation events. However, after one-day in vitro recovery, methylation status was similar to control apices. To improve the quality of methylation data interpretation, a simple and fast method for MSAP markers analysis, based on R programming, has been developed which allows the statistical comparison of treatments to control samples and its graphical representation.
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Affiliation(s)
- Miguel Angel Ibáñez
- Departamento de Economía Agraria, Estadística y Gestión de Empresas, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Av. Puerta de Hierro, nº 2 - 4, 28040, Madrid, Spain.
| | - Ana Alvarez-Mari
- Departamento de Economía Agraria, Estadística y Gestión de Empresas, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Av. Puerta de Hierro, nº 2 - 4, 28040, Madrid, Spain.
| | - Héctor Rodríguez-Sanz
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Av. Puerta de Hierro, nº 2 - 4, 28040, Madrid, Spain.
| | - Carolina Kremer
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Av. Puerta de Hierro, nº 2 - 4, 28040, Madrid, Spain.
| | - María Elena González-Benito
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Av. Puerta de Hierro, nº 2 - 4, 28040, Madrid, Spain.
| | - Carmen Martín
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Av. Puerta de Hierro, nº 2 - 4, 28040, Madrid, Spain.
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8
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Ke X, Johnson H, Jing X, Michalkiewicz T, Huang YW, Lane RH, Konduri GG. Persistent pulmonary hypertension alters the epigenetic characteristics of endothelial nitric oxide synthase gene in pulmonary artery endothelial cells in a fetal lamb model. Physiol Genomics 2018; 50:828-836. [PMID: 30004838 DOI: 10.1152/physiolgenomics.00047.2018] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Decreased expression of endothelial nitric oxide synthase (eNOS), a key mediator of perinatal transition, characterizes persistent pulmonary hypertension of the newborn (PPHN) in neonates and a fetal lamb model; the mechanisms are unclear. We investigated whether increased DNA CpG methylation at the eNOS promoter in estrogen response elements (EREs) and altered histone code together contribute to decreased eNOS expression in PPHN. We isolated pulmonary artery endothelial cells (PAEC) from fetal lambs with PPHN induced by prenatal ductus arteriosus constriction from 128 to 136 days gestation or gestation-matched twin controls. We measured right ventricular systolic pressure (RVSP) and Fulton index and determined eNOS expression in PAEC in control and PPHN lambs. We determined DNA CpG methylation by pyrosequencing and activity of ten eleven translocase demethylases (TET) by colorimetric assay. We quantified the occupancy of transcription factors, specificity protein 1 (Sp1), and estrogen receptors and density of four histone marks around Sp1 binding sites by chromatin immunoprecipitation (ChIP) assays. Fetal lambs with PPHN developed increased RVSP and Fulton index. Levels of eNOS mRNA and protein were decreased in PAEC from PPHN lambs. PPHN significantly increased the DNA CpG methylation in eNOS promoter and decreased TET activity in PAEC. PPHN decreased Sp1 occupancy and density of the active mark, lysine 12 acetylation of histone 4, and increased density of the repression mark, lysine 9 trimethylation of histone 3 around Sp1 binding sites in eNOS promoter. These results suggest that epigenetic modifications are primed to decrease Sp1 binding at the eNOS gene promoter in PPHN.
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Affiliation(s)
- Xingrao Ke
- Division of Neonatology, Department of Pediatrics, Medical College of Wisconsin , Milwaukee, Wisconsin
| | - Hollis Johnson
- Division of Neonatology, Department of Pediatrics, Medical College of Wisconsin , Milwaukee, Wisconsin
| | - Xigang Jing
- Division of Neonatology, Department of Pediatrics, Medical College of Wisconsin , Milwaukee, Wisconsin
| | - Teresa Michalkiewicz
- Division of Neonatology, Department of Pediatrics, Medical College of Wisconsin , Milwaukee, Wisconsin
| | - Yi-Wen Huang
- Department of Obstetrics and Gynecology, Medical College of Wisconsin , Milwaukee, Wisconsin
| | - Robert H Lane
- Division of Neonatology, Department of Pediatrics, Medical College of Wisconsin , Milwaukee, Wisconsin
| | - Girija G Konduri
- Division of Neonatology, Department of Pediatrics, Medical College of Wisconsin , Milwaukee, Wisconsin
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9
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Tirado-Magallanes R, Rebbani K, Lim R, Pradhan S, Benoukraf T. Whole genome DNA methylation: beyond genes silencing. Oncotarget 2018; 8:5629-5637. [PMID: 27895318 PMCID: PMC5354935 DOI: 10.18632/oncotarget.13562] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 11/07/2016] [Indexed: 11/25/2022] Open
Abstract
The combination of DNA bisulfite treatment with high-throughput sequencing technologies has enabled investigation of genome-wide DNA methylation at near base pair level resolution, far beyond that of the kilobase-long canonical CpG islands that initially revealed the biological relevance of this covalent DNA modification. The latest high-resolution studies have revealed a role for very punctual DNA methylation in chromatin plasticity, gene regulation and splicing. Here, we aim to outline the major biological consequences of DNA methylation recently discovered. We also discuss the necessity of tuning DNA methylation resolution into an adequate scale to ease the integration of the methylome information with other chromatin features and transcription events such as gene expression, nucleosome positioning, transcription factors binding dynamic, gene splicing and genomic imprinting. Finally, our review sheds light on DNA methylation heterogeneity in cell population and the different approaches used for its assessment, including the contribution of single cell DNA analysis technology.
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Affiliation(s)
- Roberto Tirado-Magallanes
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore, Singapore.,Computational Systems Biology Team, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), INSERM, Ecole Normale Supérieure, PSL Research University, 75005 Paris, France
| | - Khadija Rebbani
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore, Singapore
| | - Ricky Lim
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore, Singapore
| | | | - Touati Benoukraf
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore, Singapore
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Lyons DB, Zilberman D. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. eLife 2017; 6:e30674. [PMID: 29140247 PMCID: PMC5728721 DOI: 10.7554/elife.30674] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 11/14/2017] [Indexed: 12/17/2022] Open
Abstract
Cytosine methylation regulates essential genome functions across eukaryotes, but the fundamental question of whether nucleosomal or naked DNA is the preferred substrate of plant and animal methyltransferases remains unresolved. Here, we show that genetic inactivation of a single DDM1/Lsh family nucleosome remodeler biases methylation toward inter-nucleosomal linker DNA in Arabidopsis thaliana and mouse. We find that DDM1 enables methylation of DNA bound to the nucleosome, suggesting that nucleosome-free DNA is the preferred substrate of eukaryotic methyltransferases in vivo. Furthermore, we show that simultaneous mutation of DDM1 and linker histone H1 in Arabidopsis reproduces the strong linker-specific methylation patterns of species that diverged from flowering plants and animals over a billion years ago. Our results indicate that in the absence of remodeling, nucleosomes are strong barriers to DNA methyltransferases. Linker-specific methylation can evolve simply by breaking the connection between nucleosome remodeling and DNA methylation.
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Affiliation(s)
- David B Lyons
- Department of Plant and Microbial BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Daniel Zilberman
- Department of Plant and Microbial BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Department of Cell and Developmental BiologyJohn Innes CentreNorwichUnited Kingdom
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11
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Geyer KK, Niazi UH, Duval D, Cosseau C, Tomlinson C, Chalmers IW, Swain MT, Cutress DJ, Bickham-Wright U, Munshi SE, Grunau C, Yoshino TP, Hoffmann KF. The Biomphalaria glabrata DNA methylation machinery displays spatial tissue expression, is differentially active in distinct snail populations and is modulated by interactions with Schistosoma mansoni. PLoS Negl Trop Dis 2017; 11:e0005246. [PMID: 28510608 PMCID: PMC5433704 DOI: 10.1371/journal.pntd.0005246] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 12/10/2016] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND The debilitating human disease schistosomiasis is caused by infection with schistosome parasites that maintain a complex lifecycle alternating between definitive (human) and intermediate (snail) hosts. While much is known about how the definitive host responds to schistosome infection, there is comparably less information available describing the snail's response to infection. METHODOLOGY/PRINCIPLE FINDINGS Here, using information recently revealed by sequencing of the Biomphalaria glabrata intermediate host genome, we provide evidence that the predicted core snail DNA methylation machinery components are associated with both intra-species reproduction processes and inter-species interactions. Firstly, methyl-CpG binding domain protein (Bgmbd2/3) and DNA methyltransferase 1 (Bgdnmt1) genes are transcriptionally enriched in gonadal compared to somatic tissues with 5-azacytidine (5-AzaC) treatment significantly inhibiting oviposition. Secondly, elevated levels of 5-methyl cytosine (5mC), DNA methyltransferase activity and 5mC binding in pigmented hybrid- compared to inbred (NMRI)- B. glabrata populations indicate a role for the snail's DNA methylation machinery in maintaining hybrid vigour or heterosis. Thirdly, locus-specific detection of 5mC by bisulfite (BS)-PCR revealed 5mC within an exonic region of a housekeeping protein-coding gene (Bg14-3-3), supporting previous in silico predictions and whole genome BS-Seq analysis of this species' genome. Finally, we provide preliminary evidence for parasite-mediated host epigenetic reprogramming in the schistosome/snail system, as demonstrated by the increase in Bgdnmt1 and Bgmbd2/3 transcript abundance following Bge (B. glabrata embryonic cell line) exposure to parasite larval transformation products (LTP). CONCLUSIONS/SIGNIFICANCE The presence of a functional DNA methylation machinery in B. glabrata as well as the modulation of these gene products in response to schistosome products, suggests a vital role for DNA methylation during snail development/oviposition and parasite interactions. Further deciphering the role of this epigenetic process during Biomphalaria/Schistosoma co-evolutionary biology may reveal key factors associated with disease transmission and, moreover, enable the discovery of novel lifecycle intervention strategies.
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Affiliation(s)
- Kathrin K. Geyer
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais Campus, Aberystwyth, United Kingodm
| | - Umar H. Niazi
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais Campus, Aberystwyth, United Kingodm
| | - David Duval
- Université Perpignan Via Domitia, CNRS, IFREMER, Perpignan, France
| | - Céline Cosseau
- Université Perpignan Via Domitia, CNRS, IFREMER, Perpignan, France
| | - Chad Tomlinson
- Genome Sequencing Center, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Iain W. Chalmers
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais Campus, Aberystwyth, United Kingodm
| | - Martin T. Swain
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais Campus, Aberystwyth, United Kingodm
| | - David J. Cutress
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais Campus, Aberystwyth, United Kingodm
| | - Utibe Bickham-Wright
- Department of Pathobiological Sciences, School of Veterinary Medicine University of Wisconsin, Madison, United States of America
| | - Sabrina E. Munshi
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais Campus, Aberystwyth, United Kingodm
| | - Christoph Grunau
- Université Perpignan Via Domitia, CNRS, IFREMER, Perpignan, France
| | - Timothy P. Yoshino
- Department of Pathobiological Sciences, School of Veterinary Medicine University of Wisconsin, Madison, United States of America
| | - Karl F. Hoffmann
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais Campus, Aberystwyth, United Kingodm
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12
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Bandyopadhyay AK, Paul S, Adak S, Giri AK. Reduced LINE-1 methylation is associated with arsenic-induced genotoxic stress in children. Biometals 2016; 29:731-41. [DOI: 10.1007/s10534-016-9950-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 07/08/2016] [Indexed: 10/21/2022]
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13
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Adu-Gyamfi R, Wetten A, Marcelino Rodríguez López C. Effect of Cryopreservation and Post-Cryopreservation Somatic Embryogenesis on the Epigenetic Fidelity of Cocoa (Theobroma cacao L.). PLoS One 2016; 11:e0158857. [PMID: 27403857 PMCID: PMC4942035 DOI: 10.1371/journal.pone.0158857] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 06/22/2016] [Indexed: 11/24/2022] Open
Abstract
UNLABELLED While cocoa plants regenerated from cryopreserved somatic embryos can demonstrate high levels of phenotypic variability, little is known about the sources of the observed variability. Previous studies have shown that the encapsulation-dehydration cryopreservation methodology imposes no significant extra mutational load since embryos carrying high levels of genetic variability are selected against during protracted culture. Also, the use of secondary rather than primary somatic embryos has been shown to further reduce the incidence of genetic somaclonal variation. Here, the effect of in vitro conservation, cryopreservation and post-cryopreservation generation of somatic embryos on the appearance of epigenetic somaclonal variation were comparatively assessed. To achieve this we compared the epigenetic profiles, generated using Methylation Sensitive Amplified Polymorphisms, of leaves collected from the ortet tree and from cocoa somatic embryos derived from three in vitro conditions: somatic embryos, somatic embryos cryopreserved in liquid nitrogen and somatic embryos generated from cryoproserved somatic embryos. Somatic embryos accumulated epigenetic changes but these were less extensive than in those regenerated after storage in LN. Furthermore, the passage of cryopreserved embryos through another embryogenic stage led to further increase in variation. Interestingly, this detected variability appears to be in some measure reversible. The outcome of this study indicates that the cryopreservation induced phenotypic variability could be, at least partially, due to DNA methylation changes. KEY MESSAGE Phenotypic variability observed in cryostored cocoa somatic-embryos is epigenetic in nature. This variability is partially reversible, not stochastic in nature but a directed response to the in-vitro culture and cryopreservation.
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Affiliation(s)
- Raphael Adu-Gyamfi
- Faculty of Agriculture, University for Development Studies, P.O. Box TL 1882, Tamale, Ghana
| | - Andy Wetten
- School of Agriculture, Policy and Development, University of Reading, Whiteknights, Reading, Berks, RG6 6AS, United Kingdom
| | - Carlos Marcelino Rodríguez López
- Environmental Epigenetics and Genetics Group, Plant Research Centre, School of Agriculture, Food and Wine, Faculty of Sciences, University of Adelaide, Waite Campus, PMB1, Glen Osmond, SA, 5064, Australia
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14
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DNA methylation effects on tetra-nucleosome compaction and aggregation. Biophys J 2015; 107:1629-36. [PMID: 25296315 DOI: 10.1016/j.bpj.2014.05.055] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 05/27/2014] [Accepted: 05/30/2014] [Indexed: 12/19/2022] Open
Abstract
DNA CpG methylation has been associated with chromatin compaction and gene silencing. Whether DNA methylation directly contributes to chromatin compaction remains an open question. In this study, we used fluorescence fluctuation spectroscopy (FFS) to evaluate the compaction and aggregation of tetra-nucleosomes containing specific CpG patterns and methylation levels. The compactness of both unmethylated and methylated tetra-nucleosomes is dependent on DNA sequences. Specifically, methylation of the CpG sites located in the central dyad and the major grooves of DNA seem to have opposite effects on modulating the compactness of tetra-nucleosomes. The interactions among tetra-nucleosomes, however, seem to be enhanced because of DNA methylation independent of sequence contexts. Our finding can shed light on understanding the role of DNA methylation in determining nucleosome positioning pattern and chromatin compactness.
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15
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Saint-Carlier E, Riviere G. Regulation of Hox orthologues in the oyster Crassostrea gigas evidences a functional role for promoter DNA methylation in an invertebrate. FEBS Lett 2015; 589:1459-66. [PMID: 25943713 DOI: 10.1016/j.febslet.2015.04.043] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 04/11/2015] [Accepted: 04/20/2015] [Indexed: 11/28/2022]
Abstract
DNA methylation within promoter regions (PRDM) controls vertebrate early gene transcription and thereby development, but is neglected outside this group. However, epigenetic features in the oyster Crassostrea gigas suggest functional significance of PDRM in invertebrates. To investigate this, reporter constructs containing in vitro methylated oyster Hox gene promoters were transfected into oyster embryos. The influence of in vivo methylation was studied using bisulfite sequencing and DNA methyltransferase inhibition during development. Our results demonstrate that methylation controls the transcriptional activity of the promoters investigated, unraveling a functional role for PRDM in a lophotrochozoan, an important finding regarding the evolution of epigenetic regulation.
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Affiliation(s)
- Emma Saint-Carlier
- IBFA, Institute for Fundamental and Applied Biology, University of Caen, Caen, France; UMR BOREA 'Biologie des organismes et écosystèmes aquatiques' Université de Caen Basse-Normandie, CNRS-7208, IRD-207, MNHN, UPMC, UCBN, UAG, F-14032 Caen, France
| | - Guillaume Riviere
- IBFA, Institute for Fundamental and Applied Biology, University of Caen, Caen, France; UMR BOREA 'Biologie des organismes et écosystèmes aquatiques' Université de Caen Basse-Normandie, CNRS-7208, IRD-207, MNHN, UPMC, UCBN, UAG, F-14032 Caen, France.
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16
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Lee JY, Lee J, Yue H, Lee TH. Dynamics of nucleosome assembly and effects of DNA methylation. J Biol Chem 2014; 290:4291-303. [PMID: 25550164 DOI: 10.1074/jbc.m114.619213] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The nucleosome is the fundamental packing unit of the eukaryotic genome, and CpG methylation is an epigenetic modification associated with gene repression and silencing. We investigated nucleosome assembly mediated by histone chaperone Nap1 and the effects of CpG methylation based on three-color single molecule FRET measurements, which enabled direct monitoring of histone binding in the context of DNA wrapping. According to our observation, (H3-H4)2 tetramer incorporation must precede H2A-H2B dimer binding, which is independent of DNA termini wrapping. Upon CpG methylation, (H3-H4)2 tetramer incorporation and DNA termini wrapping are facilitated, whereas proper incorporation of H2A-H2B dimers is inhibited. We suggest that these changes are due to rigidified DNA and increased random binding of histones to DNA. According to the results, CpG methylation expedites nucleosome assembly in the presence of abundant DNA and histones, which may help facilitate gene packaging in chromatin. The results also indicate that the slowest steps in nucleosome assembly are DNA termini wrapping and tetramer positioning, both of which are affected heavily by changes in the physical properties of DNA.
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Affiliation(s)
- Ju Yeon Lee
- From the Department of Chemistry and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Jaehyoun Lee
- From the Department of Chemistry and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Hongjun Yue
- From the Department of Chemistry and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Tae-Hee Lee
- From the Department of Chemistry and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802
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17
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Abstract
Repetitive genomic sequences can adopt a number of alternative DNA structures that differ from the canonical B-form duplex (i.e. non-B DNA). These non-B DNA-forming sequences have been shown to have many important biological functions related to DNA metabolic processes; for example, they may have regulatory roles in DNA transcription and replication. In addition to these regulatory functions, non-B DNA can stimulate genetic instability in the presence or absence of DNA damage, via replication-dependent and/or replication-independent pathways. This review focuses on the interactions of non-B DNA conformations with DNA repair proteins and how these interactions impact genetic instability.
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Affiliation(s)
- Guliang Wang
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd. R1800, Austin, TX 78723, United States
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd. R1800, Austin, TX 78723, United States.
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18
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Yusufaly TI, Li Y, Olson WK. 5-Methylation of cytosine in CG:CG base-pair steps: a physicochemical mechanism for the epigenetic control of DNA nanomechanics. J Phys Chem B 2013; 117:16436-42. [PMID: 24313757 DOI: 10.1021/jp409887t] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
van der Waals density functional theory is integrated with analysis of a non-redundant set of protein-DNA crystal structures from the Nucleic Acid Database to study the stacking energetics of CG:CG base-pair steps, specifically the role of cytosine 5-methylation. Principal component analysis of the steps reveals the dominant collective motions to correspond to a tensile "opening" mode and two shear "sliding" and "tearing" modes in the orthogonal plane. The stacking interactions of the methyl groups globally inhibit CG:CG step overtwisting while simultaneously softening the modes locally via potential energy modulations that create metastable states. Additionally, the indirect effects of the methyl groups on possible base-pair steps neighboring CG:CG are observed to be of comparable importance to their direct effects on CG:CG. The results have implications for the epigenetic control of DNA mechanics.
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Affiliation(s)
- Tahir I Yusufaly
- Department of Physics and Astronomy, Rutgers, the State University of New Jersey , Piscataway, New Jersey 08854, United States
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19
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Vasquez KM, Wang G. The yin and yang of repair mechanisms in DNA structure-induced genetic instability. Mutat Res 2013; 743-744:118-131. [PMID: 23219604 PMCID: PMC3661696 DOI: 10.1016/j.mrfmmm.2012.11.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 11/21/2012] [Accepted: 11/24/2012] [Indexed: 01/14/2023]
Abstract
DNA can adopt a variety of secondary structures that deviate from the canonical Watson-Crick B-DNA form. More than 10 types of non-canonical or non-B DNA secondary structures have been characterized, and the sequences that have the capacity to adopt such structures are very abundant in the human genome. Non-B DNA structures have been implicated in many important biological processes and can serve as sources of genetic instability, implicating them in disease and evolution. Non-B DNA conformations interact with a wide variety of proteins involved in replication, transcription, DNA repair, and chromatin architectural regulation. In this review, we will focus on the interactions of DNA repair proteins with non-B DNA and their roles in genetic instability, as the proteins and DNA involved in such interactions may represent plausible targets for selective therapeutic intervention.
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Affiliation(s)
- Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd. R1800, Austin, TX 78723, United States.
| | - Guliang Wang
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd. R1800, Austin, TX 78723, United States
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20
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Jung JS, Jee MK, Cho HT, Choi JI, Im YB, Kwon OH, Kang SK. MBD6 is a direct target of Oct4 and controls the stemness and differentiation of adipose tissue-derived stem cells. Cell Mol Life Sci 2013; 70:711-28. [PMID: 23052207 PMCID: PMC11114067 DOI: 10.1007/s00018-012-1157-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Revised: 08/29/2012] [Accepted: 08/30/2012] [Indexed: 01/07/2023]
Abstract
Argonaute 2 (Ago2) is a pivotal regulator of cell fate in adult stem cells. Its expression is significantly downregulated in late passages of cells, concomitant with a prominent increase in Ago2 cytosolic localization in single cells. Nuclear localization of Ago2 is crucial for the survival, proliferation, and differentiation of hATSCs (human adipose tissue-derived stem cells), mediated by the specific binding of the regulatory regions of functional genes, which positively or negatively altered gene expression. Ago2 targets genes that control stemness, reactive oxygen species scavenging, and microRNA expression, all of which are crucial for hATSC survival and self-renewal. Ago2 promotes cell proliferation and self-renewal by activating the expression of octamer-binding transcription factor 4 (Oct4). We confirmed the direct regulation of Oct4 activity by Ago2, as indicated by the results of the ChIP analysis. Methyl-CpG-binding protein 6 (MBD6) was detected as an Oct4 regulatory gene. As predicted, knockdown of MBD6 expression attenuated cell proliferation and eventually induced cell death. We hypothesized that MBD6 functions downstream of Oct4 in the regulation of stemness-related genes, cell proliferation, self-renewal activity, and survival. MBD6 also promoted cell transdifferentiation into neural and endodermal β-cells while significantly attenuating differentiation into the mesodermal lineage. We demonstrate that MBD6 is regulated by Ago2 via an interaction with Oct4, which alters self-renewal and gene expression in hATSCs. MBD6 was promoted cell proliferation through a novel set of signal mediators that may influence differentiation by repressing MBD2 and MBD3, which are possibly recruited by germ cell nuclear factor (GCNF).
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Affiliation(s)
- Jin Sun Jung
- Laboratory of Stem Cell Biology, Department of Biotechnology, College of Veterinary Medicine, Seoul National University, Seoul, 151-742 Republic of Korea
| | - Min Ki Jee
- Laboratory of Stem Cell Biology, Department of Biotechnology, College of Veterinary Medicine, Seoul National University, Seoul, 151-742 Republic of Korea
| | - Hyun Tae Cho
- Laboratory of Stem Cell Biology, Department of Biotechnology, College of Veterinary Medicine, Seoul National University, Seoul, 151-742 Republic of Korea
| | - Jee In Choi
- Laboratory of Stem Cell Biology, Department of Biotechnology, College of Veterinary Medicine, Seoul National University, Seoul, 151-742 Republic of Korea
| | - Young Bin Im
- Laboratory of Stem Cell Biology, Department of Biotechnology, College of Veterinary Medicine, Seoul National University, Seoul, 151-742 Republic of Korea
| | - Oh Hyun Kwon
- Laboratory of Stem Cell Biology, Department of Biotechnology, College of Veterinary Medicine, Seoul National University, Seoul, 151-742 Republic of Korea
| | - Soo Kyung Kang
- Laboratory of Stem Cell Biology, Department of Biotechnology, College of Veterinary Medicine, Seoul National University, Seoul, 151-742 Republic of Korea
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21
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Collings CK, Waddell PJ, Anderson JN. Effects of DNA methylation on nucleosome stability. Nucleic Acids Res 2013; 41:2918-31. [PMID: 23355616 PMCID: PMC3597673 DOI: 10.1093/nar/gks893] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Methylation of DNA at CpG dinucleotides represents one of the most important epigenetic mechanisms involved in the control of gene expression in vertebrate cells. In this report, we conducted nucleosome reconstitution experiments in conjunction with high-throughput sequencing on 572 KB of human DNA and 668 KB of mouse DNA that was unmethylated or methylated in order to investigate the effects of this epigenetic modification on the positioning and stability of nucleosomes. The results demonstrated that a subset of nucleosomes positioned by nucleotide sequence was sensitive to methylation where the modification increased the affinity of these sequences for the histone octamer. The features that distinguished these nucleosomes from the bulk of the methylation-insensitive nucleosomes were an increase in the frequency of CpG dinucleotides and a unique rotational orientation of CpGs such that their minor grooves tended to face toward the histones in the nucleosome rather than away. These methylation-sensitive nucleosomes were preferentially associated with exons as compared to introns while unmethylated CpG islands near transcription start sites became enriched in nucleosomes upon methylation. The results of this study suggest that the effects of DNA methylation on nucleosome stability in vitro can recapitulate what has been observed in the cell and provide a direct link between DNA methylation and the structure and function of chromatin.
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Affiliation(s)
- Clayton K Collings
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
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22
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Kelly RDW, Mahmud A, McKenzie M, Trounce IA, St John JC. Mitochondrial DNA copy number is regulated in a tissue specific manner by DNA methylation of the nuclear-encoded DNA polymerase gamma A. Nucleic Acids Res 2012; 40:10124-38. [PMID: 22941637 PMCID: PMC3488228 DOI: 10.1093/nar/gks770] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
DNA methylation is an essential mechanism controlling gene expression during differentiation and development. We investigated the epigenetic regulation of the nuclear-encoded, mitochondrial DNA (mtDNA) polymerase γ catalytic subunit (PolgA) by examining the methylation status of a CpG island within exon 2 of PolgA. Bisulphite sequencing identified low methylation levels (<10%) within exon 2 of mouse oocytes, blastocysts and embryonic stem cells (ESCs), while somatic tissues contained significantly higher levels (>40%). In contrast, induced pluripotent stem (iPS) cells and somatic nuclear transfer ESCs were hypermethylated (>20%), indicating abnormal epigenetic reprogramming. Real time PCR analysis of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) immunoprecipitated DNA suggests active DNA methylation and demethylation within exon 2 of PolgA. Moreover, neural differentiation of ESCs promoted de novo methylation and demethylation at the exon 2 locus. Regression analysis demonstrates that cell-specific PolgA expression levels were negatively correlated with DNA methylation within exon 2 and mtDNA copy number. Finally, using chromatin immunoprecipitation (ChIP) against RNA polymerase II (RNApII) phosphorylated on serine 2, we show increased DNA methylation levels are associated with reduced RNApII transcriptional elongation. This is the first study linking nuclear DNA epigenetic regulation with mtDNA regulation during differentiation and cell specialization.
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Affiliation(s)
- Richard D W Kelly
- Mitochondrial Genetics Group, Centre for Reproduction and Development, Monash Institute of Medical Research, Monash University, 27-31 Wright Street, Clayton, Victoria 3168, Australia
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23
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Chatterjee R, Vinson C. CpG methylation recruits sequence specific transcription factors essential for tissue specific gene expression. BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1819:763-70. [PMID: 22387149 PMCID: PMC3371161 DOI: 10.1016/j.bbagrm.2012.02.014] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Revised: 02/13/2012] [Accepted: 02/14/2012] [Indexed: 01/22/2023]
Abstract
CG methylation is an epigenetically inherited chemical modification of DNA found in plants and animals. In mammals it is essential for accurate regulation of gene expression and normal development. Mammalian genomes are depleted for the CG dinucleotide, a result of the chemical deamination of methyl-cytosine in CG resulting in TpG. Most CG dinucleotides are methylated, but ~15% are unmethylated. Five percent of CGs cluster into ~20,000 regions termed CG islands (CGI) which are generally unmethylated. About half of CGIs are associated with housekeeping genes. In contrast, the gene body, repeats and transposable elements in which CGs are generally methylated. Unraveling the epigenetic machinery operating in normal cells is important for understanding the epigenetic aberrations that are involved in human diseases including cancer. With the advent of high-throughput sequencing technologies, it is possible to identify the CG methylation status of all 30million unique CGs in the human genome, and monitor differences in distinct cell types during differentiation and development. Here we summarize the present understanding of DNA methylation in normal cells and discuss recent observations that CG methylation can have an effect on tissue specific gene expression. We also discuss how aberrant CG methylation can lead to cancer. This article is part of a Special Issue entitled: Chromatin in time and space.
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24
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Rach EA, Winter DR, Benjamin AM, Corcoran DL, Ni T, Zhu J, Ohler U. Transcription initiation patterns indicate divergent strategies for gene regulation at the chromatin level. PLoS Genet 2011; 7:e1001274. [PMID: 21249180 PMCID: PMC3020932 DOI: 10.1371/journal.pgen.1001274] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Accepted: 12/13/2010] [Indexed: 11/18/2022] Open
Abstract
The application of deep sequencing to map 5' capped transcripts has confirmed the existence of at least two distinct promoter classes in metazoans: "focused" promoters with transcription start sites (TSSs) that occur in a narrowly defined genomic span and "dispersed" promoters with TSSs that are spread over a larger window. Previous studies have explored the presence of genomic features, such as CpG islands and sequence motifs, in these promoter classes, but virtually no studies have directly investigated the relationship with chromatin features. Here, we show that promoter classes are significantly differentiated by nucleosome organization and chromatin structure. Dispersed promoters display higher associations with well-positioned nucleosomes downstream of the TSS and a more clearly defined nucleosome free region upstream, while focused promoters have a less organized nucleosome structure, yet higher presence of RNA polymerase II. These differences extend to histone variants (H2A.Z) and marks (H3K4 methylation), as well as insulator binding (such as CTCF), independent of the expression levels of affected genes. Notably, differences are conserved across mammals and flies, and they provide for a clearer separation of promoter architectures than the presence and absence of CpG islands or the occurrence of stalled RNA polymerase. Computational models support the stronger contribution of chromatin features to the definition of dispersed promoters compared to focused start sites. Our results show that promoter classes defined from 5' capped transcripts not only reflect differences in the initiation process at the core promoter but also are indicative of divergent transcriptional programs established within gene-proximal nucleosome organization.
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Affiliation(s)
- Elizabeth A. Rach
- Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina, United States of America
| | - Deborah R. Winter
- Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina, United States of America
| | - Ashlee M. Benjamin
- Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina, United States of America
| | - David L. Corcoran
- Institute for Genome Sciences and Policy, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Ting Ni
- Institute for Genome Sciences and Policy, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Cell Biology, Duke University, Durham, North Carolina, United States of America
| | - Jun Zhu
- Institute for Genome Sciences and Policy, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Cell Biology, Duke University, Durham, North Carolina, United States of America
| | - Uwe Ohler
- Institute for Genome Sciences and Policy, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Computer Science, Duke University, Durham, North Carolina, United States of America
- * E-mail:
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25
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Yang F, Zhang L, Li J, Huang J, Wen R, Ma L, Zhou D, Li L. Trichostatin A and 5-azacytidine both cause an increase in global histone H4 acetylation and a decrease in global DNA and H3K9 methylation during mitosis in maize. BMC PLANT BIOLOGY 2010; 10:178. [PMID: 20718950 PMCID: PMC3095308 DOI: 10.1186/1471-2229-10-178] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Accepted: 08/18/2010] [Indexed: 05/04/2023]
Abstract
BACKGROUND Modifications of DNA and histones in various combinations are correlated with many cellular processes. In this study, we investigated the possible relationship between histone H4 tetraacetylation, DNA methylation and histone H3 dimethylation at lysine 9 during mitosis in maize root meristems. RESULTS Treatment with trichostatin A, which inhibits histone deacetylases, resulted in increased histone H4 acetylation accompanied by the decondensation of interphase chromatin and a decrease in both global H3K9 dimethylation and DNA methylation during mitosis in maize root tip cells. These observations suggest that histone acetylation may affect DNA and histone methylation during mitosis. Treatment with 5-azacytidine, a cytosine analog that reduces DNA methylation, caused chromatin decondensation and mediated an increase in H4 acetylation, in addition to reduced DNA methylation and H3K9 dimethylation during interphase and mitosis. These results suggest that decreased DNA methylation causes a reduction in H3K9 dimethylation and an increase in H4 acetylation. CONCLUSIONS The interchangeable effects of 5-azacytidine and trichostatin A on H4 acetylation, DNA methylation and H3K9 dimethylation indicate a mutually reinforcing action between histone acetylation, DNA methylation and histone methylation with respect to chromatin modification. Treatment with trichostatin A and 5-azacytidine treatment caused a decrease in the mitotic index, suggesting that H4 deacetylation and DNA and H3K9 methylation may contain the necessary information for triggering mitosis in maize root tips.
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Affiliation(s)
- Fei Yang
- Key laboratory of MOE for Plant Developmental Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Lu Zhang
- Key laboratory of MOE for Plant Developmental Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jun Li
- Key laboratory of MOE for Plant Developmental Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jing Huang
- Key laboratory of MOE for Plant Developmental Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Ruoyu Wen
- Key laboratory of MOE for Plant Developmental Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Lu Ma
- Key laboratory of MOE for Plant Developmental Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Dongfeng Zhou
- Tongji medical colleges, Huazhong Science and Technology University, Wuhan 430030, China
| | - Lijia Li
- Key laboratory of MOE for Plant Developmental Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
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26
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Bauer AP, Leikam D, Krinner S, Notka F, Ludwig C, Längst G, Wagner R. The impact of intragenic CpG content on gene expression. Nucleic Acids Res 2010; 38:3891-908. [PMID: 20203083 PMCID: PMC2896515 DOI: 10.1093/nar/gkq115] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The development of vaccine components or recombinant therapeutics critically depends on sustained expression of the corresponding transgene. This study aimed to determine the contribution of intragenic CpG content to expression efficiency in transiently and stably transfected mammalian cells. Based upon a humanized version of green fluorescent protein (GFP) containing 60 CpGs within its coding sequence, a CpG-depleted variant of the GFP reporter was established by carefully modulating the codon usage. Interestingly, GFP reporter activity and detectable protein amounts in stably transfected CHO and 293 cells were significantly decreased upon CpG depletion and independent from promoter usage (CMV, EF1α). The reduction in protein expression associated with CpG depletion was likewise observed for other unrelated reporter genes and was clearly reflected by a decline in mRNA copy numbers rather than translational efficiency. Moreover, decreased mRNA levels were neither due to nuclear export restrictions nor alternative splicing or mRNA instability. Rather, the intragenic CpG content influenced de novo transcriptional activity thus implying a common transcription-based mechanism of gene regulation via CpGs. Increased high CpG transcription correlated with changed nucleosomal positions in vitro albeit histone density at the two genes did not change in vivo as monitored by ChIP.
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Affiliation(s)
- Asli Petra Bauer
- Institute of Medical Microbiology and Hygiene, Molecular Microbiology & Gene Therapy Unit, University of Regensburg, Regensburg, Germany
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27
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Bettecken T, Trifonov EN. Repertoires of the nucleosome-positioning dinucleotides. PLoS One 2009; 4:e7654. [PMID: 19888331 PMCID: PMC2765632 DOI: 10.1371/journal.pone.0007654] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Accepted: 10/02/2009] [Indexed: 11/18/2022] Open
Abstract
It is generally accepted that the organization of eukaryotic DNA into chromatin is strongly governed by a code inherent in the genomic DNA sequence. This code, as well as other codes, is superposed on the triplets coding for amino acids. The history of the chromatin code started three decades ago with the discovery of the periodic appearance of certain dinucleotides, with AA/TT and RR/YY giving the strongest signals, all with a period of 10.4 bases. Every base-pair stack in the DNA duplex has specific deformation properties, thus favoring DNA bending in a specific direction. The appearance of the corresponding dinucleotide at the distance 10.4 xn bases will facilitate DNA bending in that direction, which corresponds to the minimum energy of DNA folding in the nucleosome. We have analyzed the periodic appearances of all 16 dinucleotides in the genomes of thirteen different eukaryotic organisms. Our data show that a large variety of dinucleotides (if not all) are, apparently, contributing to the nucleosome positioning code. The choice of the periodical dinucleotides differs considerably from one organism to another. Among other 10.4 base periodicities, a strong and very regular 10.4 base signal was observed for CG dinucleotides in the genome of the honey bee A. mellifera. Also, the dinucleotide CG appears as the only periodical component in the human genome. This observation seems especially relevant since CpG methylation is well known to modulate chromatin packing and regularity. Thus, the selection of the dinucleotides contributing to the chromatin code is species specific, and may differ from region to region, depending on the sequence context.
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Affiliation(s)
- Thomas Bettecken
- CAGT-Center for Applied Genotyping, Max Planck Institute of Psychiatry, Munich, Germany.
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28
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Salih F, Salih B, Kogan S, Trifonov EN. Epigenetic nucleosomes: Alu sequences and CG as nucleosome positioning element. J Biomol Struct Dyn 2008; 26:9-16. [PMID: 18533722 DOI: 10.1080/07391102.2008.10507219] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Alu sequences carry periodical pattern with CG dinucleotides (CpG) repeating every 31-32 bases. Similar distances are observed in distribution of DNA curvature in crystallized nucleosomes, at positions +/-1.5 and +/-4.5 periods of DNA from nucleosome DNA dyad. Since CG elements are also found to impart to nucleosomes higher stability when positioned at +/-1.5 sites, it suggests that CG dinucleotides may play a role in modulation of the nucleosome strength when the CG elements are methylated. Thus, Alu sequences may harbor special epigenetic nucleosomes with methylation-dependent regulatory functions. Nucleosome DNA sequence probe is suggested to detect locations of such regulatory nucleosomes in the sequences.
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Affiliation(s)
- F Salih
- Genome Diversity Center, Institute of Evolution, University of Haifa, Israel
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29
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Abstract
The methyl-CpG-binding protein MeCP2 was discovered over 15 years ago as part of a search for proteins that selectively bind methylated DNA. It is a nuclear protein that is largely chromatin-bound and has a strong preference for binding to methylated DNA sequences in vivo. Evidence from model systems shows that MeCP2 can recruit the Sin3a co-repressor complex to promoters leading to transcriptional repression, therefore suggesting that MeCP2 can interpret the DNA methylation signal to bring about gene silencing. Mutations in the human MECP2 gene cause the autism spectrum disorder Rett Syndrome. MeCP2 is most highly expressed in neurons, and mice lacking this protein show symptoms that strikingly parallel those of Rett patients. Surprisingly, these symptoms are efficiently reversed by delayed activation of a ‘stopped’ Mecp2 gene, raising hopes that human Rett syndrome may also be reversible. Future studies of MeCP2 promise to shed light upon brain function, neurological disease and the biology of DNA methylation.
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30
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Abstract
DNA methylation is an epigenetic modification which plays an important role in chromatin organization and gene expression. DNA methylation can silence genes and repetitive elements through a process which leads to the alteration of chromatin structure. The mechanisms which target DNA methylation to specific sites in the genome are not fully understood. In this review, we will discuss the mechanisms which lead to the long-term silencing of genes and will survey the progression that has been made in determining the targeted mechanisms for de novo DNA methylation.
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Affiliation(s)
- Tina Branscombe Miranda
- Department of Urology, Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
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31
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Wong B, Chen S, Kwon JA, Rich A. Characterization of Z-DNA as a nucleosome-boundary element in yeast Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 2007; 104:2229-34. [PMID: 17284586 PMCID: PMC1892989 DOI: 10.1073/pnas.0611447104] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In this article, the effect of a d(CG) DNA dinucleotide repeat sequence on RNA polymerase II transcription is examined in yeast Saccharomyces cerevisiae. Our previous report shows that a d(CG)n dinucleotide repeat sequence located proximally upstream of the TATA box enhances transcription from a minimal CYC1 promoter in a manner that depends on its surrounding negative supercoiling. Here, we demonstrate that the d(CG)9 repeat sequence stimulates gene activity by forming a Z-DNA secondary structure. Furthermore, the extent of transcriptional enhancement by Z-DNA is promoter-specific and determined by its separation distance relative to the TATA box. The stimulatory effect exerted by promoter proximal Z-DNA is not affected by helical phasing relative to the TATA box, suggesting that Z-DNA effects transcription without interacting with the general transcription machinery by looping-out the intervening DNA. A nucleosome-scanning assay reveals that the d(CG)9 repeat sequence in the Z conformation blocks nucleosome formation, and it is found in the linker DNA with two flanking nucleosomes. This result suggests that Z-DNA formation proximally upstream of a promoter is sufficient to demarcate the boundaries of its neighboring nucleosomes, which produces transcriptionally favorable locations for the TATA box near the nucleosomal DNA-entry site and at dyad positions on the nucleosome. These findings suggest that Z-DNA formation in chromatin is a part of the "genomic code" for nucleosome positioning in vivo.
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Affiliation(s)
- Ben Wong
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139
| | - Shuai Chen
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139
| | - Jin-Ah Kwon
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139
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32
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Brackertz M, Gong Z, Leers J, Renkawitz R. p66alpha and p66beta of the Mi-2/NuRD complex mediate MBD2 and histone interaction. Nucleic Acids Res 2006; 34:397-406. [PMID: 16415179 PMCID: PMC1331983 DOI: 10.1093/nar/gkj437] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Mi-2/NuRD complex is a multi-subunit protein complex with enzymatic activities involving chromatin remodeling and histone deacetylation. Targeting of Mi-2/NuRD to methylated CpG sequences mediates gene repression. The function of p66alpha and of p66beta within the multiple subunits has not been addressed. Here, we analyzed the in vivo function and binding of both p66-paralogs. Both factors function in synergy, since knocking-down p66alpha affects the repressive function of p66beta and vice versa. Both proteins interact with MBD2 functionally and biochemically. Mutation of a single amino acid of p66alpha abolishes in vivo binding to MBD2 and interferes with MBD2-mediated repression. This loss of binding results in a diffuse nuclear localization in contrast to wild-type p66alpha that shows a speckled nuclear distribution. Furthermore, wild-type subnuclear distribution of p66alpha and p66beta depends on the presence of MBD2. Both proteins interact with the tails of all octamer histones in vitro, and acetylation of histone tails interferes with p66 binding. The conserved region 2 of p66alpha is required for histone tail interaction as well as for wild-type subnuclear distribution. These results suggest a two-interaction forward feedback binding mode, with a stable chromatin association only after deacetylation of the histones has occurred.
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Affiliation(s)
| | | | | | - Rainer Renkawitz
- To whom correspondence should be addressed. Tel: +49 641 99 35460; Fax: +49 641 99 35469;
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33
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Abstract
Studies of histone modification patterns and their role in gene regulation have led to the proposal that there is a "histone code." We have developed a method for nucleosome immunoprecipitation that can precisely identify the specific nucleosomes that carry a posttranslational modification of interest. The process involves the isolation and micrococcal nuclease digestion of minichromosomes to generate nucleosome core particles. These are then used in immunoprecipitation reactions with an antibody directed against the histone modification of interest. Subsequently, nucleosome core particle DNA is purified and end labeled. The original locations of the nucleosomes in the immunoprecipitate can be determined at low resolution (using a modified Southern blot hybridization procedure) or at maximal resolution (using the monomer extension method). Using the latter method, the positions of specific nucleosomes that carry the posttranslational modification of interest can be identified precisely. This method is sensitive, provides maximal resolution, and is inexpensive. The approach described here may serve as a paradigm for the study of histone-modifying patterns.
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Affiliation(s)
- David J Clark
- Laboratory of Molecular Growth Regulation, NICHD, National Institutes of Health, Bethesda, Maryland, USA
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34
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Zhu Y, Brown HN, Zhang Y, Holford TR, Zheng T. Genotypes and haplotypes of the methyl-CpG-binding domain 2 modify breast cancer risk dependent upon menopausal status. Breast Cancer Res 2005; 7:R745-52. [PMID: 16168120 PMCID: PMC1242141 DOI: 10.1186/bcr1283] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2004] [Revised: 06/07/2005] [Accepted: 06/24/2005] [Indexed: 01/02/2023] Open
Abstract
Introduction MBD2, the gene encoding methyl-CpG-binding domain (MBD)2, is a major methylation related gene and functions as a transcriptional repressor that can specifically bind to the methylated regions of other genes. MBD2 may also mediate gene activation because of its potential DNA demethylase activity. The present case-control study investigated associations between two single nucleotide polymorphisms (SNPs) in the MBD2 gene and breast cancer risk. Methods DNA samples from 393 Caucasian patients with breast cancer (cases) and 436 matched control individuals, collected in a recently completed breast cancer case–control study conducted in Connecticut, were included in the study. Because no coding SNPs were found in the MBD2 gene, one SNP in the noncoding exon (rs1259938) and another in the intron 3 (rs609791) were genotyped. Odds ratios (ORs) with 95% confidence intervals (CIs) were calculated to estimate cancer risk associated with the variant genotypes and the reconstructed haplotypes. Results The variant genotypes at both SNP loci were significantly associated with reduced risk among premenopausal women (OR = 0.41 for rs1259938; OR = 0.54 for rs609791). Further haplotype analyses showed that the two rare haplotypes (A-C and A-G) were significantly associated with reduced breast cancer risk (OR = 0.40, 95% CI = 0.20–0.83 for A-C; OR = 0.47, 95% CI = 0.26–0.84 for A-G) in premenopausal women. No significant associations were detected in the postmenopausal women and the whole population. Conclusion Our results demonstrate a role for the MBD2 gene in breast carcinogenesis in premenopausal women. These findings suggest that genetic variations in methylation related genes may potentially serve as a biomarker in risk estimates for breast cancer.
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Affiliation(s)
- Yong Zhu
- Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Heather N Brown
- Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Yawei Zhang
- Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Theodore R Holford
- Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Tongzhang Zheng
- Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, Connecticut, USA
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Davey CS, Pennings S, Reilly C, Meehan RR, Allan J. A determining influence for CpG dinucleotides on nucleosome positioning in vitro. Nucleic Acids Res 2004; 32:4322-31. [PMID: 15310836 PMCID: PMC514372 DOI: 10.1093/nar/gkh749] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
DNA sequence information that directs the translational positioning of nucleosomes can be attenuated by cytosine methylation when a short run of CpG dinucleotides is located close to the dyad axis of the nucleosome. Here, we show that point mutations introduced to re-pattern methylation at the (CpG)3 element in the chicken betaA-globin promoter sequence themselves strongly influenced nucleosome formation in reconstituted chromatin. The disruptive effect of cytosine methylation on nucleosome formation was found to be determined by the sequence context of CpG dinucleotides, not just their location in the positioning sequence. Additional mutations indicated that methylation can also promote the occupation of certain nucleosome positions. DNase I analysis demonstrated that these genetic and epigenetic modifications altered the structural characteristics of the (CpG)3 element. Our findings support a proposal that the intrinsic structural properties of the DNA at the -1.5 site, as occupied by (CpG)3 in the nucleosome studied, can be decisive for nucleosome formation and stability, and that changes in anisotropic DNA bending or flexibility at this site explain why nucleosome positioning can be exquisitely sensitive to genetic and epigenetic modification of the DNA sequence.
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Affiliation(s)
- Colin S Davey
- Institute of Cell and Molecular Biology, University of Edinburgh, Darwin Building, King's Buildings, West Mains Road, Edinburgh EH9 3JR, UK
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36
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Chan Y, Fish JE, D'Abreo C, Lin S, Robb GB, Teichert AM, Karantzoulis-Fegaras F, Keightley A, Steer BM, Marsden PA. The cell-specific expression of endothelial nitric-oxide synthase: a role for DNA methylation. J Biol Chem 2004; 279:35087-100. [PMID: 15180995 DOI: 10.1074/jbc.m405063200] [Citation(s) in RCA: 186] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The basis for the endothelial cell-restricted expression of endothelial nitric-oxide synthase (eNOS) is not known. While transgenic promoter/reporter mice demonstrated endothelium cell-specific eNOS expression, we found robust expression of episomal eNOS promoter/reporter constructs in cell types that do not express the native eNOS transcript. To explore the mechanism underlying this differential activity pattern of chromatin-versus episome-based eNOS promoters, we examined the methylation status of 5'-regulatory sequences of the human eNOS gene. DNA methylation differed dramatically between endothelial and nonendothelial cell types, including vascular smooth muscle cells. This same cell type-specific methylation pattern was observed in vivo in endothelial and vascular smooth muscle cells of the mouse aorta at the native murine eNOS promoter. We addressed the functional consequences of methylation on eNOS transcription using transient transfection of in vitro methylated promoter/reporter constructs and found that methylated constructs exhibited a marked decrease in the synergistic action of Sp1, Sp3, and Ets1 on eNOS promoter activity. The addition of methyl-CpG-binding protein 2 further reduced the transcriptional activity of methylated eNOS constructs. Importantly, chromatin immunoprecipitation demonstrated the presence of Sp1, Sp3, and Ets1 at the native eNOS promoter in endothelial cells but not in vascular smooth muscle cells. Finally, robust expression of eNOS mRNA was induced in nonendothelial cell types following inhibition of DNA methyltransferase activity with 5-azacytidine, demonstrating the importance of DNA methylation-mediated repression. This report is the first to show that promoter DNA methylation plays an important role in the cell-specific expression of a constitutively expressed gene in the vascular endothelium.
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MESH Headings
- Animals
- Aorta/pathology
- Azacitidine/pharmacology
- Cattle
- Cell Line
- Cell Line, Tumor
- Cells, Cultured
- Chromatin/metabolism
- CpG Islands
- DNA Methylation
- DNA-Binding Proteins/metabolism
- Drosophila
- Endothelium, Vascular/cytology
- Endothelium, Vascular/metabolism
- Genes, Reporter
- Genetic Vectors
- Humans
- Jurkat Cells
- Luciferases/metabolism
- Mice
- Muscle, Smooth, Vascular/metabolism
- Nitric Oxide Synthase/biosynthesis
- Nitric Oxide Synthase Type II
- Nitric Oxide Synthase Type III
- Precipitin Tests
- Promoter Regions, Genetic
- Proto-Oncogene Protein c-ets-1
- Proto-Oncogene Proteins/metabolism
- Proto-Oncogene Proteins c-ets
- RNA, Messenger/metabolism
- Ribonucleases/metabolism
- Sp1 Transcription Factor/metabolism
- Sp3 Transcription Factor
- Sulfites/pharmacology
- Transcription Factors/metabolism
- Transcription, Genetic
- Transfection
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Affiliation(s)
- Yvonne Chan
- Renal Division and Department of Medicine, St. Michael's Hospital and University of Toronto, Toronto, Ontario M5S 1A8, Canada
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37
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Davey C, Allan J. Nucleosome positioning signals and potential H-DNA within the DNA sequence of the imprinting control region of the mouse Igf2r gene. ACTA ACUST UNITED AC 2004; 1630:103-16. [PMID: 14654240 DOI: 10.1016/j.bbaexp.2003.09.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The imprinting control region within the second intron of the mouse Igf2r gene contains a CpG island comprising direct repeats, an imprinting box and the Air antisense promoter which is blocked by the methylation imprint on the active maternal allele. We have investigated the structural features of this DNA, including a mapping of all nucleosome positioning signals within the nucleotide sequence. A discrete series of strong positioning signals distinguished the direct repeat region from the much more diverse positioning capacity of the sequence encompassing the known regulatory elements. At only a few locations did CpG methylation modulate the use of this positioning information. Direct effects upon histone-DNA interactions are therefore unlikely to contribute significantly to the means by which the imprint may establish allele-specific chromatin architecture and determine Air expression. A strand-specific obstruction to DNA polymerase was observed between the repeat and regulatory regions. The same region adopts triple-stranded H-DNA structures in supercoiled DNA, according to pH and divalent cation exposure. Methylation did not modulate the occurrence or form of this structure under the conditions tested. This finding nevertheless adds to the repertoire of potential H-DNA structures found in the vicinity of regulatory sequences-here, in an imprinting context.
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Affiliation(s)
- C Davey
- Institute of Cell and Molecular Biology, University of Edinburgh, UK
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38
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Gilbert N, Gilchrist S, Bickmore WA. Chromatin organization in the mammalian nucleus. INTERNATIONAL REVIEW OF CYTOLOGY 2004; 242:283-336. [PMID: 15598472 DOI: 10.1016/s0074-7696(04)42007-5] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mammalian cells package their DNA into chromatin and arrange it in the nucleus as chromosomes. In interphase cells chromosomes are organized in a radial distribution with the most gene-dense chromosomes toward the center of the nucleus. Gene transcription, replication, and repair are influenced by the underlying chromatin architecture, which in turn is affected by the formation of chromosome territories. This arrangement in the nucleus presumably facilitates cellular functions to occur in an efficient and ordered fashion and exploring the link between transcription and nuclear organization will be an exciting area of further research.
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Affiliation(s)
- Nick Gilbert
- MRC Human Genetics Unit, Western General Hospital, Edinburgh EH4 2XU, UK
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39
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Rothem L, Stark M, Kaufman Y, Mayo L, Assaraf YG. Reduced folate carrier gene silencing in multiple antifolate-resistant tumor cell lines is due to a simultaneous loss of function of multiple transcription factors but not promoter methylation. J Biol Chem 2003; 279:374-84. [PMID: 14551190 DOI: 10.1074/jbc.m309092200] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The human reduced folate carrier (hRFC) is the major uptake route for antifolates used in cancer chemotherapy. Here we explored the molecular basis for the decrease or loss of hRFC gene expression in seventeen tumor cell lines with resistance to multiple antifolates due to impaired antifolate transport. We studied the role of various cis-acting elements including CRE/AP-1-like element and GC-box in hRFC promoters A and B, respectively, as well as AP-2, Mzf-1 and E-box that are contained within or near four tandemly repeated sequences upstream of promoter A. Decreased or abolished binding either to [32P]GC-box, Mzf-1, AP-1, E-box, or CRE oligonucleotides was detected in approximately 50-80% of antifolate-resistant cell lines. Strikingly, approximately 80% of the cell lines displayed a simultaneously decreased binding to three or more of these hRFC promoter elements, whereas normal AP-2 binding was retained. The possible contribution of promoter methylation to hRFC gene silencing was also explored. None of the antifolate-resistant cell lines, except for MDA-MB-231 cells, showed hRFC promoter methylation; consistently, MDA-MB-231 was the only cell line that retained binding to all six cis-acting elements. Western blot analysis demonstrated decreased expression of transcriptional activators (pCREB-1, pATF-1, USF-1, c-Fos, c-Jun, Sp1, and Sp3) and/or increased expression of repressors (short Sp3 isoforms), whereas normal AP2alpha levels were retained. Transient expression of the relevant transcription factors restored, at least partially, both promoter binding and hRFC gene expression. This is the first report that transcriptional silencing of the hRFC gene in multiple tumor cell lines with resistance to various novel antifolates is a result of a simultaneous loss of function of multiple transcription factors but not promoter methylation.
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Affiliation(s)
- Lilah Rothem
- Department of Biology, The Technion-Israel Institute of Technology, Haifa 32000, Israel
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40
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GORELICK ROOT. Transposable elements suppress recombination in all meiotic eukaryotes, including automictic ancient asexuals: a reply to Schön and Martens. J NAT HIST 2003. [DOI: 10.1080/0022293021000007705] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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41
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Abstract
Nuclear transfer experiments have demonstrated that epigenetic mechanisms operate to limit gene expression during animal development. In somatic cells, silenced genes are associated with defined chromatin states which are characterised by hypermethylation of DNA, hypoacetylation of histones and specific patterns of methylation at distinct residues of the N-terminal tails of histone H3 and H4. This review describes the role of the DNA methylation-mediated repression system (Dnmt1's, MeCPs and MBDs and associated chromatin remodelling activities) in animal development. DNA methylation is essential for normal vertebrate development but has distinct regulatory roles in non-mammalian and mammalian vertebrates. In mammals, DNA methylation has an additional role in regulating imprinting. This suggests that epigenetic regulation is plastic in its application and should be considered in a developmental context that may be species specific.
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Affiliation(s)
- Richard R Meehan
- Genes and Development Group, Department of Biomedical Sciences, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh, Scotland EH8 9XD, UK
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42
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Davey C, Fraser R, Smolle M, Simmen MW, Allan J. Nucleosome positioning signals in the DNA sequence of the human and mouse H19 imprinting control regions. J Mol Biol 2003; 325:873-87. [PMID: 12527297 DOI: 10.1016/s0022-2836(02)01340-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We have investigated the sequences of the mouse and human H19 imprinting control regions (ICRs) to see whether they contain nucleosome positioning information pertinent to their function as a methylation-regulated chromatin boundary. Positioning signals were identified by an in vitro approach that employs reconstituted chromatin to comprehensively describe the contribution of the DNA to the most basic, underlying level of chromatin structure. Signals in the DNA sequence of both ICRs directed nucleosomes to flank and encompass the short conserved sequences that constitute the binding sites for the zinc finger protein CTCF, an essential mediator of insulator activity. The repeat structure of the human ICR presented a conserved array of strong positioning signals that would preferentially flank these CTCF binding sites with positioned nucleosomes, a chromatin structure that would tend to maintain their accessibility. Conversely, all four CTCF binding sites in the mouse sequence were located close to the centre of positioning signals that were stronger than those in their flanks; these binding sites might therefore be expected to be more readily incorporated into positioned nucleosomes. We found that CpG methylation did not effect widespread repositioning of nucleosomes on either ICR, indicating that allelic methylation patterns were unlikely to establish allele-specific chromatin structures for H19 by operating directly upon the underlying DNA-histone interactions; instead, epigenetic modulation of ICR chromatin structure is likely to be mediated principally at higher levels of control. DNA methylation did, however, both promote and inhibit nucleosome positioning at several sites in both ICRs and substantially negated one of the strongest nucleosome positioning signals in the human sequence, observations that underline the fact that this epigenetic modification can, nevertheless, directly and decisively modulate core histone-DNA interactions within the nucleosome.
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Affiliation(s)
- C Davey
- Institute of Cell and Molecular Biology, University of Edinburgh, Darwin Building, King's Buildings, West Mains Road, Scotland EH9 3JR, Edinburgh, UK
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43
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Steward N, Ito M, Yamaguchi Y, Koizumi N, Sano H. Periodic DNA methylation in maize nucleosomes and demethylation by environmental stress. J Biol Chem 2002; 277:37741-6. [PMID: 12124387 DOI: 10.1074/jbc.m204050200] [Citation(s) in RCA: 197] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
When maize seedlings were exposed to cold stress, a genome-wide demethylation occurred in root tissues. Screening of genomic DNA identified one particular fragment that was demethylated during chilling. This 1.8-kb fragment, designated ZmMI1, contained part of the coding region of a putative protein and part of a retrotransposon-like sequence. ZmMI1 was transcribed only under cold stress. Direct methylation mapping revealed that hypomethylated regions spanning 150 bases alternated with hypermethylated regions spanning 50 bases. Analysis of nuclear DNA digested with micrococcal nuclease indicated that these regions corresponded to nucleosome cores and linkers, respectively. Cold stress induced severe demethylation in core regions but left linker regions relatively intact. Thus, methylation and demethylation were periodic in nucleosomes. The following biological significance is conceivable. First, because DNA methylation in nucleosomes induces alteration of gene expression by changing chromatin structures, vast demethylation may serve as a common switch for many genes that are simultaneously controlled upon environmental cues. Second, because artificial demethylation induces heritable changes in plant phenotype (Sano, H., Kamada, I., Youssefian, S., Katsumi, M., and Wabilko, H. (1990) Mol. Gen. Genet. 220, 441-447), altered DNA methylation may result in epigenetic inheritance, in which gene expression is modified without changing the nucleotide sequence.
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Affiliation(s)
- Nicolas Steward
- Research and Education Center for Genetic Information, Nara Institute of Science and Technology, Nara 630-0101, Japan
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44
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El-Osta A. FMR1 silencing and the signals to chromatin: a unified model of transcriptional regulation. Biochem Biophys Res Commun 2002; 295:575-81. [PMID: 12099676 DOI: 10.1016/s0006-291x(02)00682-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Understanding the effect of DNA methylation requires an appreciation of the determinants responsible for gene expression. To this end, we and others have demonstrated the exquisite silencing properties of methylation-dependent repressors that belong to the methyl-CpG binding domain (MBD) protein family. It is crucial, to establish a direct connection between the remodelling events observed with the fragile X mental retardation gene 1 (FMR1) promoter if we are to understand the mechanism of control. In this paper contrasting but not mutually exclusive models are discussed, which conceptually and experimentally reflects an appreciation of the surrounding chromatin environment. Examining general transcription systems controlled by DNA methylation, proteins that recognize the methyl-CpG moiety and the enzyme that maintains methylation, a unified model of FMR1 gene silencing are discussed.
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Affiliation(s)
- Assam El-Osta
- Sir Donald and Lady Trescowthick Research Laboratories, Peter MacCallum Cancer Institute, St. Andrews Place, East Melbourne, Vic. 3002, Australia.
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45
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MESH Headings
- Acute Disease
- Angiogenesis Inhibitors/therapeutic use
- Animals
- Antineoplastic Agents/therapeutic use
- Antineoplastic Agents, Alkylating/adverse effects
- Antineoplastic Agents, Alkylating/therapeutic use
- Chromosome Deletion
- Chromosomes, Human, Pair 11/genetics
- Chromosomes, Human, Pair 11/ultrastructure
- Chromosomes, Human, Pair 7/genetics
- Chromosomes, Human, Pair 7/ultrastructure
- DNA Methylation
- DNA-Binding Proteins/genetics
- Enzyme Inhibitors/adverse effects
- Enzyme Inhibitors/therapeutic use
- Forecasting
- Genes, Tumor Suppressor
- Hematopoietic Stem Cells/drug effects
- Histone Deacetylase Inhibitors
- Histone-Lysine N-Methyltransferase
- Humans
- Leukemia, Experimental/etiology
- Leukemia, Experimental/pathology
- Leukemia, Myeloid/chemically induced
- Leukemia, Myeloid/drug therapy
- Leukemia, Myeloid/genetics
- Leukemia, Radiation-Induced/pathology
- Mice
- Mice, Inbred NOD
- Mice, SCID
- Myeloid-Lymphoid Leukemia Protein
- Neoplasm Proteins/antagonists & inhibitors
- Neoplasms/drug therapy
- Neoplasms/radiotherapy
- Neoplasms, Second Primary/chemically induced
- Neoplasms, Second Primary/drug therapy
- Neoplasms, Second Primary/genetics
- Neoplastic Stem Cells/drug effects
- Neovascularization, Pathologic/drug therapy
- Neovascularization, Pathologic/pathology
- Oncogene Proteins, Fusion/genetics
- Proto-Oncogenes
- Stromal Cells/pathology
- Topoisomerase II Inhibitors
- Transcription Factors
- Translocation, Genetic
- Xenograft Model Antitumor Assays
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Affiliation(s)
- I Gojo
- University of Maryland School of Medicine, Marlene and Stewart Greenebaum Cancer Center, Baltimore, MD, USA
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46
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Karrer KM, VanNuland TA. Methylation of adenine in the nuclear DNA of Tetrahymena is internucleosomal and independent of histone H1. Nucleic Acids Res 2002; 30:1364-70. [PMID: 11884634 PMCID: PMC101364 DOI: 10.1093/nar/30.6.1364] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
There are about 50 copies of each chromosome in the somatic macronucleus of the ciliated protozoan TETRAHYMENA: Approximately 0.8% of the adenine residues in the macronuclear DNA of Tetrahymena are methylated to N6-methyladenine. The degree of methylation varies between sites from a very low percentage to >90%. In this study a correlation was found between nucleosome positioning and DNA methylation. Eight GATC sites with different levels of methylation were examined. There was a direct correlation between the degree of methylation and proximity to linker DNA at these sites. Although methylation occurs preferentially in linker DNA, the patterns and extent of methylation in a histone H1 knockout strain were virtually indistinguishable from those in wild-type cells.
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Affiliation(s)
- Kathleen M Karrer
- Department of Biology, Wehr Life Sciences, Marquette University, PO Box 1881, Milwaukee, WI 53201-1881, USA.
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47
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Abstract
We used cyclization kinetics experiments and Monte Carlo simulations to determine a structural model for a DNA decamer containing the EcoRI restriction site. Our findings agree well with recent crystal and NMR structures of the EcoRI dodecamer, where an overall bend of seven degrees is distributed symmetrically over the molecule. Monte Carlo simulations indicate that the sequence has a higher flexibility, assumed to be isotropic, compared to that of a "generic" DNA sequence. This model was used as a starting point for the investigation of the effect of cytosine methylation on DNA bending and flexibility. While methylation did not affect bend magnitude or direction, it resulted in a reduction in bending flexibility and under-winding of the methylated nucleotides. We demonstrate that our approach can augment the understanding of DNA structure and dynamics by adding information about the global structure and flexibility of the sequence. We also show that cyclization kinetics can be used to study the properties of modified nucleotides.
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Affiliation(s)
- Dafna Nathan
- Departments of Chemistry, Yale University, New Haven, CT 06520, USA
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48
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Karymov MA, Tomschik M, Leuba SH, Caiafa P, Zlatanova J. DNA methylation-dependent chromatin fiber compaction in vivo and in vitro: requirement for linker histone. FASEB J 2001; 15:2631-41. [PMID: 11726539 DOI: 10.1096/fj.01-0345com] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Dynamic alterations in chromatin structure mediated by postsynthetic histone modifications and DNA methylation constitute a major regulatory mechanism in DNA functioning. DNA methylation has been implicated in transcriptional silencing, in part by inducing chromatin condensation. To understand the methylation-dependent chromatin structure, we performed atomic force microscope (AFM) studies of fibers isolated from cultured cells containing normal or elevated levels of m5C. Chromatin fibers were reconstituted on control or methylated DNA templates in the presence or absence of linker histone. Visual inspection of AFM images, combined with quantitative analysis of fiber structural parameters, suggested that DNA methylation induced fiber compaction only in the presence of linker histones. This conclusion was further substantiated by biochemical results.
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Affiliation(s)
- M A Karymov
- Physical Molecular Biology, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-5055, USA
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49
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Chen C, Yang TP. Nucleosomes are translationally positioned on the active allele and rotationally positioned on the inactive allele of the HPRT promoter. Mol Cell Biol 2001; 21:7682-95. [PMID: 11604504 PMCID: PMC99939 DOI: 10.1128/mcb.21.22.7682-7695.2001] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2001] [Accepted: 08/20/2001] [Indexed: 11/20/2022] Open
Abstract
Differential chromatin structure is one of the hallmarks distinguishing active and inactive genes. For the X-linked human hypoxanthine phosphoribosyltransferase gene (HPRT), this difference in chromatin structure is evident in the differential general DNase I sensitivity and hypersensitivity of the promoter regions on active versus inactive X chromosomes. Here we characterize the nucleosomal organization responsible for the differential chromatin structure of the active and inactive HPRT promoters. The micrococcal nuclease digestion pattern of chromatin from the active allele in permeabilized cells reveals an ordered array of translationally positioned nucleosomes in the promoter region except over a 350-bp region that is either nucleosome free or contains structurally altered nucleosomes. This 350-bp region includes the entire minimal promoter and all of the multiple transcription initiation sites of the HPRT gene. It also encompasses all of the transcription factor binding sites identified by either dimethyl sulfate or DNase I in vivo footprinting of the active allele. In contrast, analysis of the inactive HPRT promoter reveals no hypersensitivity to either DNase I or a micrococcal nuclease and no translational positioning of nucleosomes. Although nucleosomes on the inactive promoter are not translationally positioned, high-resolution DNase I cleavage analysis of permeabilized cells indicates that nucleosomes are rotationally positioned over a region of at least 210 bp on the inactive promoter, which coincides with the 350-bp nuclease-hypersensitive region on the active allele, including the entire minimal promoter. This rotational positioning of nucleosomes is not observed on the active promoter. These results suggest a model in which the silencing of the HPRT promoter during X chromosome inactivation involves remodeling a transcriptionally competent, translationally positioned nucleosomal array into a transcriptionally repressed architecture consisting of rotationally but not translationally positioned nucleosomal arrays.
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Affiliation(s)
- C Chen
- Department of Biochemistry and Molecular Biology, Center for Mammalian Genetics, University of Florida, Gainesville, 32610, USA
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50
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Meints GA, Drobny GP. Dynamic impact of methylation at the M. Hhai target site: a solid-state deuterium NMR study. Biochemistry 2001; 40:12436-43. [PMID: 11591165 DOI: 10.1021/bi0102555] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Base methylation plays an important role in numerous biological functions of DNA, from inhibition of cleavage by endonucleases to inhibition of transcription factor binding. Studies of nucleic acid structure have shown little differences in unmethylated DNAs and the identical sequence containing methylated analogues. We have investigated changes in the local dynamics of DNA upon substitution of a methylated cytosine analogue for cytosine using solid-state deuterium NMR. In particular, we have observed changes in the local dynamics at the target site of the M. HhaI restriction system. These studies observe changes in the amplitudes of the local backbone dynamics at the actual target site of the HhaI methyltransferase. This conclusion is another indication that the significant result of base methylation is to perturb the local dynamics, and therefore the local conformational flexibility, of the DNA helix, inhibiting or restricting the protein's ability to manipulate the DNA helix in order to perform its chemical alterations.
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Affiliation(s)
- G A Meints
- Department of Chemistry, University of Washington, Seattle, 98195, USA
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