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Lüth T, Laβ J, Schaake S, Wohlers I, Pozojevic J, Jamora RDG, Rosales RL, Brüggemann N, Saranza G, Diesta CCE, Schlüter K, Tse R, Reyes CJ, Brand M, Busch H, Klein C, Westenberger A, Trinh J. Elucidating Hexanucleotide Repeat Number and Methylation within the X-Linked Dystonia-Parkinsonism (XDP)-Related SVA Retrotransposon in TAF1 with Nanopore Sequencing. Genes (Basel) 2022; 13:genes13010126. [PMID: 35052466 PMCID: PMC8775018 DOI: 10.3390/genes13010126] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/05/2022] [Accepted: 01/07/2022] [Indexed: 12/13/2022] Open
Abstract
Background: X-linked dystonia-parkinsonism (XDP) is an adult-onset neurodegenerative disorder characterized by progressive dystonia and parkinsonism. It is caused by a SINE-VNTR-Alu (SVA) retrotransposon insertion in the TAF1 gene with a polymorphic (CCCTCT)n domain that acts as a genetic modifier of disease onset and expressivity. Methods: Herein, we used Nanopore sequencing to investigate SVA genetic variability and methylation. We used blood-derived DNA from 96 XDP patients for amplicon-based deep Nanopore sequencing and validated it with fragment analysis which was performed using fluorescence-based PCR. To detect methylation from blood- and brain-derived DNA, we used a Cas9-targeted approach. Results: High concordance was observed for hexanucleotide repeat numbers detected with Nanopore sequencing and fragment analysis. Within the SVA locus, there was no difference in genetic variability other than variations of the repeat motif between patients. We detected high CpG methylation frequency (MF) of the SVA and flanking regions (mean MF = 0.94, SD = ±0.12). Our preliminary results suggest only subtle differences between the XDP patient and the control in predicted enhancer sites directly flanking the SVA locus. Conclusions: Nanopore sequencing can reliably detect SVA hexanucleotide repeat numbers, methylation and, lastly, variation in the repeat motif.
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Affiliation(s)
- Theresa Lüth
- Institute of Neurogenetics, University of Luebeck, 23538 Luebeck, Germany; (T.L.); (J.L.); (S.S.); (J.P.); (N.B.); (K.S.); (R.T.); (C.J.R.); (M.B.); (C.K.); (A.W.)
| | - Joshua Laβ
- Institute of Neurogenetics, University of Luebeck, 23538 Luebeck, Germany; (T.L.); (J.L.); (S.S.); (J.P.); (N.B.); (K.S.); (R.T.); (C.J.R.); (M.B.); (C.K.); (A.W.)
| | - Susen Schaake
- Institute of Neurogenetics, University of Luebeck, 23538 Luebeck, Germany; (T.L.); (J.L.); (S.S.); (J.P.); (N.B.); (K.S.); (R.T.); (C.J.R.); (M.B.); (C.K.); (A.W.)
| | - Inken Wohlers
- Medical Systems Biology Division, Luebeck Institute of Experimental Dermatology, University of Luebeck, 23538 Luebeck, Germany; (I.W.); (H.B.)
- Institute for Cardiogenetics, University of Luebeck, 23538 Luebeck, Germany
| | - Jelena Pozojevic
- Institute of Neurogenetics, University of Luebeck, 23538 Luebeck, Germany; (T.L.); (J.L.); (S.S.); (J.P.); (N.B.); (K.S.); (R.T.); (C.J.R.); (M.B.); (C.K.); (A.W.)
| | - Roland Dominic G. Jamora
- Department of Neurosciences, College of Medicine, Philippine General Hospital, University of the Philippines Manila, Manila 1000, Philippines;
| | - Raymond L. Rosales
- Department of Neurology and Psychiatry, The Hospital Neuroscience Institute, University of Santo Tomas, Manila 1008, Philippines;
| | - Norbert Brüggemann
- Institute of Neurogenetics, University of Luebeck, 23538 Luebeck, Germany; (T.L.); (J.L.); (S.S.); (J.P.); (N.B.); (K.S.); (R.T.); (C.J.R.); (M.B.); (C.K.); (A.W.)
- Department of Neurology, University of Luebeck, 23538 Luebeck, Germany
| | - Gerard Saranza
- Section of Neurology, Department of Internal Medicine, Chong Hua Hospital, Cebu City 6000, Philippines;
| | - Cid Czarina E. Diesta
- Department of Neurosciences, Movement Disorders Clinic, Makati Medical Center, Makati 1229, Philippines;
| | - Kathleen Schlüter
- Institute of Neurogenetics, University of Luebeck, 23538 Luebeck, Germany; (T.L.); (J.L.); (S.S.); (J.P.); (N.B.); (K.S.); (R.T.); (C.J.R.); (M.B.); (C.K.); (A.W.)
| | - Ronnie Tse
- Institute of Neurogenetics, University of Luebeck, 23538 Luebeck, Germany; (T.L.); (J.L.); (S.S.); (J.P.); (N.B.); (K.S.); (R.T.); (C.J.R.); (M.B.); (C.K.); (A.W.)
| | - Charles Jourdan Reyes
- Institute of Neurogenetics, University of Luebeck, 23538 Luebeck, Germany; (T.L.); (J.L.); (S.S.); (J.P.); (N.B.); (K.S.); (R.T.); (C.J.R.); (M.B.); (C.K.); (A.W.)
| | - Max Brand
- Institute of Neurogenetics, University of Luebeck, 23538 Luebeck, Germany; (T.L.); (J.L.); (S.S.); (J.P.); (N.B.); (K.S.); (R.T.); (C.J.R.); (M.B.); (C.K.); (A.W.)
| | - Hauke Busch
- Medical Systems Biology Division, Luebeck Institute of Experimental Dermatology, University of Luebeck, 23538 Luebeck, Germany; (I.W.); (H.B.)
- Institute for Cardiogenetics, University of Luebeck, 23538 Luebeck, Germany
| | - Christine Klein
- Institute of Neurogenetics, University of Luebeck, 23538 Luebeck, Germany; (T.L.); (J.L.); (S.S.); (J.P.); (N.B.); (K.S.); (R.T.); (C.J.R.); (M.B.); (C.K.); (A.W.)
| | - Ana Westenberger
- Institute of Neurogenetics, University of Luebeck, 23538 Luebeck, Germany; (T.L.); (J.L.); (S.S.); (J.P.); (N.B.); (K.S.); (R.T.); (C.J.R.); (M.B.); (C.K.); (A.W.)
| | - Joanne Trinh
- Institute of Neurogenetics, University of Luebeck, 23538 Luebeck, Germany; (T.L.); (J.L.); (S.S.); (J.P.); (N.B.); (K.S.); (R.T.); (C.J.R.); (M.B.); (C.K.); (A.W.)
- Correspondence:
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Abstract
Multicellular eukaryotic genomes show enormous differences in size. A substantial part of this variation is due to the presence of transposable elements (TEs). They contribute significantly to a cell's mass of DNA and have the potential to become involved in host gene control. We argue that the suppression of their activities by methylation of the C-phosphate-G (CpG) dinucleotide in DNA is essential for their long-term accommodation in the host genome and, therefore, to its expansion. An inevitable consequence of cytosine methylation is an increase in C-to-T transition mutations via deamination, which causes CpG loss. Cytosine deamination is often needed for TEs to take on regulatory functions in the host genome. Our study of the whole-genome sequences of 53 organisms showed a positive correlation between the size of a genome and the percentage of TEs it contains, as well as a negative correlation between size and the CpG observed/expected (O/E) ratio in both TEs and the host DNA. TEs are seldom found at promoters and transcription start sites, but they are found more at enhancers, particularly after they have accumulated C-to-T and other mutations. Therefore, the methylation of TE DNA allows for genome expansion and also leads to new opportunities for gene control by TE-based regulatory sites.
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Li B, Hu P, Zhu LB, You LL, Cao HH, Wang J, Zhang SZ, Liu MH, Toufeeq S, Huang SJ, Xu JP. DNA Methylation Is Correlated with Gene Expression during Diapause Termination of Early Embryonic Development in the Silkworm ( Bombyx mori). Int J Mol Sci 2020; 21:E671. [PMID: 31968548 PMCID: PMC7013401 DOI: 10.3390/ijms21020671] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 01/16/2020] [Accepted: 01/16/2020] [Indexed: 12/13/2022] Open
Abstract
DNA modification is a naturally occurring DNA modification in prokaryotic and eukaryotic organisms and is involved in several biological processes. Although genome-wide methylation has been studied in many insects, the understanding of global and genomic DNA methylation during insect early embryonic development, is lacking especially for insect diapause. In this study, we analyzed the relationship between DNA methylomes and transcriptomes in diapause-destined eggs compared to diapause-terminated eggs in the silkworm, Bombyx mori (B. mori). The results revealed that methylation was sparse in this species, as previously reported. Moreover, methylation levels in diapause-terminated eggs (HCl-treated) were 0.05% higher than in non-treated eggs, mainly due to the contribution of CG methylation sites. Methylation tends to occur in the coding sequences and promoter regions, especially at transcription initiation sites and short interspersed elements. Additionally, 364 methylome- and transcriptome-associated genes were identified, which showed significant differences in methylation and expression levels in diapause-destined eggs when compared with diapause-terminated eggs, and 74% of methylome and transcriptome associated genes showed both hypermethylation and elevated expression. Most importantly, Kyoto Encyclopaedia of Genes and Genomes (KEGG) analyses showed that methylation may be positively associated with Bombyx mori embryonic development, by regulating cell differentiation, metabolism, apoptosis pathways and phosphorylation. Through analyzing the G2/M phase-specific E3 ubiquitin-protein ligase (G2E3), we speculate that methylation may affect embryo diapause by regulating the cell cycle in Bombyx mori. These findings will help unravel potential linkages between DNA methylation and gene expression during early insect embryonic development and insect diapause.
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Affiliation(s)
- Bing Li
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China; (B.L.); (P.H.); (L.-B.Z.); (L.-L.Y.); (H.-H.C.); (J.W.); (S.-Z.Z.); (S.T.)
- Institute of Sericulture, Anhui Academy of Agricultural Sciences, Hefei 230061, Anhui, China;
| | - Pei Hu
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China; (B.L.); (P.H.); (L.-B.Z.); (L.-L.Y.); (H.-H.C.); (J.W.); (S.-Z.Z.); (S.T.)
- Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, Hefei 230036, Anhui, China
| | - Lin-Bao Zhu
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China; (B.L.); (P.H.); (L.-B.Z.); (L.-L.Y.); (H.-H.C.); (J.W.); (S.-Z.Z.); (S.T.)
- Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, Hefei 230036, Anhui, China
| | - Ling-Ling You
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China; (B.L.); (P.H.); (L.-B.Z.); (L.-L.Y.); (H.-H.C.); (J.W.); (S.-Z.Z.); (S.T.)
- Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, Hefei 230036, Anhui, China
| | - Hui-Hua Cao
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China; (B.L.); (P.H.); (L.-B.Z.); (L.-L.Y.); (H.-H.C.); (J.W.); (S.-Z.Z.); (S.T.)
- Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, Hefei 230036, Anhui, China
| | - Jie Wang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China; (B.L.); (P.H.); (L.-B.Z.); (L.-L.Y.); (H.-H.C.); (J.W.); (S.-Z.Z.); (S.T.)
- Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, Hefei 230036, Anhui, China
| | - Shang-Zhi Zhang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China; (B.L.); (P.H.); (L.-B.Z.); (L.-L.Y.); (H.-H.C.); (J.W.); (S.-Z.Z.); (S.T.)
- Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, Hefei 230036, Anhui, China
| | - Ming-Hui Liu
- Institute of Sericulture, Anhui Academy of Agricultural Sciences, Hefei 230061, Anhui, China;
| | - Shahzad Toufeeq
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China; (B.L.); (P.H.); (L.-B.Z.); (L.-L.Y.); (H.-H.C.); (J.W.); (S.-Z.Z.); (S.T.)
- Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, Hefei 230036, Anhui, China
| | - Shou-Jun Huang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China; (B.L.); (P.H.); (L.-B.Z.); (L.-L.Y.); (H.-H.C.); (J.W.); (S.-Z.Z.); (S.T.)
- Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, Hefei 230036, Anhui, China
| | - Jia-Ping Xu
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China; (B.L.); (P.H.); (L.-B.Z.); (L.-L.Y.); (H.-H.C.); (J.W.); (S.-Z.Z.); (S.T.)
- Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, Hefei 230036, Anhui, China
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Navarro E, Funtikova AN, Fíto M, Schröder H. Prenatal nutrition and the risk of adult obesity: Long-term effects of nutrition on epigenetic mechanisms regulating gene expression. J Nutr Biochem 2017; 39:1-14. [DOI: 10.1016/j.jnutbio.2016.03.012] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 03/23/2016] [Accepted: 03/27/2016] [Indexed: 12/19/2022]
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Yu DH, Waterland RA, Zhang P, Schady D, Chen MH, Guan Y, Gadkari M, Shen L. Targeted p16(Ink4a) epimutation causes tumorigenesis and reduces survival in mice. J Clin Invest 2014; 124:3708-12. [PMID: 25061879 DOI: 10.1172/jci76507] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 06/05/2014] [Indexed: 01/14/2023] Open
Abstract
Cancer has long been viewed as a genetic disease; however, epigenetic silencing as the result of aberrant promoter DNA methylation is frequently associated with cancer development, suggesting an epigenetic component to the disease. Nonetheless, it has remained unclear whether an epimutation (an aberrant change in epigenetic regulation) can induce tumorigenesis. Here, we exploited a functionally validated cis-acting regulatory element and devised a strategy to induce developmentally regulated genomic targeting of DNA methylation. We used this system to target DNA methylation within the p16(Ink4a) promoter in mice in vivo. Engineered p16(Ink4a) promoter hypermethylation led to transcriptional suppression in somatic tissues during aging and increased the incidence of spontaneous cancers in these mice. Further, mice carrying a germline p16(Ink4a) mutation in one allele and a somatic epimutation in the other had accelerated tumor onset and substantially shortened tumor-free survival. Taken together, these results provide direct functional evidence that p16(Ink4a) epimutation drives tumor formation and malignant progression and validate a targeted methylation approach to epigenetic engineering.
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Rebollo R, Miceli-Royer K, Zhang Y, Farivar S, Gagnier L, Mager DL. Epigenetic interplay between mouse endogenous retroviruses and host genes. Genome Biol 2012; 13:R89. [PMID: 23034137 PMCID: PMC3491417 DOI: 10.1186/gb-2012-13-10-r89] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 10/03/2012] [Indexed: 11/15/2022] Open
Abstract
Background Transposable elements are often the targets of repressive epigenetic modifications such as DNA methylation that, in theory, have the potential to spread toward nearby genes and induce epigenetic silencing. To better understand the role of DNA methylation in the relationship between transposable elements and genes, we assessed the methylation state of mouse endogenous retroviruses (ERVs) located near genes. Results We found that ERVs of the ETn/MusD family show decreased DNA methylation when near transcription start sites in tissues where the nearby gene is expressed. ERVs belonging to the IAP family, however, are generally heavily methylated, regardless of the genomic environment and the tissue studied. Furthermore, we found full-length ETn and IAP copies that display differential DNA methylation between their two long terminal repeats (LTRs), suggesting that the environment surrounding gene promoters can prevent methylation of the nearby LTR. Spreading from methylated ERV copies to nearby genes was rarely observed, with the regions between the ERVs and genes apparently acting as a boundary, enriched in H3K4me3 and CTCF, which possibly protects the unmethylated gene promoter. Furthermore, the flanking regions of unmethylated ERV copies harbor H3K4me3, consistent with spreading of euchromatin from the host gene toward ERV insertions. Conclusions We have shown that spreading of DNA methylation from ERV copies toward active gene promoters is rare. We provide evidence that genes can be protected from ERV-induced heterochromatin spreading by either blocking the invasion of repressive marks or by spreading euchromatin toward the ERV copy.
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Zhang Y, Shu J, Si J, Shen L, Estecio MRH, Issa JPJ. Repetitive elements and enforced transcriptional repression co-operate to enhance DNA methylation spreading into a promoter CpG-island. Nucleic Acids Res 2012; 40:7257-68. [PMID: 22600741 PMCID: PMC3424568 DOI: 10.1093/nar/gks429] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Repression of many tumor suppressor genes in cancer is concurrent with aberrantly increased DNA methylation levels at promoter CpG islands (CGIs). About one-fourth of empirically defined human promoters are surrounded by or contain clustered repetitive elements. It was previously observed that a sharp transition of methylation exists between highly methylated repetitive elements and unmethylated promoter-CGIs in normal tissues. The factors that lead to aberrant CGI hypermethylation in cancer remain poorly understood. Here, we established a site-specific integration system with enforced local transcriptional repression in colorectal cancer cells and monitored the occurrence of initial de novo methylation at specific CG sites adjacent to the CGI of the INSL6 promoter, which could be accelerated by binding a KRAB-containing transcriptional factor. Additional repetitive elements from P16 and RIL (PDLIM4), if situated adjacent to the promoter of INSL6, could confer DNA methylation spreading into the CGI particularly in the setting of KRAB-factor binding. However, a repressive chromatin alone was not sufficient to initiate DNA methylation, which required specific DNA sequences and was integration-site (and/or cell-line) specific. Overall, these results demonstrate a requirement for specific DNA sequences to trigger de novo DNA methylation, and repetitive elements as cis-regulatory factors to cooperate with advanced transcriptional repression in promoting methylation spreading.
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Affiliation(s)
- Yan Zhang
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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Bire S, Rouleux-Bonnin F. Transposable elements as tools for reshaping the genome: it is a huge world after all! Methods Mol Biol 2012; 859:1-28. [PMID: 22367863 DOI: 10.1007/978-1-61779-603-6_1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Transposable elements (TEs) are discrete pieces of DNA that can move from one site to another within genomes and sometime between genomes. They are found in all major branches of life. Because of their wide distribution and considerable diversity, they are a considerable source of genomic variation and as such, they constitute powerful drivers of genome evolution. Moreover, it is becoming clear that the epigenetic regulation of certain genes is derived from defense mechanisms against the activity of ancestral transposable elements. TEs now tend to be viewed as natural molecular tools that can reshape the genome, which challenges the idea that TEs are natural tools used to answer biological questions. In the first part of this chapter, we review the classification and distribution of TEs, and look at how they have contributed to the structural and transcriptional reshaping of genomes. In the second part, we describe methodological innovations that have modified their contribution as molecular tools.
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Affiliation(s)
- Solenne Bire
- GICC, UMR CNRS 6239, Université François Rabelais, UFR des Sciences et Technques, Tours, France
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Abstract
Colorectal cancer (CRC) is a leading cause of cancer deaths worldwide. It results from an accumulation of genetic and epigenetic changes in colon epithelial cells, which transforms them into adenocarcinomas. Over the past decade, major advances have been made in understanding cancer epigenetics, particularly regarding aberrant DNA methylation. Assessment of the colon cancer epigenome has revealed that virtually all CRCs have aberrantly methylated genes and that the average CRC methylome has hundreds to thousands of abnormally methylated genes. As with gene mutations in the cancer genome, a subset of these methylated genes, called driver genes, is presumed to have a functional role in CRC. The assessment of methylated genes in CRCs has also revealed a unique molecular subgroup of CRCs called CpG island methylator phenotype (CIMP) cancers; these tumors have a particularly high frequency of methylated genes. These advances in our understanding of aberrant methylation in CRC have led to epigenetic alterations being developed as clinical biomarkers for diagnostic, prognostic and therapeutic applications. Progress in this field suggests that these epigenetic alterations will be commonly used in the near future to direct the prevention and treatment of CRC.
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Affiliation(s)
- Victoria Valinluck Lao
- Department of Surgery, University of Washington, Seattle, WA,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - William M. Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA,Department of Medicine, University of Washington Medical School, Seattle, WA
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Retrotransposon-induced heterochromatin spreading in the mouse revealed by insertional polymorphisms. PLoS Genet 2011; 7:e1002301. [PMID: 21980304 PMCID: PMC3183085 DOI: 10.1371/journal.pgen.1002301] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Accepted: 08/04/2011] [Indexed: 12/13/2022] Open
Abstract
The "arms race" relationship between transposable elements (TEs) and their host has promoted a series of epigenetic silencing mechanisms directed against TEs. Retrotransposons, a class of TEs, are often located in repressed regions and are thought to induce heterochromatin formation and spreading. However, direct evidence for TE-induced local heterochromatin in mammals is surprisingly scarce. To examine this phenomenon, we chose two mouse embryonic stem (ES) cell lines that possess insertionally polymorphic retrotransposons (IAP, ETn/MusD, and LINE elements) at specific loci in one cell line but not the other. Employing ChIP-seq data for these cell lines, we show that IAP elements robustly induce H3K9me3 and H4K20me3 marks in flanking genomic DNA. In contrast, such heterochromatin is not induced by LINE copies and only by a minority of polymorphic ETn/MusD copies. DNA methylation is independent of the presence of IAP copies, since it is present in flanking regions of both full and empty sites. Finally, such spreading into genes appears to be rare, since the transcriptional start sites of very few genes are less than one Kb from an IAP. However, the B3galtl gene is subject to transcriptional silencing via IAP-induced heterochromatin. Hence, although rare, IAP-induced local heterochromatin spreading into nearby genes may influence expression and, in turn, host fitness.
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Estécio MRH, Issa JPJ. Dissecting DNA hypermethylation in cancer. FEBS Lett 2011; 585:2078-86. [PMID: 21146531 PMCID: PMC3378045 DOI: 10.1016/j.febslet.2010.12.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Revised: 12/02/2010] [Accepted: 12/03/2010] [Indexed: 12/31/2022]
Abstract
There is compelling evidence to support the importance of DNA methylation alterations in cancer development. Both losses and gains of DNA methylation are observed, thought to contribute pathophysiologically by inactivating tumor suppressor genes, inducing chromosomal instability and ectopically activating gene expression. Lesser known are the causes of aberrant DNA methylation. Recent studies have pointed out that intrinsic gene susceptibility to DNA methylation, environmental factors and gene function all have an intertwined participation in this process. Overall, these data support a deterministic rather than a stochastic mechanism for de novo DNA methylation in cancer. In this review article, we discuss the technologies available to study DNA methylation and the endogenous and exogenous factors that influence the onset of de novo methylation in cancer.
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Affiliation(s)
- Marcos R H Estécio
- Department of Leukemia, UT MD Anderson Cancer Center, Houston, TX 77030, United States.
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Cowley M, de Burca A, McCole RB, Chahal M, Saadat G, Oakey RJ, Schulz R. Short interspersed element (SINE) depletion and long interspersed element (LINE) abundance are not features universally required for imprinting. PLoS One 2011; 6:e18953. [PMID: 21533089 PMCID: PMC3080381 DOI: 10.1371/journal.pone.0018953] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Accepted: 03/18/2011] [Indexed: 01/22/2023] Open
Abstract
Genomic imprinting is a form of gene dosage regulation in which a gene is expressed from only one of the alleles, in a manner dependent on the parent of origin. The mechanisms governing imprinted gene expression have been investigated in detail and have greatly contributed to our understanding of genome regulation in general. Both DNA sequence features, such as CpG islands, and epigenetic features, such as DNA methylation and non-coding RNAs, play important roles in achieving imprinted expression. However, the relative importance of these factors varies depending on the locus in question. Defining the minimal features that are absolutely required for imprinting would help us to understand how imprinting has evolved mechanistically. Imprinted retrogenes are a subset of imprinted loci that are relatively simple in their genomic organisation, being distinct from large imprinting clusters, and have the potential to be used as tools to address this question. Here, we compare the repeat element content of imprinted retrogene loci with non-imprinted controls that have a similar locus organisation. We observe no significant differences that are conserved between mouse and human, suggesting that the paucity of SINEs and relative abundance of LINEs at imprinted loci reported by others is not a sequence feature universally required for imprinting.
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Affiliation(s)
- Michael Cowley
- Department of Medical & Molecular Genetics, King's College London, Guy's Hospital, London, United Kingdom
| | - Anna de Burca
- Department of Medical & Molecular Genetics, King's College London, Guy's Hospital, London, United Kingdom
| | - Ruth B. McCole
- Department of Medical & Molecular Genetics, King's College London, Guy's Hospital, London, United Kingdom
| | - Mandeep Chahal
- Department of Medical & Molecular Genetics, King's College London, Guy's Hospital, London, United Kingdom
| | - Ghazal Saadat
- Department of Medical & Molecular Genetics, King's College London, Guy's Hospital, London, United Kingdom
| | - Rebecca J. Oakey
- Department of Medical & Molecular Genetics, King's College London, Guy's Hospital, London, United Kingdom
| | - Reiner Schulz
- Department of Medical & Molecular Genetics, King's College London, Guy's Hospital, London, United Kingdom
- * E-mail:
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Oyer JA, Yates PA, Godsey S, Turker MS. Aberrantly silenced promoters retain a persistent memory of the silenced state after long-term reactivation. Mutat Res 2010; 706:21-7. [PMID: 21035468 DOI: 10.1016/j.mrfmmm.2010.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Revised: 10/10/2010] [Accepted: 10/20/2010] [Indexed: 10/18/2022]
Abstract
A hallmark of aberrant DNA methylation-associated silencing is reversibility. However, long-term stability of reactivated promoters has not been explored. To examine this issue, spontaneous reactivant clones were isolated from mouse embryonal carcinoma cells bearing aberrantly silenced Aprt alleles and re-silencing frequencies were determined as long as three months after reactivation occurred. Despite continuous selection for expression of the reactivated Aprt alleles, exceptionally high spontaneous re-silencing frequencies were observed. A DNA methylation analysis demonstrated retention of sporadic methylation of CpG sites in a protected region of the Aprt promoter in many reactivant alleles suggesting a role for these methylated sites in the re-silencing process. In contrast, a chromatin immunoprecipitation (ChIP) analysis for methyl-H3K4, acetyl-H3K9, and dimethyl-H3K9 levels failed to reveal a specific histone modification that could explain high frequency re-silencing. These results demonstrate that aberrantly silenced and reactivated promoters retain a persistent memory of having undergone the silencing process and suggest the failure to eliminate all CpG methylation as a potential contributing mechanism.
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Affiliation(s)
- Jon A Oyer
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
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14
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Estécio MR, Gallegos J, Vallot C, Castoro RJ, Chung W, Maegawa S, Oki Y, Kondo Y, Jelinek J, Shen L, Hartung H, Aplan PD, Czerniak BA, Liang S, Issa JPJ. Genome architecture marked by retrotransposons modulates predisposition to DNA methylation in cancer. Genome Res 2010; 20:1369-82. [DOI: 10.1101/gr.107318.110] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Epigenetic silencing plays an important role in cancer development. An attractive hypothesis is that local DNA features may participate in differential predisposition to gene hypermethylation. We found that, compared with methylation-resistant genes, methylation-prone genes have a lower frequency of SINE and LINE retrotransposons near their transcription start site. In several large testing sets, this distribution was highly predictive of promoter methylation. Genome-wide analysis showed that 22% of human genes were predicted to be methylation-prone in cancer; these tended to be genes that are down-regulated in cancer and that function in developmental processes. Moreover, retrotransposon distribution marks a larger fraction of methylation-prone genes compared to Polycomb group protein (PcG) marking in embryonic stem cells; indeed, PcG marking and our predictive model based on retrotransposon frequency appear to be correlated but also complementary. In summary, our data indicate that retrotransposon elements, which are widespread in our genome, are strongly associated with gene promoter DNA methylation in cancer and may in fact play a role in influencing epigenetic regulation in normal and abnormal physiological states.
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Muramoto H, Yagi S, Hirabayashi K, Sato S, Ohgane J, Tanaka S, Shiota K. Enrichment of short interspersed transposable elements to embryonic stem cell-specific hypomethylated gene regions. Genes Cells 2010; 15:855-65. [DOI: 10.1111/j.1365-2443.2010.01423.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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16
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Devlin AM, Singh R, Bottiglieri T, Innis SM, Green TJ. Hepatic acyl-coenzyme a:cholesterol acyltransferase-2 expression is decreased in mice with hyperhomocysteinemia. J Nutr 2010; 140:231-7. [PMID: 20018805 DOI: 10.3945/jn.109.112920] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Alterations in lipid metabolism may contribute to the pathology of hyperhomocysteinemia (HHcy). Our objective in this study was to test the hypothesis that HHcy is associated with changes in liver acyl CoA:cholesterol acyl transferase 2 (ACAT2) expression and cholesteryl esters (CE) in mice with HHcy. ACAT2 is encoded by Soat2 and functions to catalyze the esterification of cholesterol with acyl-CoA. Mice heterozygous for disruption of the cystathionine-beta-synthase gene (Cbs +/-) and C57BL/6 mice (Cbs +/+) were fed a control diet or a diet high in l-methionine (8.60 g/kg) and low in folic acid (0.20 mg/kg) to induce HHcy (HH diet). Lower Soat2 mRNA (P < 0.05) and ACAT protein (P < 0.001), higher total oleic acid [18:1(n-9)], and lower CE 18:1(n-9) was found in liver from Cbs +/- mice fed the HH diet, with higher plasma total homocysteine concentrations, than Cbs +/+ mice fed the control diet (35.01 +/- 5.6 vs. 2.21 +/- 0.6 mumol/L, respectively). In silico searches identified a CpG-rich region in the 5' portion of the Soat2 gene, which was differentially methylated (P < 0.05) in Cbs +/- mice fed the HH diet than in Cbs +/+ mice fed the control diet and was accompanied by higher (P < 0.05) B1 repeat element methylation, an indicator of global de novo methylation. These findings show altered methylation and expression of Soat2/ACAT2 in liver from mice with HHcy and suggest a role for changes in liver CE in the pathology of HHcy.
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Affiliation(s)
- Angela M Devlin
- Department of Pathology and Laboratory Medicine, Pediatrics, Child and Family Research Institute, University of British Columbia, Vancouver V5Z 4H4, Canada.
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17
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Takeshima H, Yamashita S, Shimazu T, Niwa T, Ushijima T. The presence of RNA polymerase II, active or stalled, predicts epigenetic fate of promoter CpG islands. Genome Res 2009; 19:1974-82. [PMID: 19652013 DOI: 10.1101/gr.093310.109] [Citation(s) in RCA: 113] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Instructive mechanisms are present for induction of DNA methylation, as shown by methylation of specific CpG islands (CGIs) by specific inducers and in specific cancers. However, instructive factors involved are poorly understood, except for involvement of low transcription and trimethylation of histone H3 lysine 27 (H3K27me3). Here, we used methylated DNA immunoprecipitation (MeDIP) combined with a CGI oligonucleotide microarray analysis, and identified 5510 and 521 genes with promoter CGIs resistant and susceptible, respectively, to DNA methylation in prostate cancer cell lines. Expression analysis revealed that the susceptible genes had low transcription in a normal prostatic epithelial cell line. Chromatin immunoprecipitation with microarray hybridization (CHiP-chip) analysis of RNA polymerase II (Pol II) and histone modifications showed that, even among the genes with low transcription, the presence of Pol II was associated with marked resistance to DNA methylation (OR = 0.22; 95% CI = 0.12-0.38), and H3K27me3 was associated with increased susceptibility (OR = 11.20; 95% CI = 7.14-17.55). The same was true in normal human mammary epithelial cells for 5430 and 733 genes resistant and susceptible, respectively, to DNA methylation in breast cancer cell lines. These results showed that the presence of Pol II, active or stalled, and H3K27me3 can predict the epigenetic fate of promoter CGIs independently of transcription levels.
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Affiliation(s)
- Hideyuki Takeshima
- Carcinogenesis Division, National Cancer Center Research Institute, 104-0045 Tokyo, Japan
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Carson MB, Langlois R, Lu H. Mining knowledge for the methylation status of CpG islands using alternating decision trees. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2009; 2008:3787-90. [PMID: 19163536 DOI: 10.1109/iembs.2008.4650033] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
CpG island (CpGI) methylation is an epigenetic modification that occurs in eukaryotes and is based on the addition of a methyl group to the number 5 carbon of the pyrimidine ring of cytosine. When methylation of a CpGI occurs, the associated gene (if any) is not expressed [1]. Aberrant methylation is thought to be a causative agent in disease [2] and drug sensitivity [3], [4]. In this work, we have predicted the methylation status of CpGIs in human chromosome 21 using sequence patterns. These patterns showed a significantly different distribution between methylated and unmethylated islands in a previous work [5]. Using C4.5 with bagging and cost-sensitive learning, we achieved 85.6% accuracy, 82.8% sensitivity, and 86.4% specificity.We then constructed 1000 alternating decision trees using a bootstrapping method and analyzed the nodes that were conserved between the trees. This allowed us to find specific combinations of sequence patterns that distinguished between methylated and unmethylated CpGIs. Analysis of these characteristics offers certain insight into the conditions that permit or prevent methylation.
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Affiliation(s)
- Matthew B Carson
- Bioinformatics Program, Department of Bioengineering, University of Ilinois at Chicago, IL 60607, USA
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20
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Abstract
DNA and histone methylation are linked and subjected to mitotic inheritance in mammals. Yet how methylation is propagated and maintained between successive cell divisions is not fully understood. A series of enzyme families that can add methylation marks to cytosine nucleobases, and lysine and arginine amino acid residues has been discovered. Apart from methyltransferases, there are also histone modification enzymes and accessory proteins, which can facilitate and/or target epigenetic marks. Several lysine and arginine demethylases have been discovered recently, and the presence of an active DNA demethylase is speculated in mammalian cells. A mammalian methyl DNA binding protein MBD2 and de novo DNA methyltransferase DNMT3A and DNMT3B are shown experimentally to possess DNA demethylase activity. Thus, complex mammalian epigenetic mechanisms appear to be dynamic yet reversible along with a well-choreographed set of events that take place during mammalian development.
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21
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Oyer JA, Chu A, Brar S, Turker MS. Aberrant epigenetic silencing is triggered by a transient reduction in gene expression. PLoS One 2009; 4:e4832. [PMID: 19279688 PMCID: PMC2654015 DOI: 10.1371/journal.pone.0004832] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2009] [Accepted: 02/17/2009] [Indexed: 12/31/2022] Open
Abstract
Background Aberrant epigenetic silencing plays a major role in cancer formation by inactivating tumor suppressor genes. While the endpoints of aberrant silencing are known, i.e., promoter region DNA methylation and altered histone modifications, the triggers of silencing are not known. We used the tet-off system to test the hypothesis that a transient reduction in gene expression will sensitize a promoter to undergo epigenetic silencing. Methodology/Principal Findings The tet responsive promoter (PTRE) was used to drive expression of the selectable human HPRT cDNA in independent transfectants of an Hprt deficient mouse cell line. In this system, high basal HPRT expression is greatly reduced when doxycycline (Dox) is added to the culture medium. Exposure of the PTRE-HPRT transfectants to Dox induced HPRT deficient clones in a time dependent manner. A molecular analysis demonstrated promoter region DNA methylation, loss of histone modifications associated with expression (i.e., H3 lysine 9 and 14 acetylation and lysine 4 methylation), and acquisition of the repressive histone modification H3 lysine 9 methylation. These changes, which are consistent with aberrant epigenetic silencing, were not present in the Dox-treated cultures, with the exception of reduced H3 lysine 14 acetylation. Silenced alleles readily reactivated spontaneously or after treatment of cells with inhibitors of histone deacetylation and/or DNA methylation, but re-silencing of reactivated alleles did not require a new round of Dox exposure. Inhibition of histone deacetylation inhibited both the induction of silencing and re-silencing, whereas inhibition of DNA methylation had no such effect. Conclusions/Significance This study demonstrates that a transient reduction in gene expression triggers a pathway for aberrant silencing in mammalian cells and identifies histone deacetylation as a critical early step in this process. DNA methylation, in contrast, is a secondary step in the silencing pathway under study. A model to explain these observations is offered.
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Affiliation(s)
- Jon A. Oyer
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Adrian Chu
- Center for Research on Occupational and Environmental Toxicology (CROET), Oregon Health & Science University, Portland, Oregon, United States of America,
| | - Sukhmani Brar
- Center for Research on Occupational and Environmental Toxicology (CROET), Oregon Health & Science University, Portland, Oregon, United States of America,
| | - Mitchell S. Turker
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon, United States of America
- Center for Research on Occupational and Environmental Toxicology (CROET), Oregon Health & Science University, Portland, Oregon, United States of America,
- * E-mail:
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Chen Y, Dhupelia A, Schoenherr CJ. The Igf2/H19 imprinting control region exhibits sequence-specific and cell-type-dependent DNA methylation-mediated repression. Nucleic Acids Res 2008; 37:793-803. [PMID: 19074953 PMCID: PMC2647309 DOI: 10.1093/nar/gkn985] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Methylation of CpGs is generally thought to repress transcription without significant influence from the sequence surrounding the methylated dinucleotides. Using the mouse Igf2/H19 imprinting control region (ICR), Igf2r differentially methylated region 2 (DMR2) and bacterial sequences, we addressed how methylation-dependent repression (MDR) from a distance varies with CpG number, density and surrounding sequence. In stably transfected F9 cells, the methylated ICR repressed expression from a CpG-free reporter plasmid more than 1000-fold compared with its unmethylated control. A segment of pBluescript, with a CpG number equal to the ICR's but with a higher density, repressed expression only 70-fold when methylated. A bacteriophage lambda fragment and the Igf2r DMR2 showed minimal MDR activity, despite having CpG numbers and densities similar to or greater than the ICR. By rearranging or deleting CpGs, we identified CpGs associated with three CTCF sites in the ICR that are necessary and sufficient for sequence-specific MDR. In contrast to F9 cells, the methylated ICR and pBS fragments exhibited only 3-fold reporter repression in Hela cells and none in Cos7. Our results show that the strength of MDR from a distance can vary a 1000-fold between different cell types and depends on the sequence surrounding the methylated CpGs, but does not necessarily increase with CpG number or density.
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Affiliation(s)
- Yinming Chen
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA
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23
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Abstract
Among the persistent mysteries in epigenetics are the criteria by which specific regions of the genome are chosen for deposition of distinguishing chromatin marks. Once a particular region is modified, will the newly acquired epigenetic state spill onto neighboring regions of the genome or be confined to tidy patches? The report by Henderson and Jacobsen in the the previous issue of Genes & Development (1597-1606) addresses these questions while providing insight into the utility of DNA methylation for a eukaryotic genome.
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Affiliation(s)
- Hye Ryun Woo
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130, USA
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24
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Kang MY, Lee BB, Ji YI, Jung EH, Chun HK, Song SY, Park SE, Park J, Kim DH. Association of interindividual differences in p14ARF promoter methylation with single nucleotide polymorphism in primary colorectal cancer. Cancer 2008; 112:1699-707. [PMID: 18327804 DOI: 10.1002/cncr.23335] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
BACKGROUND CpG island hypermethylation has been reported at the promoter region of many tumor suppressor genes in colorectal cancers. However, there are significant interindividual differences in the degree of DNA methylation in colorectal cancers. The objective of the current study was to understand whether single nucleotide polymorphisms (SNPs) around the promoter of a gene are implicated in the interindividual differences of CpG island hypermethylation. METHODS Promoter methylation of the p14(ARF) gene and messenger RNA (mRNA) expression levels of p14(ARF), DNA methyltransferase 1 (DNMT1), and DNMT3b were investigated by using methylation-specific polymerase chain reaction (PCR) analysis (MSP) and quantitative real-time PCR analysis in fresh tissues from 188 patients with colorectal cancer. SNPs around the p14(ARF) promoter were genotyped in DNA from peripheral blood lymphocytes in 300 healthy individuals and in 188 patients with colorectal cancer by using matrix-assisted laser desorption/ionization mass spectrometry. RESULTS p14(ARF) methylation was present in 61 of 188 colorectal cancers (32%). Fourteen SNPs among the 20 candidate SNPs were identified as monomorphic in the Korean population studied. Two individual SNPs (-4256 thymine to cytosine [T-->C] and -1477 guanine to adenine [G-->A]), which were in strong linkage disequilibrium (|D'|=0.99; correlation coefficient [r(2)]=0.95), were associated significantly with p14(ARF) methylation. Patients who had the CC variant at the-4256 locus or the AA variant at the -1477 locus had 2.42 times (95% confidence interval [95% CI], 1.07-5.46; P = .03) and 2.47 times (95% CI, 1.09-5.56; P= .03) greater risk of p14(ARF) methylation than patients who had the TT or GG homozygote, respectively, after adjusting for mRNA levels of DNMTs. Four major haplotypes were identified within a block (-4256 T-->C, -3631 T-->C, -1477 G-->A, and +20,188 T-->C). p14(ARF) promoter methylation also was associated significantly with the CCAT haplotype (odds ratio [OR], 8.31; 95% CI, 2.43-28.41; P= .0007) and the CTAC haplotype (OR, 9.71; 95% CI, 1.09-86.24; P= .04). CONCLUSIONS The current results suggested that SNPs around the p14(ARF) promoter region may be responsible for the interindividual susceptibility to p14(ARF) promoter methylation among individuals with colorectal cancer.
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Affiliation(s)
- Mi Yeon Kang
- Center for Genome Research, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Kangnam-Ku, Seoul, South Korea
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25
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Strathdee D, Whitelaw CBA, Clark AJ. Distal transgene insertion affects CpG island maintenance during differentiation. J Biol Chem 2008; 283:11509-15. [PMID: 18308728 DOI: 10.1074/jbc.m709805200] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
About half of all genes have a CpG island surrounding the promoter and transcription start site. Most promoter CpG islands are normally unmethylated in all tissues, irrespective of the expression level of the associated gene. Establishment of the appropriate patterns of DNA methylation in the genome is essential for normal development and patterns of gene expression. Aberrant methylation of CpG islands and silencing of the associated genes is frequently observed in cancer. One gene with a 5'-CpG island is cytoplasmic beta-actin, which is an abundantly expressed protein and a major component of microfilaments. Inserting a betageo cassette into the 3'-untranslated region of beta-actin gene led to widespread but not ubiquitous lacZ expression in mice heterozygous for the modified beta-actin allele. Surprisingly, embryos homozygous for this insertion died at mid-gestation. The modified beta-actin allele was expressed in undifferentiated embryonic stem cells but was turned off as these cells differentiate in vitro and in vivo. We demonstrate that the insertion affects the maintenance of the methylation status of the CpG island of the modified beta-actin allele in differentiated but not in undifferentiated embryonic cells. These data suggest that there is a two-step process to defining a CpG island, requiring both embryonic establishment and a signal that maintains the CpG island in differentiated cells. Furthermore, they indicate that features built into the CpG island are not sufficient to direct CpG island maintenance during differentiation.
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Affiliation(s)
- Douglas Strathdee
- Division of Gene Function and Development, Roslin Institute, Roslin, Midlothian EH25 9PS, United Kingdom.
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26
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Kang MI, Kim HS, Jung YC, Kim YH, Hong SJ, Kim MK, Baek KH, Kim CC, Rhyu MG. Transitional CpG methylation between promoters and retroelements of tissue-specific genes during human mesenchymal cell differentiation. J Cell Biochem 2007; 102:224-39. [PMID: 17352407 DOI: 10.1002/jcb.21291] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
In general, methylation of the promoter regions is inversely correlated with gene expression. The transitional CpG area between the promoter-associated CpG islands and the nearby retroelements is often methylated in a tissue-specific manner. This study analyzed the relationship between gene expression and the methylation of the transitional CpGs in two human stromal cells derived from the bone marrow (BMSC) and adipose tissue (ATSC), both of which have a multilineage differentiation potential. The transitional CpGs of the osteoblast-specific (RUNX2 and BGLAP), adipocyte-specific (PPARgamma2), housekeeping (CDKN2A and MLH1), and mesenchyme-unrelated (RUNX3) genes were examined by methylation-specific PCR. The expression of each gene was measured using reverse-transcription PCR analysis. The RUNX2, BGLAP, and CDKN2A genes in the BMSC, and the PPARgamma2 gene in the ATSC exhibited hypomethylation of the transitional CpGs along with the strong expression. The CpG island of RUNX3 gene not expressed in both BMSC and ATSC was hypermethylated. Transitional hypomethylation of the MLH1 gene was accompanied by the higher expression in the BMSC than in the ATSC. The weakly methylated CpGs of the PPARgamma2 gene in the BMSC became hypomethylated along with the strong expression during the osteoblastic differentiation. There were no notable changes in the transitional methylation and expression of the genes other than PPARgamma2 after the differentiation. Therefore, the transitional methylation and gene expression established in mesenchymal cells tend to be consistently preserved under the induction of differentiation. Weak transitional methylation of the PPARgamma2 gene in the BMSC suggests a methylation-dependent mechanism underlying the adiopogenesis of bone marrow.
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Affiliation(s)
- Moo-Il Kang
- Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
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Wood AJ, Bourc'his D, Bestor TH, Oakey RJ. Allele-specific demethylation at an imprinted mammalian promoter. Nucleic Acids Res 2007; 35:7031-9. [PMID: 17942418 PMCID: PMC2175309 DOI: 10.1093/nar/gkm742] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
A screen for imprinted genes on mouse Chromosome 7 recently identified Inpp5f_v2, a paternally expressed retrogene lying within an intron of Inpp5f. Here, we identify a novel paternally expressed variant of the Inpp5f gene (Inpp5f_v3) that shows a number of unusual features. Inpp5f_v3 initiates from a CpG-rich repeat region adjoining two B1 elements, despite previous reports that SINEs are generally excluded from imprinted promoters. Accordingly, we find that the Inpp5f_v3 promoter acquires methylation around the time of implantation, when many repeat families undergo de novo epigenetic silencing. Methylation is then lost specifically on the paternally derived allele during the latter stages of embryonic development, resulting in imprinted transcriptional activation on the demethylated allele. Methylation analyses in embryos lacking maternal methylation imprints suggest that the primary imprinting mark resides within an intronic CpG island ∼1 kb downstream of the Inpp5f_v3 transcriptional start site. These data support the hypothesis that SINEs can influence gene expression by attracting de novo methylation during development, a property likely to explain their exclusion from other imprinted promoters.
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Affiliation(s)
- Andrew J Wood
- Department of Medical and Molecular Genetics, King's College London, Guy's Hospital, London, SE1 9RT, UK, INSERM U741, Institut Jacques Monod, 2 Place Jussieu, 75251 Paris, CEDEX 05, France
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Shen L, Kondo Y, Guo Y, Zhang J, Zhang L, Ahmed S, Shu J, Chen X, Waterland RA, Issa JPJ. Genome-wide profiling of DNA methylation reveals a class of normally methylated CpG island promoters. PLoS Genet 2007; 3:2023-36. [PMID: 17967063 PMCID: PMC2041996 DOI: 10.1371/journal.pgen.0030181] [Citation(s) in RCA: 269] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2007] [Accepted: 09/07/2007] [Indexed: 12/25/2022] Open
Abstract
The role of CpG island methylation in normal development and cell differentiation is of keen interest, but remains poorly understood. We performed comprehensive DNA methylation profiling of promoter regions in normal peripheral blood by methylated CpG island amplification in combination with microarrays. This technique allowed us to simultaneously determine the methylation status of 6,177 genes, 92% of which include dense CpG islands. Among these 5,549 autosomal genes with dense CpG island promoters, we have identified 4.0% genes that are nearly completely methylated in normal blood, providing another exception to the general rule that CpG island methylation in normal tissue is limited to X inactivation and imprinted genes. We examined seven genes in detail, including ANKRD30A, FLJ40201, INSL6, SOHLH2, FTMT, C12orf12, and DPPA5. Dense promoter CpG island methylation and gene silencing were found in normal tissues studied except testis and sperm. In both tissues, bisulfite cloning and sequencing identified cells carrying unmethylated alleles. Interestingly, hypomethylation of several genes was associated with gene activation in cancer. Furthermore, reactivation of silenced genes could be induced after treatment with a DNA demethylating agent or in a cell line lacking DNMT1 and/or DNMT3b. Sequence analysis identified five motifs significantly enriched in this class of genes, suggesting that cis-regulatory elements may facilitate preferential methylation at these promoter CpG islands. We have identified a group of non-X–linked bona fide promoter CpG islands that are densely methylated in normal somatic tissues, escape methylation in germline cells, and for which DNA methylation is a primary mechanism of tissue-specific gene silencing. About half of all human genes contain a CpG-rich region called a “CpG island” in the 5′ area, often encompassing the promoter and transcription start site of the associated gene. DNA methylation was initially suggested to control tissue-specific gene expression in mammalian cells, but most promoter region CpG islands were found to be unmethylated regardless of tissue specificity of expression. In this study, we discovered an exceptional subset of autosomal genes associated with dense promoter CpG islands that is methylated in normal tissues. We observed tissue-specific gene silencing correlated with hypermethylation in this class of genes, and provided evidence for a direct role of methylation in maintaining the silencing state. Furthermore, we identified five sequence motifs significantly enriched in this class of genes, suggesting the influence of cis-regulatory elements on the establishment and/or stability of DNA methylation. Together, these results provide important new insights into the role of CpG island methylation in normal development and differentiation.
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Affiliation(s)
- Lanlan Shen
- Department of Leukemia, The University of Texas at M. D. Anderson Cancer Center, Houston, Texas, USA.
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Jiang Y, Sun T, Xiong J, Cao J, Li G, Wang S. Hyperhomocysteinemia-mediated DNA hypomethylation and its potential epigenetic role in rats. Acta Biochim Biophys Sin (Shanghai) 2007; 39:657-67. [PMID: 17805460 DOI: 10.1111/j.1745-7270.2007.00327.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Hyperhomocysteinemia (HHcy), which is an independent risk factor for atherosclerosis, might cause dysregulation of gene expression, but the characteristics and key links involved in its pathogenic mechanisms are still poorly understood. The objective of the present study was to investigate the effect of HHcy on DNA methylation and the underlying mechanism of homocysteine (Hcy)-induced DNA methylation. HHcy was induced in Sprague-Dawley rats after 4 weeks of a low, medium or high methionine diet. The levels of total homocysteine, S-adenosylmethionine (AdoMet) and S-adenosylhomocysteine (AdoHcy) were detected by high-performance liquid chromatography. The expression levels of genes and proteins of S-adenosylhomocysteine hydrolase, DNA methyltransferase and methyl-CpG-binding domain 2 were detected by real-time reverse transcription-polymerase chain reaction and Western blot analysis. A high-throughput quantitative methylation assay using fluorescence-based real-time polymerase chain reaction was employed to determine the levels of DNA methylation. The results indicated that HHcy induced the elevation of AdoHcy concentration, the decline of AdoMet concentration, the ratios of AdoMet/AdoHcy and the RNA and protein expression of S-adenosylhomocysteine hydrolase and methyl-CpG-binding domain 2, as well as an increase of DNA methyltransferase activity. With different methylation-dependent restriction endonucleases, the aberrant demethylation was found to prefer CCGG sequences to CpG islands. Increasing levels of HHcy significantly increased genome hypomethylation in B1 repetitive elements. The impacts of different levels of HHcy showed that the varied detrimental effects of HHcy could be attributed to different concentrations through different mechanisms. In mild and moderate HHcy, the Hcy might primarily influence the epigenetic regulation of gene expression through the interference of transferring methyl-group metabolism. However, at high Hcy concentrations, the impacts might be more injurious through oxidative stress, apoptosis and inflammation.
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Affiliation(s)
- Yideng Jiang
- Department of Pathophysiology, Ningxia Medical College, Yinchuan 750004, China.
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30
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Abstract
At certain evolutionary junctures, two or more mutations participating in the build-up of a new complex function may be required to become available simultaneously in the same individuals. How could this happen in higher organisms whose populations are small compared to those of microbes, and in which chances of combined nearly simultaneous highly specific favorable mutations are correspondingly low? The question can in principle be answered for regulatory evolution, one of the basic processes of evolutionary change. A combined resetting of transcription rates in several genes could occur in the same individual. It is proposed that, in eukaryotes, changes in epigenetic trends and epigenetically transforming encounters between alternative chromatin structures could arise frequently enough so as to render probable particular conjunctions of changed transcription rates. Such conjunctions could involve mutational changes with low specificity requirements in gene-associated regions of non-protein-coding sequences. The effects of such mutations, notably when they determine the use of histone variants and covalent modifications of histones, can be among those that migrate along chromatin. Changes in chromatin structure are often cellularly inheritable over at least a limited number of generations of cells, and of individuals when the germ line is involved. SINEs and LINEs, which have been considered "junk DNA", are among the repeat sequences that would appear liable to have teleregulatory effects on the function of a nearby promoter, through changes in their numbers and distribution. There may also be present preexisting unstably inheritable epigenetic trends leading to cellular variegation, trends endemic in a cell population based on DNA sequences previously established in the neighborhood. Either way, epigenetically conditioned teleregulatory trends may display only limited penetrance. The imposition at a distance of new chromatin structures with regulatory impact can occur in cis as well as in trans, and is examined as intrachromosomally spreading teleregulation and interchromosomal "gene kissing". The chances for two or more particular epigenetically determined regulatory trends to occur together in a cell are increased thanks to the proposed low specificity requirements for most of the pertinent sequence changes in intergenic and intronic DNA or in the distribution of middle repetitive sequences that have teleregulatory impact. Inheritable epigenetic changes ("epimutations") with effects at a distance would then perdure over the number of generations required for "assimilation" of the several regulatory novelties through the occurrence and selection, gene by gene, of specific classical mutations. These mutations would have effects similar to the epigenetic effects, yet would provide stability and penetrance. The described epigenetic/genetic partnership may well at times have opened the way toward certain complex new functions. Thus, the presence of "junk DNA", through co-determining the (higher or lower) order and the variants of chromatin structure with regulatory effects at a distance, might make an important contribution to the evolution of complex organisms.
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Affiliation(s)
- Emile Zuckerkandl
- Department of Biological Sciences, Stanford University, Stanford, California 94305, USA
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31
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Kim YH, Hong SJ, Jung YC, Kim SJ, Seo EJ, Choi SW, Rhyu MG. The 5'-end transitional CpGs between the CpG islands and retroelements are hypomethylated in association with loss of heterozygosity in gastric cancers. BMC Cancer 2006; 6:180. [PMID: 16827945 PMCID: PMC1552088 DOI: 10.1186/1471-2407-6-180] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2006] [Accepted: 07/10/2006] [Indexed: 01/28/2023] Open
Abstract
Background A loss of heterozygosity (LOH) represents a unilateral chromosomal loss that reduces the dose of highly repetitive Alu, L1, and LTR retroelements. The aim of this study was to determine if the LOH events can affect the spread of retroelement methylation in the 5'-end transitional area between the CpG islands and their nearest retroelements. Methods The 5'-transitional area of all human genes (22,297) was measured according to the nearest retroelements to the transcription start sites. For 50 gastric cancer specimens, the level of LOH events on eight cancer-associated chromosomes was estimated using the microsatellite markers, and the 5'-transitional CpGs of 20 selected genes were examined by methylation analysis using the bisulfite-modified DNA. Results The extent of the transitional area was significantly shorter with the nearest Alu elements than with the nearest L1 and LTR elements, as well as in the extragenic regions containing a higher density of retroelements than in the intragenic regions. The CpG islands neighbouring a high density of Alu elements were consistently hypomethylated in both normal and tumor tissues. The 5'-transitional methylated CpG sites bordered by a low density of Alu elements or the L1 and LTR elements were hypomethylated more frequently in the high-level LOH cases than in the low-level LOH cases. Conclusion The 5'-transitional methylated CpG sites not completely protected by the Alu elements were hypomethylated in association with LOH events in gastric cancers. This suggests that an irreversible unbalanced decrease in the genomic dose reduces the spread of L1 methylation in the 5'-end regions of genes.
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Affiliation(s)
- Young-Ho Kim
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Seung-Jin Hong
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Yu-Chae Jung
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Sung-Ja Kim
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Eun-Joo Seo
- Department of Clinical Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Sang-Wook Choi
- Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Mun-Gan Rhyu
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
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Feltus FA, Lee EK, Costello JF, Plass C, Vertino PM. DNA motifs associated with aberrant CpG island methylation. Genomics 2006; 87:572-9. [PMID: 16487676 DOI: 10.1016/j.ygeno.2005.12.016] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2005] [Revised: 12/20/2005] [Accepted: 12/21/2005] [Indexed: 02/06/2023]
Abstract
Epigenetic silencing involving the aberrant methylation of promoter region CpG islands is widely recognized as a tumor suppressor silencing mechanism in cancer. However, the molecular pathways underlying aberrant DNA methylation remain elusive. Recently we showed that, on a genome-wide level, CpG island loci differ in their intrinsic susceptibility to aberrant methylation and that this susceptibility can be predicted based on underlying sequence context. These data suggest that there are sequence/structural features that contribute to the protection from or susceptibility to aberrant methylation. Here we use motif elicitation coupled with classification techniques to identify DNA sequence motifs that selectively define methylation-prone or methylation-resistant CpG islands. Motifs common to 28 methylation-prone or 47 methylation-resistant CpG island-containing genomic fragments were determined using the MEME and MAST algorithms (). The five most discriminatory motifs derived from methylation-prone sequences were found to be associated with CpG islands in general and were nonrandomly distributed throughout the genome. In contrast, the eight most discriminatory motifs derived from the methylation-resistant CpG islands were randomly distributed throughout the genome. Interestingly, this latter group tended to associate with Alu and other repetitive sequences. Used together, the frequency of occurrence of these motifs successfully discriminated methylation-prone and methylation-resistant CpG island groups with an accuracy of 87% after 10-fold cross-validation. The motifs identified here are candidate methylation-targeting or methylation-protection DNA sequences.
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Affiliation(s)
- F Alex Feltus
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, 1365-C Clifton Road. NE, Atlanta, GA 30322, USA.
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33
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Kang MI, Rhyu MG, Kim YH, Jung YC, Hong SJ, Cho CS, Kim HS. The length of CpG islands is associated with the distribution of Alu and L1 retroelements. Genomics 2006; 87:580-90. [PMID: 16488573 DOI: 10.1016/j.ygeno.2006.01.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2005] [Revised: 01/10/2006] [Accepted: 01/10/2006] [Indexed: 11/20/2022]
Abstract
Alu and L1 retroelements have been suggested to initiate the spread of CpG methylation. In this study, the spread of CpG methylation was estimated based on the distance between the CpG islands and the nearest retroelements. All human genes (23,116) were examined and the correlations between the length of the CpG islands and the distance and density of the confronting retroelements were examined using nonoverlapping 5-kb windows. There was a linear relationship between the length of the CpG islands and the density of the Alu elements and an inverse relationship between the CpG islands and the L1 elements located more distantly, suggesting a suppressive effect of the Alu's on the spread of L1 methylation. Methylation analysis of the transitional CpG sites between the CpG islands and the nearest retroelements upstream of 16 genes was then carried out using DNA preparations from 11 different human tissues. Methylation-variable transitional CpGs were observed for the selected genes and the different tissues.
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Affiliation(s)
- Moo-Il Kang
- Department of Internal Medicine, The Catholic University of Korea, 505 Banpo-dong, Socho-gu, Seoul 137-701, Korea
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34
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Sironi M, Menozzi G, Comi GP, Cereda M, Cagliani R, Bresolin N, Pozzoli U. Gene function and expression level influence the insertion/fixation dynamics of distinct transposon families in mammalian introns. Genome Biol 2006; 7:R120. [PMID: 17181857 PMCID: PMC1794433 DOI: 10.1186/gb-2006-7-12-r120] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2006] [Revised: 10/25/2006] [Accepted: 12/20/2006] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Transposable elements (TEs) represent more than 45% of the human and mouse genomes. Both parasitic and mutualistic features have been shown to apply to the host-TE relationship but a comprehensive scenario of the forces driving TE fixation within mammalian genes is still missing. RESULTS We show that intronic multispecies conserved sequences (MCSs) have been affecting TE integration frequency over time. We verify that a selective economizing pressure has been acting on TEs to decrease their frequency in highly expressed genes. After correcting for GC content, MCS density and intron size, we identified TE-enriched and TE-depleted gene categories. In addition to developmental regulators and transcription factors, TE-depleted regions encompass loci that might require subtle regulation of transcript levels or precise activation timing, such as growth factors, cytokines, hormones, and genes involved in the immune response. The latter, despite having reduced frequencies of most TE types, are significantly enriched in mammalian-wide interspersed repeats (MIRs). Analysis of orthologous genes indicated that MIR over-representation also occurs in dog and opossum immune response genes, suggesting, given the partially independent origin of MIR sequences in eutheria and metatheria, the evolutionary conservation of a specific function for MIRs located in these loci. Consistently, the core MIR sequence is over-represented in defense response genes compared to the background intronic frequency. CONCLUSION Our data indicate that gene function, expression level, and sequence conservation influence TE insertion/fixation in mammalian introns. Moreover, we provide the first report showing that a specific TE family is evolutionarily associated with a gene function category.
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Affiliation(s)
- Manuela Sironi
- Scientific Institute IRCCS E Medea, Bioinformatic Lab, Via don L Monza, 23842 Bosisio Parini (LC), Italy
| | - Giorgia Menozzi
- Scientific Institute IRCCS E Medea, Bioinformatic Lab, Via don L Monza, 23842 Bosisio Parini (LC), Italy
| | - Giacomo P Comi
- Dino Ferrari Centre, Department of Neurological Sciences, University of Milan, IRCCS Ospedale Maggiore Policlinico, Mangiagalli and Regina Elena Foundation, 20100 Milan, Italy
| | - Matteo Cereda
- Scientific Institute IRCCS E Medea, Bioinformatic Lab, Via don L Monza, 23842 Bosisio Parini (LC), Italy
| | - Rachele Cagliani
- Scientific Institute IRCCS E Medea, Bioinformatic Lab, Via don L Monza, 23842 Bosisio Parini (LC), Italy
| | - Nereo Bresolin
- Scientific Institute IRCCS E Medea, Bioinformatic Lab, Via don L Monza, 23842 Bosisio Parini (LC), Italy
- Dino Ferrari Centre, Department of Neurological Sciences, University of Milan, IRCCS Ospedale Maggiore Policlinico, Mangiagalli and Regina Elena Foundation, 20100 Milan, Italy
| | - Uberto Pozzoli
- Scientific Institute IRCCS E Medea, Bioinformatic Lab, Via don L Monza, 23842 Bosisio Parini (LC), Italy
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35
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Jeong KS, Lee S. Estimating the total mouse DNA methylation according to the B1 repetitive elements. Biochem Biophys Res Commun 2005; 335:1211-6. [PMID: 16115613 DOI: 10.1016/j.bbrc.2005.08.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2005] [Accepted: 08/02/2005] [Indexed: 12/31/2022]
Abstract
Measuring the degree of methylation of the B1 element in mouse may represent the global DNA methylation status because about 30,000 copies of the B1 element are randomly dispersed in the total mouse genome. Six CpG dinucleotides are located within each 163 bp size of B1 element, and each CpG dinucleotide was partially methylated. We quantitated the DNA methylation of the B1 repetitive elements by performing PCR for the methylation specific PCR (MSP) and also by the pyrosequencing. Each CpG dinucleotide was methylated at an average of 9% in the mouse genome by the pyrosequencing and MSP. Especially, we checked whether CpG methylation of the B1 element could respond to a treatment of the DNA methylation inhibitor, 5-azacytidine (5-AzaC). Consequently, the calibration graph resulting from measuring the relative CpG methylation percentage of the B1 element is linearly decreased with the increasing amount of 5-AzaC (up to 50 ng/ml concentration) in the NIH3T3 cells with a standard deviation of only 1.73% between three independent assays. Our methods can be applied to the routine analysis of the global DNA methylation changes in mouse in vivo and in vitro in pharmaceuticals and basic epigenetic research with efforts being less labor-intensive.
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Affiliation(s)
- Kyoung-Sin Jeong
- Functional Genomics Lab, CHA Research Institute, Bundang Campus, College of Medicine, Pochon CHA University, 222 Yatap-Dong, Bundang-Gu, Sungnam-Si, Kyunggi-Do, 463-836, Republic of Korea
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36
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von Sternberg R, Shapiro JA. How repeated retroelements format genome function. Cytogenet Genome Res 2005; 110:108-16. [PMID: 16093662 DOI: 10.1159/000084942] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2004] [Accepted: 08/03/2004] [Indexed: 11/19/2022] Open
Abstract
Genomes operate as sophisticated information storage systems. Generic repeated signals in the DNA format expression of coding sequence files and organize additional functions essential for genome replication and accurate transmission to progeny cells. Retroelements comprise a major fraction of many genomes and contain a surprising diversity of functional signals. In this article, we summarize some features of the taxonomic distribution of retroelements, especially mammalian SINEs, tabulate functional roles documented for different classes of retroelements, and discuss their potential roles as genome organizers. In particular, the fact that certain retroelements serve as boundaries for heterochromatin domains and provide a significant fraction of scaffolding/matrix attachment regions (S/MARs) suggests that the reversed transcribed component of the genome plays a major architectonic role in higher order physical structuring. Employing an information science model, the "functionalist" perspective on repetitive DNA leads to new ways of thinking about the systemic organization of cellular genomes and provides several novel possibilities involving retroelements in evolutionarily significant genome reorganization.
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Affiliation(s)
- R von Sternberg
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
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37
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Abstract
There are clear theoretical reasons and many well-documented examples which show that repetitive, DNA is essential for genome function. Generic repeated signals in the DNA are necessary to format expression of unique coding sequence files and to organise additional functions essential for genome replication and accurate transmission to progeny cells. Repetitive DNA sequence elements are also fundamental to the cooperative molecular interactions forming nucleoprotein complexes. Here, we review the surprising abundance of repetitive DNA in many genomes, describe its structural diversity, and discuss dozens of cases where the functional importance of repetitive elements has been studied in molecular detail. In particular, the fact that repeat elements serve either as initiators or boundaries for heterochromatin domains and provide a significant fraction of scaffolding/matrix attachment regions (S/MARs) suggests that the repetitive component of the genome plays a major architectonic role in higher order physical structuring. Employing an information science model, the 'functionalist' perspective on repetitive DNA leads to new ways of thinking about the systemic organisation of cellular genomes and provides several novel possibilities involving repeat elements in evolutionarily significant genome reorganisation. These ideas may facilitate the interpretation of comparisons between sequenced genomes, where the repetitive DNA component is often greater than the coding sequence component.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago, 920 E. 58th Street, Chicago, IL 60637, USA.
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38
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Meunier J, Khelifi A, Navratil V, Duret L. Homology-dependent methylation in primate repetitive DNA. Proc Natl Acad Sci U S A 2005; 102:5471-6. [PMID: 15797989 PMCID: PMC556223 DOI: 10.1073/pnas.0408986102] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2004] [Indexed: 01/12/2023] Open
Abstract
In mammals, several studies have suggested that levels of methylation are higher in repetitive DNA than in nonrepetitive DNA, possibly reflecting a genome-wide defense mechanism against deleterious effects associated with transposable elements (TEs). To analyze the determinants of methylation patterns in primate repetitive DNA, we took advantage of the fact that the methylation rate in the germ line is reflected by the transition rate at CpG sites. We assessed the variability of CpG substitution rates in nonrepetitive DNA and in various TE and retropseudogene families. We show that, unlike other substitution rates, the rate of transition at CpG sites is significantly (37%) higher in repetitive DNA than in nonrepetitive DNA. Moreover, this rate of CpG transition varies according to the number of repeats, their length, and their level of divergence from the ancestral sequence (up to 2.7 times higher in long, lowly divergent TEs compared with unique sequences). This observation strongly suggests the existence of a homology-dependent methylation (HDM) mechanism in mammalian genomes. We propose that HDM is a direct consequence of interfering RNA-induced transcriptional gene silencing.
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Affiliation(s)
- Julien Meunier
- Unité Mixte de Recherche 5558 Centre National de la Recherche Scientifique, Université Claude Bernard-Lyon I, 16 Rue Raphael Dubois, 69622 Villeurbanne Cedex, France
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39
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Waterland RA, Jirtle RL. Early nutrition, epigenetic changes at transposons and imprinted genes, and enhanced susceptibility to adult chronic diseases. Nutrition 2004; 20:63-8. [PMID: 14698016 DOI: 10.1016/j.nut.2003.09.011] [Citation(s) in RCA: 506] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Robert A Waterland
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina 27710, USA.
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40
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Affiliation(s)
- Melissa J Fazzari
- Department of Epidemiology and Social Medicine, Albert Einstein College of Medicine, Bronx, New York 10461, USA.
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41
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Kim H, Kwon YM, Kim JS, Lee H, Park JH, Shim YM, Han J, Park J, Kim DH. Tumor-Specific Methylation in Bronchial Lavage for the Early Detection of Non-Small-Cell Lung Cancer. J Clin Oncol 2004; 22:2363-70. [PMID: 15197197 DOI: 10.1200/jco.2004.10.077] [Citation(s) in RCA: 118] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PurposeThe aim of this study was to identify tumor-specific methylation in bronchial lavage for the early detection of non-small-cell lung cancer (NSCLC) by differentiating the age-related methylation from the tumor-specific methylation in NSCLC.Patients and MethodsEighty-five NSCLC patients and 127 cancer-free subjects participated in this study. Aberrant methylation at the promoters of the p16, Ras association domain family 1A (RASSF1A), fragile histidine triad (FHIT), H-cadherin, and retinoic acid receptor β (RARβ) genes were evaluated in the resected tumor tissues and bronchial lavage samples of NSCLC patients and in the bronchial lavage samples of cancer-free subjects by methylation-specific polymerase chain reaction.ResultsOf the 127 cancer-free samples, methylation was detected in 6% for p16, 13% for RARβ, 3% for H-cadherin, 4% for RASSF1A, and 28% for FHIT. Hypermethylation of the p16, RARβ, H-cadherin, and RASSF1A genes was not associated with patient age and smoking, whereas hypermethylation of the FHIT promoter occurred more frequently in older patients (P = .02) and was associated with exposure to tobacco smoke (P = .001). A strong correlation between age and smoking was found in patients with hypermethylation of the FHIT gene (r = 0.36; P = .03). A total of 68% of the bronchial lavage samples from the 85 NSCLC patients showed methylation of at least one of p16, RARβ, H-cadherin, and RASSF1A genes.ConclusionOur study suggests that tumor-specific methylation of the p16, RASSF1A, H-cadherin, and RARβ genes may be a valuable biomarker for the early detection of NSCLC in bronchial lavage, and that the age-related methylation of FHIT gene in the normal bronchial epithelium is related to the exposure to tobacco smoke.
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Affiliation(s)
- Hojoong Kim
- Department of Thoracic Surgery, Sungkyunkwan University, School of Medicine, Seoul, Korea
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42
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Spillane C, Baroux C, Escobar-Restrepo JM, Page DR, Laoueille S, Grossniklaus U. Transposons and tandem repeats are not involved in the control of genomic imprinting at the MEDEA locus in Arabidopsis. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2004; 69:465-75. [PMID: 16117682 DOI: 10.1101/sqb.2004.69.465] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Affiliation(s)
- C Spillane
- Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, 8008 Zürich, Switzerland
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Feltus FA, Lee EK, Costello JF, Plass C, Vertino PM. Predicting aberrant CpG island methylation. Proc Natl Acad Sci U S A 2003; 100:12253-8. [PMID: 14519846 PMCID: PMC218745 DOI: 10.1073/pnas.2037852100] [Citation(s) in RCA: 193] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Epigenetic silencing associated with aberrant methylation of promoter region CpG islands is one mechanism leading to loss of tumor suppressor function in human cancer. Profiling of CpG island methylation indicates that some genes are more frequently methylated than others, and that each tumor type is associated with a unique set of methylated genes. However, little is known about why certain genes succumb to this aberrant event. To address this question, we used Restriction Landmark Genome Scanning to analyze the susceptibility of 1,749 unselected CpG islands to de novo methylation driven by overexpression of DNA cytosine-5-methyltransferase 1 (DNMT1). We found that although the overall incidence of CpG island methylation was increased in cells overexpressing DNMT1, not all loci were equally affected. The majority of CpG islands (69.9%) were resistant to de novo methylation, regardless of DNMT1 overexpression. In contrast, we identified a subset of methylation-prone CpG islands (3.8%) that were consistently hypermethylated in multiple DNMT1 overexpressing clones. Methylation-prone and methylation-resistant CpG islands were not significantly different with respect to size, C+G content, CpG frequency, chromosomal location, or promoter association. We used DNA pattern recognition and supervised learning techniques to derive a classification function based on the frequency of seven novel sequence patterns that was capable of discriminating methylation-prone from methylation-resistant CpG islands with 82% accuracy. The data indicate that CpG islands differ in their intrinsic susceptibility to de novo methylation, and suggest that the propensity for a CpG island to become aberrantly methylated can be predicted based on its sequence context.
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Affiliation(s)
- F A Feltus
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA
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44
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Coombes C, Arnaud P, Gordon E, Dean W, Coar EA, Williamson CM, Feil R, Peters J, Kelsey G. Epigenetic properties and identification of an imprint mark in the Nesp-Gnasxl domain of the mouse Gnas imprinted locus. Mol Cell Biol 2003; 23:5475-88. [PMID: 12897124 PMCID: PMC166348 DOI: 10.1128/mcb.23.16.5475-5488.2003] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2002] [Revised: 04/07/2003] [Accepted: 05/20/2003] [Indexed: 12/19/2022] Open
Abstract
The Gnas locus in the mouse is imprinted with a complex arrangement of alternative transcripts defined by promoters with different patterns of monoallelic expression. The Gnas transcript is subject to tissue-specific imprinted expression, Nesp is expressed only from the maternal allele, and Gnasxl is expressed only from the paternal allele. The mechanisms controlling these expression patterns are not known. To identify potential imprinting regulatory regions, particularly for the reciprocally expressed Nesp and Gnasxl promoters, we examined epigenetic properties of the locus in gametes, embryonic stem cells, and fetal and adult tissues. The Nesp and Gnasxl promoter regions are contained in extensive CpG islands with methylation of the paternal allele at Nesp and the maternal allele at Gnasxl. Parental allele-specific DNase I-hypersensitive sites were found at these regions, which correlate with hypomethylation rather than actual expression status. A germ line methylation mark was identified covering the promoters for Gnasxl and the antisense transcript Nespas. Prominent DNase I-hypersensitive sites present on paternal alleles in embryonic stem cells are contained within this mark. This is the second gametic mark identified at Gnas and suggests that the Nesp and Gnasxl promoters are under separate control from the Gnas promoter. We propose models to account for the regulation of imprinting at the locus.
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MESH Headings
- Alleles
- Animals
- Blotting, Southern
- Cell Nucleus/metabolism
- Cells, Cultured
- Chromatin/metabolism
- Chromogranins
- Chromosome Mapping
- DNA Methylation
- Deoxyribonuclease I/metabolism
- Exons
- GTP-Binding Protein alpha Subunits, Gs
- Genomic Imprinting
- Heterotrimeric GTP-Binding Proteins/genetics
- Mice
- Mice, Inbred C57BL
- Models, Genetic
- Nerve Tissue Proteins/genetics
- Oligonucleotides, Antisense/metabolism
- Promoter Regions, Genetic
- Protein Structure, Tertiary
- RNA, Messenger/metabolism
- Repetitive Sequences, Nucleic Acid
- Sulfites/pharmacology
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Affiliation(s)
- Candice Coombes
- Developmental Genetics Programme, The Babraham Institute, Cambridge CB2 4AT, United Kingdom
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Yates PA, Burman R, Simpson J, Ponomoreva ON, Thayer MJ, Turker MS. Silencing of mouse Aprt is a gradual process in differentiated cells. Mol Cell Biol 2003; 23:4461-70. [PMID: 12808089 PMCID: PMC164859 DOI: 10.1128/mcb.23.13.4461-4470.2003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Mouse Aprt constructs that are highly susceptible to DNA methylation-associated inactivation in embryonal carcinoma cells were transfected into differentiated cells, where they were expressed. Construct silencing was induced by either whole-cell fusion of the expressing differentiated cells with embryonal carcinoma cells or by treatment of the differentiated cells with the DNA demethylating agent 5-aza-2'-deoxycytidine. Induction of silencing was enhanced significantly by the presence of a methylation center fragment positioned upstream of a truncated promoter comprised of two functional Sp1 binding sites. Initial silencing of the Aprt constructs was unstable, as evidenced by high spontaneous reversion frequencies ( approximately 10(-2)). Stably silenced subclones with spontaneous reversion frequencies of <10(-5) were isolated readily from the unstably silenced clones. These reversion frequencies were enhanced significantly by treatment of the cells with 5-aza-2'-deoxycytidine. A bisulfite sequence analysis demonstrated that CpG methylation initiated within the methylation center region on expressing alleles and that the induction of silencing allowed methylation to spread towards and eventually into the promoter region. Combined with the induction of revertants by 5-aza-2'-deoxycytidine, this result suggested that stabilization of silencing was due to an increased density of CpG methylation. All allelic methylation patterns were variegated, which is consistent with a gradual and evolving process. In total, our results demonstrate that silencing of mouse Aprt is a gradual process in the differentiated cells.
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Affiliation(s)
- Phillip A Yates
- Center for Research on Occupational and Environmental Toxicology, Oregon Health and Sciences University, Portland, Oregon 97239, USA
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46
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Abstract
Most 5-methylcytosine in Neurospora crassa occurs in A:T-rich sequences high in TpA dinucleotides, hallmarks of repeat-induced point mutation. To investigate how such sequences induce methylation, we developed a sensitive in vivo system. Tests of various 25- to 100-bp synthetic DNA sequences revealed that both T and A residues were required on a given strand to induce appreciable methylation. Segments composed of (TAAA)(n) or (TTAA)(n) were the most potent signals; 25-mers induced robust methylation at the special test site, and a 75-mer induced methylation elsewhere. G:C base pairs inhibited methylation, and cytosines 5' of ApT dinucleotides were particularly inhibitory. Weak signals could be strengthened by extending their lengths. A:T tracts as short as two were found to cooperate to induce methylation. Distamycin, which, like the AT-hook DNA binding motif found in proteins such as mammalian HMG-I, binds to the minor groove of A:T-rich sequences, suppressed DNA methylation and gene silencing. We also found a correlation between the strength of methylation signals and their binding to an AT-hook protein (HMG-I) and to activities in a Neurospora extract. We propose that de novo DNA methylation in Neurospora cells is triggered by cooperative recognition of the minor groove of multiple short A:T tracts. Similarities between sequences subjected to repeat-induced point mutation in Neurospora crassa and A:T-rich repeated sequences in heterochromatin in other organisms suggest that related mechanisms control silent chromatin in fungi, plants, and animals.
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Affiliation(s)
- Hisashi Tamaru
- Department of Biology and Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403-1229, USA
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47
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Patkin EL. Epigenetic mechanisms for primary differentiation in mammalian embryos. INTERNATIONAL REVIEW OF CYTOLOGY 2002; 216:81-129. [PMID: 12049211 DOI: 10.1016/s0074-7696(02)16004-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This review examines main developments related to the interface between primary mammalian cell differentiation and various aspects of chromosomal structure changes, such as heterochromatin dynamics, DNA methylation, mitotic recombination, and inter- and intrachromosomal differentiation. In particular, X chromosome difference, imprinting, chromosomal banding, methylation pattern, single-strand DNA breaks, sister chromatid exchanges (SCEs), and sister chromatid asymmetry are considered. A hypothesis is put forward which implies the existence of an epigenetic asymmetry versus mirror symmetry of sister chromatids for any DNA sequences. Such epigenetic asymmetry appears as a result of asymmetry of sister chromatid organization and of SCE and is a necessary (not sufficient) condition for creating cell diversity. The sister chromatid asymmetry arises as a result of consecutive rounds of active and passive demethylation which leads after chromatin assembly events to chromatid difference. Single-strand DNA breaks that emerge during demethylation trigger reparation machinery, provend as sister chromatid exchanges, which are not epigenetically neutral in this case. Taken together, chromatid asymmetry and SCE lead to cell diversity regarding their future fate. Such cells are considered pluripotent stem cells which after interplay between a set of chromosomal domains and certain substances localized within the cytoplasmic compartments (and possibly cell interactions) can cause sister cells to express different gene chains. A model is suggested that may be useful for stem cell technology and studies of carcinogenesis.
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Affiliation(s)
- Eugene L Patkin
- Department of Molecular Genetics, Institute of Experimental Medicine, Russian Academy of Medical Sciences, St Petersburg
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von Sternberg R. On the roles of repetitive DNA elements in the context of a unified genomic-epigenetic system. Ann N Y Acad Sci 2002; 981:154-88. [PMID: 12547679 DOI: 10.1111/j.1749-6632.2002.tb04917.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Repetitive DNA sequences comprise a substantial portion of most eukaryotic and some prokaryotic chromosomes. Despite nearly forty years of research, the functions of various sequence families as a whole and their monomer units remain largely unknown. The inability to map specific functional roles onto many repetitive DNA elements (REs), coupled with the taxon-specificity of sequence families, have led many to speculate that these genomic components are "selfish" replicators generating genomic "junk." The purpose of this paper is to critically examine the selfishness, evolutionary effects, and functionality of REs. First, a brief overview of the range of ideas pertaining to RE function is presented. Second, the argument is presented that the selfish DNA "hypothesis" is actually a narrative scheme, that it serves to protect neo-Darwinian assumptions from criticism, and that this story is untestable and therefore not a hypothesis. Third, attempts to synthesize the selfish DNA concept with complex systems models of the genome and RE functionality are critiqued. Fourth, the supposed connection between RE-induced mutations and macroevolutionary events are stated to be at variance with empirical evidence and theoretical considerations. Hypotheses that base phylogenetic transitions in repetitive sequence changes thus remain speculative. Fifth and finally, the case is made for viewing REs as integrally functional components of chromosomes, genomes, and cells. It is argued throughout that a new conceptual framework is needed for understanding the roles of repetitive DNA in genomic/epigenetic systems, and that neo-Darwinian "narratives" have been the primary obstacle to elucidating the effects of these enigmatic components of chromosomes.
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Affiliation(s)
- Richard von Sternberg
- Department of Systematic Biology, NHB-163, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA.
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Neumeister P, Albanese C, Balent B, Greally J, Pestell RG. Senescence and epigenetic dysregulation in cancer. Int J Biochem Cell Biol 2002; 34:1475-90. [PMID: 12200040 DOI: 10.1016/s1357-2725(02)00079-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Mammalian cells have a finite proliferative lifespan, at the end of which they are unable to enter S phase in response to mitogenic stimuli. They undergo morphological changes and synthesize an altered repertoire of cell type-specific proteins. This non-proliferative state is termed replicative senescence and is regarded as a major tumor suppressor mechanism. The ability to overcome senescence and obtain a limitless replicative potential is called immortalization, and considered to be one of the prerequisites of cancer formation. While senescence mainly represents a genetically governed process, epigenetic changes in cancer have received increasing attention as an alternative mechanism for mediating gene expression changes in transformed cells. DNA methylation of promoter-containing CpG islands has emerged as an epigenetic mechanism of silencing tumor suppressor genes. New insights are being gained into the mechanisms causing aberrant methylation in cancer and evidence suggests that aging is accompanied by accumulation of cells with aberrant CpG island methylation. Aberrant methylation may contribute to many of the physiological and pathological changes associated with aging including tumor development. Finally, we describe how genes involved in promoting longevity might inhibit pathways promoting tumorigenesis.
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Affiliation(s)
- Peter Neumeister
- Department of Development and Molecular Biology, Division of Hormone-Responsive Tumors, Albert Einstein Cancer Center, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
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Abstract
Abstract
We explore the extent and sources of epigenetic variation in cytosine methylation in natural accessions of the flowering plant, Arabidopsis thaliana, by focusing on the methylation of the major rRNA gene repeats at the two nucleolus organizer regions (NOR). Our findings indicate that natural variation in NOR methylation results from a combination of genetic and epigenetic mechanisms. Genetic variation in rRNA gene copy number and trans-acting modifier loci account for some of the natural variation in NOR methylation. Our results also suggest that divergence and inheritance of epigenetic information, independent of changes in underlying nucleotide sequence, may play an important role in maintaining natural variation in cytosine methylation.
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Affiliation(s)
- Nicole C Riddle
- Department of Biology, Washington University, Saint Louis, Missouri 63130, USA
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