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Anwar F, Davenport MP, Ebrahimi D. Footprint of APOBEC3 on the genome of human retroelements. J Virol 2013; 87:8195-204. [PMID: 23698293 PMCID: PMC3700199 DOI: 10.1128/jvi.00298-13] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 05/10/2013] [Indexed: 01/01/2023] Open
Abstract
Almost half of the human genome is composed of transposable elements. The genomic structures and life cycles of some of these elements suggest they are a result of waves of retroviral infection and transposition over millions of years. The reduction of retrotransposition activity in primates compared to that in nonprimates, such as mice, has been attributed to the positive selection of several antiretroviral factors, such as apolipoprotein B mRNA editing enzymes. Among these, APOBEC3G is known to mutate G to A within the context of GG in the genome of endogenous as well as several exogenous retroelements (the underlining marks the G that is mutated). On the other hand, APOBEC3F and to a lesser extent other APOBEC3 members induce G-to-A changes within the nucleotide GA. It is known that these enzymes can induce deleterious mutations in the genome of retroviral sequences, but the evolution and/or inactivation of retroelements as a result of mutation by these proteins is not clear. Here, we analyze the mutation signatures of these proteins on large populations of long interspersed nuclear element (LINE), short interspersed nuclear element (SINE), and endogenous retrovirus (ERV) families in the human genome to infer possible evolutionary pressure and/or hypermutation events. Sequence context dependency of mutation by APOBEC3 allows investigation of the changes in the genome of retroelements by inspecting the depletion of G and enrichment of A within the APOBEC3 target and product motifs, respectively. Analysis of approximately 22,000 LINE-1 (L1), 24,000 SINE Alu, and 3,000 ERV sequences showed a footprint of GG→AG mutation by APOBEC3G and GA→AA mutation by other members of the APOBEC3 family (e.g., APOBEC3F) on the genome of ERV-K and ERV-1 elements but not on those of ERV-L, LINE, or SINE.
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Affiliation(s)
- Firoz Anwar
- Centre for Vascular Research, The University of New South Wales, Kensington, NSW, Australia
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Ashbrook DG, Hager R. Empirical testing of hypotheses about the evolution of genomic imprinting in mammals. Front Neuroanat 2013; 7:6. [PMID: 23641202 PMCID: PMC3639422 DOI: 10.3389/fnana.2013.00006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 04/10/2013] [Indexed: 01/01/2023] Open
Abstract
The close interaction between mother and offspring in mammals is thought to contribute to the evolution of genomic imprinting or parent-of-origin dependent gene expression. Empirical tests of theories about the evolution of imprinting have been scant for several reasons. Models make different assumptions about the traits affected by imprinted genes and the scenarios in which imprinting is predicted to have been selected for. Thus, competing hypotheses cannot readily be tested against each other. Further, it is far from clear how predictions about expression patterns of genes with specific phenotypic effects can be tested given current methodology of assaying gene expression levels, be it in the brain or in other tissues. We first set out a scenario for testing competing hypotheses and delineate the different assumptions and predictions of models. We then outline how predictions may be tested using mouse models such as intercrosses or recombinant inbred (RI) systems that can be phenotyped for traits relevant to imprinting theories. Further, we briefly discuss different molecular approaches that may be used in conjunction with experiments to ascertain expression patterns of imprinted genes and thus the testing of predictions.
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Affiliation(s)
- David G Ashbrook
- Computational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester Manchester, UK
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Renfree MB, Suzuki S, Kaneko-Ishino T. The origin and evolution of genomic imprinting and viviparity in mammals. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120151. [PMID: 23166401 DOI: 10.1098/rstb.2012.0151] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Genomic imprinting is widespread in eutherian mammals. Marsupial mammals also have genomic imprinting, but in fewer loci. It has long been thought that genomic imprinting is somehow related to placentation and/or viviparity in mammals, although neither is restricted to mammals. Most imprinted genes are expressed in the placenta. There is no evidence for genomic imprinting in the egg-laying monotreme mammals, despite their short-lived placenta that transfers nutrients from mother to embryo. Post natal genomic imprinting also occurs, especially in the brain. However, little attention has been paid to the primary source of nutrition in the neonate in all mammals, the mammary gland. Differentially methylated regions (DMRs) play an important role as imprinting control centres in each imprinted region which usually comprises both paternally and maternally expressed genes (PEGs and MEGs). The DMR is established in the male or female germline (the gDMR). Comprehensive comparative genome studies demonstrated that two imprinted regions, PEG10 and IGF2-H19, are conserved in both marsupials and eutherians and that PEG10 and H19 DMRs emerged in the therian ancestor at least 160 Ma, indicating the ancestral origin of genomic imprinting during therian mammal evolution. Importantly, these regions are known to be deeply involved in placental and embryonic growth. It appears that most maternal gDMRs are always associated with imprinting in eutherian mammals, but emerged at differing times during mammalian evolution. Thus, genomic imprinting could evolve from a defence mechanism against transposable elements that depended on DNA methylation established in germ cells.
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Affiliation(s)
- Marilyn B Renfree
- Department of Zoology, The University of Melbourne, Victoria 3010, Australia.
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Laska MJ, Nissen KK, Nexø BA. (Some) cellular mechanisms influencing the transcription of human endogenous retrovirus, HERV-Fc1. PLoS One 2013; 8:e53895. [PMID: 23382858 PMCID: PMC3557288 DOI: 10.1371/journal.pone.0053895] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 12/06/2012] [Indexed: 11/18/2022] Open
Abstract
DNA methylation and histone acetylation are epigenetic modifications that act as regulators of gene expression. DNA methylation is considered an important mechanism for silencing of retroelements in the mammalian genome. However, the methylation of human endogenous retroviruses (HERVs) is not well investigated. The aim of this study was to investigate the transcriptional potential of HERV-Fc1 proviral 5'LTR in more detail, and examined the specific influence of CpG methylation on this LTR in number of cell lines. Specifically, the role of demethylating chemicals e.g. 5-aza-2' deoxycytidine and Trichostatin-A, in inducing or reactivating expression of HERV-Fc1 specific sequences and the mechanisms were investigated. In our present study, 5-aza-dC is shown to be a powerful inducer of HERV-Fc1, and at the same time it strongly inhibits methylation of DNA. Treatment with this demethylating agent 5-aza-dC, results in significantly increased levels of HERV-Fc1 expression in cells previously not expressing HERV-Fc1, or with a very low expression level. The extent of expression of HERV-Fc1 RNAs precisely correlates with the apparent extent of demethylation of the related DNA sequences. In conclusion, the results suggest that inhibition of DNA methylation/histone deacetylase can interfere with gene silencing mechanisms affecting HERV-Fc1 expression in human cells.
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Abstract
What good are transposable elements (TEs)? Although their activity can be harmful to host genomes and can cause disease, they nevertheless represent an important source of genetic variation that has helped shape genomes. In this review, we examine the impact of TEs, collectively referred to as the mobilome, on the transcriptome. We explore how TEs—particularly retrotransposons—contribute to transcript diversity and consider their potential significance as a source of small RNAs that regulate host gene transcription. We also discuss a critical role for the mobilome in engineering transcriptional networks, permitting coordinated gene expression, and facilitating the evolution of novel physiological processes.
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Affiliation(s)
- Michael Cowley
- Department of Medical & Molecular Genetics, King's College London, London, United Kingdom
| | - Rebecca J. Oakey
- Department of Medical & Molecular Genetics, King's College London, London, United Kingdom
- * E-mail:
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Abstract
Genomic imprinting is an epigenetic phenomenon in which either the paternal or the maternal allele of imprinted genes is expressed in somatic cells. It is unique to eutherian mammals, marsupials, and flowering plants. It is absolutely required for normal mammalian development. Dysregulation of genomic imprinting can cause a variety of human diseases. About 150 imprinted genes have been identified so far in mammals and many of them are clustered such that they are coregulated by a cis-acting imprinting control region, called the ICR. One hallmark of the ICR is that it contains a germ line-derived differentially methylated region that is methylated on the paternal chromosome or on the maternal chromosome. The DNA methylation imprint is reset in the germ line and differential methylation at an ICR is restored upon fertilization. The DNA methylation imprint is resistant to a genome-wide demethylation process in early embryos and is stably maintained in postimplantation embryos. Maintenance of the DNA methylation imprint is dependent on two distinct maternal effect genes (Zfp57 and PGC7/Stella). In germ cells, around midgestation, the DNA methylation imprint is erased and undergoes another round of the DNA methylation imprint cycle that includes erasure, resetting, restoration, and maintenance of differential DNA methylation.
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Affiliation(s)
- Xiajun Li
- Black Family Stem Cell Institute, Mount Sinai School of Medicine, New York, USA.
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Gutierrez-Marcos JF, Constância M, Burton GJ. Maternal to offspring resource allocation in plants and mammals. Placenta 2012; 33 Suppl 2:e3-10. [PMID: 22995735 DOI: 10.1016/j.placenta.2012.08.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 08/28/2012] [Accepted: 08/30/2012] [Indexed: 12/26/2022]
Abstract
Appropriate allocation of resources to the offspring is critical for successful reproduction, particularly in species that reproduce on more than one occasion. The offspring must be provisioned adequately to ensure its vigour, whereas the parent must not become so depleted such that its survival is endangered. In both flowering plants and mammals specialised structures have evolved to support the offspring during its development. In this review we consider common themes that may indicate conservation of nutrient transfer function and regulation by genomic imprinting across the two kingdoms.
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Affiliation(s)
- J F Gutierrez-Marcos
- School of Life Sciences, University of Warwick, Wellesbourne Campus, Coventry CV4 7AL, UK.
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58
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Jiang H, Köhler C. Evolution, function, and regulation of genomic imprinting in plant seed development. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:4713-22. [PMID: 22922638 DOI: 10.1093/jxb/ers145] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Genomic imprinting is an epigenetic phenomenon whereby genetically identical alleles are differentially expressed dependent on their parent-of-origin. Genomic imprinting has independently evolved in flowering plants and mammals. In both organism classes, imprinting occurs in embryo-nourishing tissues, the placenta and the endosperm, respectively, and it has been proposed that imprinted genes regulate the transfer of nutrients to the developing progeny. Many imprinted genes are located in the vicinity of DNA-methylated transposon or repeat sequences, implying that transposon insertions are associated with the evolution of imprinted loci. The antagonistic action of DNA methylation and Polycomb group-mediated histone methylation seems important for the regulation of many imprinted plant genes, whereby the position of such epigenetic modifications can determine whether a gene will be mainly expressed from either the maternally or paternally inherited alleles. Furthermore, long non-coding RNAs seem to play an as yet underappreciated role for the regulation of imprinted plant genes. Imprinted expression of a number of genes is conserved between monocots and dicots, suggesting that long-term selection can maintain imprinted expression at some loci.
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Affiliation(s)
- Hua Jiang
- Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center of Plant Biology, 750 07 Uppsala, Sweden
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60
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Abstract
DNA methylation mediates imprinted gene expression by passing an epigenomic state across generations and differentially marking specific regulatory regions on maternal and paternal alleles. Imprinting has been tied to the evolution of the placenta in mammals and defects of imprinting have been associated with human diseases. Although recent advances in genome sequencing have revolutionized the study of DNA methylation, existing methylome data remain largely untapped in the study of imprinting. We present a statistical model to describe allele-specific methylation (ASM) in data from high-throughput short-read bisulfite sequencing. Simulation results indicate technical specifications of existing methylome data, such as read length and coverage, are sufficient for full-genome ASM profiling based on our model. We used our model to analyze methylomes for a diverse set of human cell types, including cultured and uncultured differentiated cells, embryonic stem cells and induced pluripotent stem cells. Regions of ASM identified most consistently across methylomes are tightly connected with known imprinted genes and precisely delineate the boundaries of several known imprinting control regions. Predicted regions of ASM common to multiple cell types frequently mark noncoding RNA promoters and represent promising starting points for targeted validation. More generally, our model provides the analytical complement to cutting-edge experimental technologies for surveying ASM in specific cell types and across species.
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DeVeale B, van der Kooy D, Babak T. Critical evaluation of imprinted gene expression by RNA-Seq: a new perspective. PLoS Genet 2012; 8:e1002600. [PMID: 22479196 PMCID: PMC3315459 DOI: 10.1371/journal.pgen.1002600] [Citation(s) in RCA: 190] [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: 07/27/2011] [Accepted: 01/18/2012] [Indexed: 01/05/2023] Open
Abstract
In contrast to existing estimates of approximately 200 murine imprinted genes, recent work based on transcriptome sequencing uncovered parent-of-origin allelic effects at more than 1,300 loci in the developing brain and two adult brain regions, including hundreds present in only males or females. Our independent replication of the embryonic brain stage, where the majority of novel imprinted genes were discovered and the majority of previously known imprinted genes confirmed, resulted in only 12.9% concordance among the novel imprinted loci. Further analysis and pyrosequencing-based validation revealed that the vast majority of the novel reported imprinted loci are false-positives explained by technical and biological variation of the experimental approach. We show that allele-specific expression (ASE) measured with RNA–Seq is not accurately modeled with statistical methods that assume random independent sampling and that systematic error must be accounted for to enable accurate identification of imprinted expression. Application of a robust approach that accounts for these effects revealed 50 candidate genes where allelic bias was predicted to be parent-of-origin–dependent. However, 11 independent validation attempts through a range of allelic expression biases confirmed only 6 of these novel cases. The results emphasize the importance of independent validation and suggest that the number of imprinted genes is much closer to the initial estimates. Typically both copies of mammalian genes are expressed, but in some cases, “imprinting” restricts expression to the maternal or paternal copy. Having two copies of each gene is considered advantageous since in enables compensation when one does not function properly. Why imprinting evolved and its utility to each sex is widely debated, and having a complete catalog of imprinted genes and their functions is essential for fully characterizing this phenomenon. 25 years of screening has revealed about 130 imprinted genes, and the slowing rate of discovery suggests that we are reaching saturation. Two recent studies based on high-throughput sequencing of RNA reported more than 1,300 imprinted genes. To understand the basis of this paradigm shift, we first attempted to reproduce these results. Unable to do so, we performed additional analyses that show that most of these discoveries are due to noise in the experimental approach and assay. We remedy this with new methods that account for this noise and applied them to identify 50 novel putative imprinted genes. These methods will be useful for identifying genuine novel cases of imprinted expression as this type of screening approach becomes broadly utilized.
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Affiliation(s)
- Brian DeVeale
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
| | - Derek van der Kooy
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
| | - Tomas Babak
- Department of Biology, Stanford University, Stanford, California, United States of America
- * E-mail:
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62
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Okamoto K. Epigenetics: A way to understand the origin and biology of testicular germ cell tumors. Int J Urol 2012; 19:504-11. [DOI: 10.1111/j.1442-2042.2012.02986.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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63
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Mann JR, Mattiske DM. RNA interference in mammalian DNA methylation1This review is part of Special Issue entitled Asilomar Chromatin and has undergone the Journal’s usual peer review process. Biochem Cell Biol 2012; 90:70-7. [DOI: 10.1139/o11-050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
RNAi and Dicer-dependent siRNAs are required for constitutive heterochromatin formation in fission yeast and for establishing DNA methylation at repetitive elements in plants. In the mammalian male germ line, DICER1-independent piRNAs are required for the full establishment of DNA methylation of dispersed repetitive transposable elements. However, in other mammalian cell types, no clear picture has yet emerged of the role of RNAi in establishing heterochromatin and DNA methylation. In mouse embryonic stem cells, which remain viable on loss of DICER1 and ablation of RNAi, while no firm evidence has been obtained for defective heterochromatin formation, there are indications of defective DNA methylation. The latter has been attributed to an indirect effect of reduced DNA methyltransferase (DNMT) activity due to a loss of miRNA-mediated gene regulation. However, it is unclear whether the reductions in DNMT activity were sufficient to affect DNA methylation. We consider it equally likely that the defects in DNA methylation that can be observed in DICER1-deficient embryonic stem cells are the result of nonspecific effects related to RNAi loss aside from reduced DNMT activity.
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Affiliation(s)
- Jeffrey R. Mann
- Theme of Genetic Disorders, Murdoch Childrens Research Institute, The Royal Children’s Hospital, Parkville 3052, Victoria, Australia
| | - Deidre M. Mattiske
- Theme of Genetic Disorders, Murdoch Childrens Research Institute, The Royal Children’s Hospital, Parkville 3052, Victoria, Australia
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64
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Köhler C, Wolff P, Spillane C. Epigenetic mechanisms underlying genomic imprinting in plants. ANNUAL REVIEW OF PLANT BIOLOGY 2012; 63:331-52. [PMID: 22404470 DOI: 10.1146/annurev-arplant-042811-105514] [Citation(s) in RCA: 126] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Genomic imprinting, the differential expression of an autosomal gene that is dependent on its parent of origin, has independently evolved in flowering plants and mammals. In both of these organism classes, imprinting occurs in embryo-nourishing tissues-the placenta and the endosperm, respectively. It has been proposed that some imprinted genes control nutrient flow from the mother to the offspring. Genome-wide analyses of imprinted genes in plants have revealed that many imprinted genes are located in the vicinity of transposon or repeat sequences, implying that transposon insertions are associated with the evolution of imprinted loci. Imprinted expression of a number of genes is conserved between monocots and dicots, suggesting that long-term selection can maintain imprinted expression at some loci. In terms of epigenetic mechanisms, imprinted expression is largely controlled by an antagonistic action of DNA methylation and Polycomb group-mediated histone methylation in the vicinity of imprinted genes, whereby the position of such epigenetic modifications can determine whether a gene will be expressed mainly from either the maternally or paternally inherited alleles.
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Affiliation(s)
- Claudia Köhler
- Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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65
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Abstract
Genomic imprinting is an epigenetic phenomenon that results in the silencing of alleles, dependent on their parent of origin. Within vertebrates, this phenomenon is restricted only to the mammals and has been identified in eutherians and marsupials but not in the egg-laying monotremes. Many hypotheses have been put forward to explain why genomic imprinting evolved, most of which are centered on the regulation of nutrient provisioning from parent to offspring. The three different mammalian lineages have adopted very different modes of reproduction and, as a result, vary widely in the amount of nutrient provisioning to the conceptus. Examining imprinting across the three mammal groups enables us to test hypotheses on the origin of this phenomenon in mammals and also to investigate changes in the genome coincident with its evolution.
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Affiliation(s)
- Andrew Pask
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.
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66
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Affiliation(s)
- Denise P. Barlow
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria;
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67
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Kaneda M. Genomic imprinting in mammals—Epigenetic parental memories. Differentiation 2011; 82:51-6. [DOI: 10.1016/j.diff.2011.05.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Revised: 04/05/2011] [Accepted: 05/09/2011] [Indexed: 01/12/2023]
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68
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Abstract
The emerging awareness of the contribution of epigenetic processes to genome function in health and disease is underpinned by decades of research in model systems. In particular, many principles of the epigenetic control of genome function have been uncovered by studies of genomic imprinting. The phenomenon of genomic imprinting, which results in some genes being expressed in a parental--origin-specific manner, is essential for normal mammalian growth and development and exemplifies the regulatory influences of DNA methylation, chromatin structure and non-coding RNA. Setting seminal discoveries in this field alongside recent progress and remaining questions shows how the study of imprinting continues to enhance our understanding of the epigenetic control of genome function in other contexts.
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Wolff P, Weinhofer I, Seguin J, Roszak P, Beisel C, Donoghue MTA, Spillane C, Nordborg M, Rehmsmeier M, Köhler C. High-resolution analysis of parent-of-origin allelic expression in the Arabidopsis Endosperm. PLoS Genet 2011; 7:e1002126. [PMID: 21698132 PMCID: PMC3116908 DOI: 10.1371/journal.pgen.1002126] [Citation(s) in RCA: 183] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 04/21/2011] [Indexed: 12/28/2022] Open
Abstract
Genomic imprinting is an epigenetic phenomenon leading to parent-of-origin specific differential expression of maternally and paternally inherited alleles. In plants, genomic imprinting has mainly been observed in the endosperm, an ephemeral triploid tissue derived after fertilization of the diploid central cell with a haploid sperm cell. In an effort to identify novel imprinted genes in Arabidopsis thaliana, we generated deep sequencing RNA profiles of F1 hybrid seeds derived after reciprocal crosses of Arabidopsis Col-0 and Bur-0 accessions. Using polymorphic sites to quantify allele-specific expression levels, we could identify more than 60 genes with potential parent-of-origin specific expression. By analyzing the distribution of DNA methylation and epigenetic marks established by Polycomb group (PcG) proteins using publicly available datasets, we suggest that for maternally expressed genes (MEGs) repression of the paternally inherited alleles largely depends on DNA methylation or PcG-mediated repression, whereas repression of the maternal alleles of paternally expressed genes (PEGs) predominantly depends on PcG proteins. While maternal alleles of MEGs are also targeted by PcG proteins, such targeting does not cause complete repression. Candidate MEGs and PEGs are enriched for cis-proximal transposons, suggesting that transposons might be a driving force for the evolution of imprinted genes in Arabidopsis. In addition, we find that MEGs and PEGs are significantly faster evolving when compared to other genes in the genome. In contrast to the predominant location of mammalian imprinted genes in clusters, cluster formation was only detected for few MEGs and PEGs, suggesting that clustering is not a major requirement for imprinted gene regulation in Arabidopsis.
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Affiliation(s)
- Philip Wolff
- Department of Biology and Zurich-Basel Plant Science Center, Swiss Federal Institute of Technology, Zurich, Switzerland
- Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Isabelle Weinhofer
- Department of Biology and Zurich-Basel Plant Science Center, Swiss Federal Institute of Technology, Zurich, Switzerland
| | - Jonathan Seguin
- Department of Biology and Zurich-Basel Plant Science Center, Swiss Federal Institute of Technology, Zurich, Switzerland
| | - Pawel Roszak
- Department of Biology and Zurich-Basel Plant Science Center, Swiss Federal Institute of Technology, Zurich, Switzerland
| | - Christian Beisel
- Department Biosystems Science and Engineering, Swiss Federal Institute of Technology, Basel, Switzerland
| | - Mark T. A. Donoghue
- Genetics and Biotechnology Lab, Botany and Plant Science, National University of Ireland Galway, Aras de Brun, Ireland
| | - Charles Spillane
- Genetics and Biotechnology Lab, Botany and Plant Science, National University of Ireland Galway, Aras de Brun, Ireland
| | - Magnus Nordborg
- Gregor Mendel Institute of Molecular Plant Biology GmbH, Vienna, Austria
| | - Marc Rehmsmeier
- Gregor Mendel Institute of Molecular Plant Biology GmbH, Vienna, Austria
| | - Claudia Köhler
- Department of Biology and Zurich-Basel Plant Science Center, Swiss Federal Institute of Technology, Zurich, Switzerland
- Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Labialle S, Cavaillé J. Do repeated arrays of regulatory small-RNA genes elicit genomic imprinting?: Concurrent emergence of large clusters of small non-coding RNAs and genomic imprinting at four evolutionarily distinct eutherian chromosomal loci. Bioessays 2011; 33:565-73. [PMID: 21618561 DOI: 10.1002/bies.201100032] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Indexed: 12/26/2022]
Abstract
The basic premise of the host-defense theory is that genomic imprinting, the parent-of-origin expression of a subset of mammalian genes, derives from mechanisms originally dedicated to silencing repeated and retroviral-like sequences that deeply colonized mammalian genomes. We propose that large clusters of tandemly-repeated C/D-box small nucleolar RNAs (snoRNAs) or microRNAs represent a novel category of sequences recognized as "genomic parasites", contributing to the emergence of genomic imprinting in a subset of chromosomal regions that contain them. Such a view is supported by evidence derived from studies of the imprinted snoRNA- and/or miRNA-encoding Dlk1-Dio3, Snurf-Snrpn, Sfbmt2, and C19MC domains. While adding a new piece to the challenging puzzle of mammalian genome history, this hypothesis also reinforces the notion that dissecting the features and molecular mechanisms that discriminate between "foreign" and "endogenous" sequences is of crucial importance in the field of mammalian epigenetics.
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Affiliation(s)
- Stéphane Labialle
- Laboratoire de Biologie Moléculaire Eucaryote, Université de Toulouse, UPS, Toulouse, France
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Bauer MJ, Fischer RL. Genome demethylation and imprinting in the endosperm. CURRENT OPINION IN PLANT BIOLOGY 2011; 14:162-7. [PMID: 21435940 PMCID: PMC3082360 DOI: 10.1016/j.pbi.2011.02.006] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 01/07/2011] [Accepted: 02/21/2011] [Indexed: 05/19/2023]
Abstract
Imprinting occurs in the endosperm of flowering plants. The endosperm, a product of central cell fertilization, is critical for embryo and seed development. Imprinting in the endosperm is mainly due to the inherited differences in gamete epigenetic composition. Studies have also shown that there are differences in genomic DNA methylation patterns between embryo and endosperm. Examining those differences, along with mutations in the DNA demethylase gene DEMETER, gives insight into the number of imprinted genes and how an antagonistic relationship between TE defense and gene regulation could evolutionarily affect imprinting establishment. Finally, studies demonstrate that DEMETER demethylase activity influences endosperm chromatin composition, and could possibly enhance DNA de novo methylation activity.
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Affiliation(s)
| | - Robert L. Fischer
- Corresponding author: , Telephone: +1-510-642-1314, Fax: +1-510-642-4995
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72
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Kownacki M, Sobczyńska M, Zwierzchowski L. Population study on the inheritance of Lac-Z gene in transgenic mice. J Anim Breed Genet 2011. [DOI: 10.1111/j.1439-0388.1998.tb00338.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Genome-wide transcript profiling of endosperm without paternal contribution identifies parent-of-origin-dependent regulation of AGAMOUS-LIKE36. PLoS Genet 2011; 7:e1001303. [PMID: 21379330 PMCID: PMC3040660 DOI: 10.1371/journal.pgen.1001303] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2010] [Accepted: 01/11/2011] [Indexed: 11/26/2022] Open
Abstract
Seed development in angiosperms is dependent on the interplay among different transcriptional programs operating in the embryo, the endosperm, and the maternally-derived seed coat. In angiosperms, the embryo and the endosperm are products of double fertilization during which the two pollen sperm cells fuse with the egg cell and the central cell of the female gametophyte. In Arabidopsis, analyses of mutants in the cell-cycle regulator CYCLIN DEPENDENT KINASE A;1 (CKDA;1) have revealed the importance of a paternal genome for the effective development of the endosperm and ultimately the seed. Here we have exploited cdka;1 fertilization as a novel tool for the identification of seed regulators and factors involved in parent-of-origin–specific regulation during seed development. We have generated genome-wide transcription profiles of cdka;1 fertilized seeds and identified approximately 600 genes that are downregulated in the absence of a paternal genome. Among those, AGAMOUS-LIKE (AGL) genes encoding Type-I MADS-box transcription factors were significantly overrepresented. Here, AGL36 was chosen for an in-depth study and shown to be imprinted. We demonstrate that AGL36 parent-of-origin–dependent expression is controlled by the activity of METHYLTRANSFERASE1 (MET1) maintenance DNA methyltransferase and DEMETER (DME) DNA glycosylase. Interestingly, our data also show that the active maternal allele of AGL36 is regulated throughout endosperm development by components of the FIS Polycomb Repressive Complex 2 (PRC2), revealing a new type of dual epigenetic regulation in seeds. Seeds of flowering plants consist of three different organisms that develop in parallel. In contrast to animals, a double fertilization event takes place in plants, producing two fertilization products, the embryo and the endosperm. Imprinting, the parent-of-origin–specific expression of genes, typically takes place in the mammalian placenta and in the plant endosperm. A prevailing hypothesis predicts that a parental tug-of-war on the allocation of available recourses to the developing progeny has led to the evolution of imprinting systems where genes expressed from the mother dampen growth whereas genes expressed from the father are growth enhancers. The number of imprinted genes identified in plants is low compared to mammals, and this precludes the elucidation of the epigenetic mechanisms responsible for this specialized expression system. Here, we have used genome-wide transcript profiling of endosperm without paternal contribution to identify seed regulators and, among these, imprinted genes. We identified a cluster of downregulated MADS-box transcription factors, including AGL36, that was subsequently shown to be imprinted by an epigenetic mechanism involving the DNA methylase MET1 and the glycosylase DME. In addition, the expression of the active AGL36 allele was dampened by the FIS Polycomb Repressive Complex, identifying a novel mode of regulation of imprinted genes.
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74
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Li M, Chen SS. The tendency to recreate ancestral CG dinucleotides in the human genome. BMC Evol Biol 2011; 11:3. [PMID: 21208429 PMCID: PMC3025853 DOI: 10.1186/1471-2148-11-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Accepted: 01/05/2011] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The CG dinucleotides are known to be deficient in the human genome, due to a high mutation rate from 5-methylated CG to TG and its complementary pair CA. Meanwhile, many cellular functions rely on these CG dinucleotides, such as gene expression controlled by cytosine methylation status. Thus, CG dinucleotides that provide essential functional substrates should be retained in genomes. How these two conflicting processes regarding the fate of CG dinucleotides - i.e., high mutation rate destroying CG dinucleotides, vs. functional processes that require their preservation remains an unsolved question. RESULTS By analyzing the mutation and frequency spectrum of newly derived alleles in the human genome, a tendency towards generating more CGs was observed, which was mainly contributed by an excess number of mutations from CA/TG to CG. Simultaneously, we found a fixation preference for CGs derived from TG/CA rather than CGs generated by other dinucleotides. These tendencies were observed both in intergenic and genic regions. An analysis of Integrated Extended Haplotype Homozygosity provided no evidence of selection for newly derived CGs. CONCLUSIONS Ancestral CG dinucleotides that were subsequently lost by mutation tend to be recreated in the human genome, as indicated by a biased mutation and fixation pattern favoring new CGs that derived from TG/CA.
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Affiliation(s)
- Mingkun Li
- CAS-MPG Partner Institute of Computational Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, 200000 Shanghai, PR China.
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75
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Raissig MT, Baroux C, Grossniklaus U. Regulation and flexibility of genomic imprinting during seed development. THE PLANT CELL 2011; 23:16-26. [PMID: 21278124 PMCID: PMC3051244 DOI: 10.1105/tpc.110.081018] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Revised: 12/29/2010] [Accepted: 01/13/2011] [Indexed: 05/05/2023]
Abstract
Genomic imprinting results in monoallelic gene expression in a parent-of-origin-dependent manner. It is achieved by the differential epigenetic marking of parental alleles. Over the past decade, studies in the model systems Arabidopsis thaliana and maize (Zea mays) have shown a strong correlation between silent or active states with epigenetic marks, such as DNA methylation and histone modifications, but the nature of the primary imprint has not been clearly established for all imprinted genes. Phenotypes and expression patterns of imprinted genes have fueled the perception that genomic imprinting is specific to the endosperm, a seed tissue that does not contribute to the next generation. However, several lines of evidence suggest a potential role for imprinting in the embryo, raising questions as to how imprints are erased and reset from one generation to the next. Imprinting regulation in flowering plants shows striking similarities, but also some important differences, compared with the mechanisms of imprinting described in mammals. For example, some imprinted genes are involved in seed growth and viability in plants, which is similar in mammals, where imprinted gene regulation is essential for embryonic development. However, it seems to be more flexible in plants, as imprinting requirements can be bypassed to allow the development of clonal offspring in apomicts.
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Affiliation(s)
| | | | - Ueli Grossniklaus
- Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, CH-8008 Zurich, Switzerland
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76
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77
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Cooper WN, Constância M. How genome-wide approaches can be used to unravel the remaining secrets of the imprintome. Brief Funct Genomics 2010; 9:315-28. [PMID: 20675687 DOI: 10.1093/bfgp/elq018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Genomic imprinting is the differential expression of genes according to their transmitting parent and is achieved by labelling of the two alleles with different epigenetic marks. The majority of described imprinted genes are present in clusters with coordinate regulation. Multiple mechanisms are known to regulate this differential expression, including repression of one allele by the action of cis-acting macro non-coding RNAs, insulator elements, allele specific histone modifications and DNA methylation. A hallmark of all imprinted regions described so far is the presence of one or more differentially methylated regions (DMRs). A DMR is a nucleotide sequence rich in CpG dinucleotides that is specifically methylated on one parental chromosome and unmethylated on the allele derived from the other parent. This parent-specific differential methylation may be imparted during spermatogenesis or oogenesis (as is the case for gametic DMRs) or may be acquired during embryogenesis (somatic DMRs). This review will describe the advantages and disadvantages of some of the techniques that can be used to compare epigenetic marks between parental chromosomes and to understand how these marks affect the 3D interactions and monoallelic expression at imprinted loci. Recent advances in sequencing technologies, in particular, provide exciting new opportunities to study imprinting. These analyses are likely to lead to the full characterization of the 'imprintome', which includes uncovering the totality of imprinted genes within a genome, their epigenetic landscape and unique features that render them resistant to epigenetic reprogramming in the early embryo.
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Affiliation(s)
- Wendy N Cooper
- Metabolic Research Laboratories, Department of Obstetrics and Gynaecology, The Rosie Hospital, Cambridge CB2 0SW, UK.
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78
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Kaneko-Ishino T, Ishino F. Retrotransposon silencing by DNA methylation contributed to the evolution of placentation and genomic imprinting in mammals. Dev Growth Differ 2010; 52:533-43. [PMID: 20646026 DOI: 10.1111/j.1440-169x.2010.01194.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The evolution of two mammalian-specific traits, viviparous reproduction with a placenta and genomic imprinting, have been addressed by multiple studies of two retrotransposon derived, mammalian-specific genes. These gene targeting experiments in mice, together with recent comparative genomic analyses among three mammalian groups, suggest that extremely rare events; namely exaptations from retrotransposons, made crucial contributions to the establishment and diversification of mammals via placental formation. We propose that nearly neutral evolution, as well as Darwinian evolution (natural selection), plays an important role in the exaptation process. Comparative genomic analysis of various imprinted regions has also revealed that an imprinting control element essential for parent-of-origin specific monoallelic expression of imprinted genes emerged in each of the imprinted regions, possibly by the insertion of exogenous DNAs, such as retrotransposons. In both cases, DNA methylation in germ cells must have been of critical importance to repress the exogenous DNAs inserted into the genomes of mammalian ancestors. We propose that the ability of germ line DNA methylation enabled the emergence of certain mammalian-specific features during the course of evolution.
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Affiliation(s)
- Tomoko Kaneko-Ishino
- School of Health Sciences, Tokai University, Bohseidai, Isehara-shi, Kanagawa, Japan
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79
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Nelissen ECM, van Montfoort APA, Dumoulin JCM, Evers JLH. Epigenetics and the placenta. Hum Reprod Update 2010; 17:397-417. [PMID: 20959349 DOI: 10.1093/humupd/dmq052] [Citation(s) in RCA: 254] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The placenta is of utmost importance for intrauterine fetal development and growth. Deregulation of placentation can lead to adverse outcomes for both mother and fetus, e.g. gestational trophoblastic disease (GTD), pre-eclampsia and fetal growth retardation. A significant factor in placental development and function is epigenetic regulation. METHODS This review summarizes the current knowledge in the field of epigenetics in relation to placental development and function. Relevant studies were identified by searching PubMed, Medline and reference sections of all relevant studies and reviews. RESULTS Epigenetic regulation of the placenta evolves during preimplantation development and further gestation. Epigenetic marks, like DNA methylation, histone modifications and non-coding RNAs, affect gene expression patterns. These expression patterns, including the important parent-of-origin-dependent gene expression resulting from genomic imprinting, play a pivotal role in proper fetal and placental development. Disturbed placental epigenetics has been demonstrated in cases of intrauterine growth retardation and small for gestational age, and also appears to be involved in the pathogenesis of pre-eclampsia and GTD. Several environmental effects have been investigated so far, e.g. ethanol, oxygen tension as well as the effect of several aspects of assisted reproduction technologies on placental epigenetics. CONCLUSIONS Studies in both animals and humans have made it increasingly clear that proper epigenetic regulation of both imprinted and non-imprinted genes is important in placental development. Its disturbance, which can be caused by various environmental factors, can lead to abnormal placental development and function with possible consequences for maternal morbidity, fetal development and disease susceptibility in later life.
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Affiliation(s)
- Ewka C M Nelissen
- Department of Obstetrics and Gynaecology, Research Institute Growth & Development (GROW), Center for Reproductive Medicine, Maastricht University Medical Centre, MUMC+, PO Box 5800, 6202 AZ Maastricht, The Netherlands.
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80
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Wu S, Zhu J, Li Y, Lin T, Gan L, Yuan X, Xu M, Wei G. Dynamic effect of di-2-(ethylhexyl) phthalate on testicular toxicity: epigenetic changes and their impact on gene expression. Int J Toxicol 2010; 29:193-200. [PMID: 20335514 DOI: 10.1177/1091581809355488] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
This study investigated epigenetic (specifically, DNA methylation) changes and their impact on gene expression in testes induced by maternal exposure to Di-2-(ethylhexyl) phthalate (DEHP) in mice. Testicular dysgenesis syndrome was induced in fetuses and pups by maternal exposure to DEHP at 500 mg/kg/d, and testes were excised for analysis on gestation day (GD) 19 and postnatal days (PNDs) 3, 21, 56, and 90. High-performance liquid chromatography (HPLC) was performed to analyze DNA methylation status, and expression levels of the DNA methyltransferases were examined by quantitative real-time polymerase chain reaction (qPCR). Testis-specific gene, insulin-like hormone 3 (Insl3), and testosterone production were also detected. DEHP significantly increased DNA methylation levels on GD 19 and PND 3 (P < .05 and P < .05) but not on PNDs 21, 56, and 90. DEHP also significantly increased the expression of DNA methyltransferases. For DNA methyltransferase 1, the difference was not significant on PND 21, and DNA methyltransferase 3a and 3b returned to normal levels on PND 56. Fetal testes were a main target for DEHP as evidenced by a reduction in Insl3 expression and testosterone production. Effects of DEHP on Insl3 expression continued until PND 21. The DEHP-induced suppression of testosterone had not recovered on PND 56. Changes in DNA methylation may play an important role in abnormal testicular function caused by environmental factors such as maternal exposure to DEHP, which may be a mechanism of DEHP-mediated testicular toxicity.
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Affiliation(s)
- Shengde Wu
- Department of Pediatric Urology Surgery, Children's Hospital of Chongqing Medical University, Chongqing, China
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81
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Noguer-Dance M, Abu-Amero S, Al-Khtib M, Lefèvre A, Coullin P, Moore GE, Cavaillé J. The primate-specific microRNA gene cluster (C19MC) is imprinted in the placenta. Hum Mol Genet 2010; 19:3566-82. [PMID: 20610438 DOI: 10.1093/hmg/ddq272] [Citation(s) in RCA: 234] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Imprinted genes play crucial roles in mammalian development and disruption of their expression is associated with many human disorders including tumourigenesis; yet, the actual number of imprinted genes in the human genome remains a matter of debate. Here, we report on the unexpected finding that the chromosome 19 microRNA cluster (C19MC), the largest human microRNA gene cluster discovered so far, is regulated by genomic imprinting with only the paternally inherited allele being expressed in the placenta. DNA methylation profiling identified a differentially methylated region (C19MC-DMR1) that overlaps an upstream CpG-rich promoter region associated with short tandem repeats. It displays a maternal-specific methylation imprint acquired in oocytes and generates a complex population of large, compartimentalized non-coding RNA (ncRNA) species retained in close proximity to the C19MC transcription site. This occurs adjacent to, but not within, a poorly characterized nuclear Alu-rich domain. Interestingly, C19MC maps near another imprinted gene, the maternally expressed ZNF331 gene, and therefore may define a novel, previously unrecognized large imprinted primate-specific chromosomal domain. Altogether, our study adds C19MC to the growing list of imprinted repeated small RNA gene clusters and further strengthens the potential involvement of small ncRNAs in the function and/or the evolution of imprinted gene networks.
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Affiliation(s)
- Marie Noguer-Dance
- Laboratoire de Biologie Moléculaire Eucaryote, Université de Toulouse, Toulouse, France
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82
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de Lima ELS, da Silva VC, da Silva HDA, Bezerra AM, de Morais VLL, de Morais AL, Cruz RV, Barros MHM, Hassan R, de Freitas AC, Muniz MTC. MTR polymorphic variant A2756G and retinoblastoma risk in Brazilian children. Pediatr Blood Cancer 2010; 54:904-8. [PMID: 20310006 DOI: 10.1002/pbc.22472] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
BACKGROUND Polymorphisms in the genes of folate and methionine metabolism enzymes have been associated with some forms of cancer by affecting DNA synthesis, repair, and methylation. PROCEDURE A case-control study of 72 retinoblastoma cases and 98 cancer-free children controls was performed to investigate whether the polymorphisms of the methylenetetrahydrofolate reductase (MTHFR C677T and A1298C), methionine synthase (MTR A2756G), carrier of reduced folate 1 (RFC-1 A80G) and thymidylate synthase (TYMS 2R > 3R) altered the risk for retinoblastoma. RESULTS MTR A2756G AG plus GG genotype frequencies were higher in patients than in controls (45% vs. 26%, P = 0.03). Individual carriers of the variant allele G had a 2.02 (95% CI: 1.05-3.92)-fold increased risk for retinoblastoma. In contrast, no association was observed with respect to MTHFR C677T and A1298C, RFC A80G, and TYMS polymorphisms. CONCLUSIONS This study presents evidence for an association between the MTR A2756G polymorphism and retinoblastoma susceptibility in a Northeast population from Brazil.
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Affiliation(s)
- Elker Lene Santos de Lima
- Laboratório de Biologia Molecular, Centro de Oncohematologia Pediátrica (CEONHPE), Hospital Universitário Oswaldo Cruz, Universidade de Pernambuco, Recife, PE, Brazil
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83
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Buiting K, Kanber D, Horsthemke B, Lohmann D. Imprinting of RB1 (the new kid on the block). Brief Funct Genomics 2010; 9:347-53. [PMID: 20551090 DOI: 10.1093/bfgp/elq014] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Recent data have revealed that the paradigmatic tumour suppressor gene RB1 on chromosome 13 is preferentially expressed from the maternal allele. Imprinted expression of RB1 is linked to a differentially methylated CpG island in intron 2 of this gene (CpG 85). On the paternal chromosome, CpG 85 is unmethylated and acts as a weak promoter of an alternative RB1 transcript. Paternal mRNA levels are probably reduced as the result of transcriptional interference of the regular promoter and the alternative promoter on this chromosome. CpG 85 is part of a truncated processed pseudogene (KIAA0649P) that integrated into the RB1 gene prior to the speciation of extant primates. It is plausible that differential penetrance and variation of age at diagnosis, which have been observed in patients with hereditary and non-hereditary retinoblastoma, respectively, are a consequence of imprinted expression of the RB1 gene. Interestingly, RB1 is imprinted in the same direction as CDKN1C, which operates upstream of RB1. The imprinting of two components of the same pathway indicates that there has been strong evolutionary selection for maternal inhibition of cell proliferation.
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84
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Abstract
DNA methylation is an epigenetic mark that has key roles in the control of genome activity in plants and mammals. It is critical for the stable silencing of repeat elements and is also involved in the epigenetic regulation of some genes. Despite similarities in the controlling functions of DNA methylation, its dynamics and deposition patterns differ in several respects between plants and mammals. One of the most striking differences is that plants tend to propagate pre-existing DNA methylation states across generations, whereas mammals re-establish them genome wide at every generation. Here, we review our current understanding of DNA methylation in the flowering plant Arabidopsis. We discuss in particular the role of RNAi in the incremental methylation and silencing of repeat elements over successive generations. We argue that paramutation, an epigenetic phenomenon first described in maize, is an extreme manifestation of this RNAi-dependent pathway.
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85
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Muñoz-López M, García-Pérez JL. DNA transposons: nature and applications in genomics. Curr Genomics 2010; 11:115-28. [PMID: 20885819 PMCID: PMC2874221 DOI: 10.2174/138920210790886871] [Citation(s) in RCA: 257] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2009] [Revised: 11/18/2009] [Accepted: 12/01/2009] [Indexed: 12/19/2022] Open
Abstract
Repeated DNA makes up a large fraction of a typical mammalian genome, and some repetitive elements are able to move within the genome (transposons and retrotransposons). DNA transposons move from one genomic location to another by a cut-and-paste mechanism. They are powerful forces of genetic change and have played a significant role in the evolution of many genomes. As genetic tools, DNA transposons can be used to introduce a piece of foreign DNA into a genome. Indeed, they have been used for transgenesis and insertional mutagenesis in different organisms, since these elements are not generally dependent on host factors to mediate their mobility. Thus, DNA transposons are useful tools to analyze the regulatory genome, study embryonic development, identify genes and pathways implicated in disease or pathogenesis of pathogens, and even contribute to gene therapy. In this review, we will describe the nature of these elements and discuss recent advances in this field of research, as well as our evolving knowledge of the DNA transposons most widely used in these studies.
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Affiliation(s)
- Martín Muñoz-López
- Andalusian Stem Cell Bank, Center for Biomedical Research, University of Granada, Avda. del Conocimiento s/n, Armilla, 18100, Granada, Spain
| | - José L. García-Pérez
- Andalusian Stem Cell Bank, Center for Biomedical Research, University of Granada, Avda. del Conocimiento s/n, Armilla, 18100, Granada, Spain
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86
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Renfree MB, Papenfuss AT, Shaw G, Pask AJ. Eggs, embryos and the evolution of imprinting: insights from the platypus genome. Reprod Fertil Dev 2010; 21:935-42. [PMID: 19874717 DOI: 10.1071/rd09092] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2009] [Accepted: 08/28/2009] [Indexed: 12/18/2022] Open
Abstract
Genomic imprinting is widespread in eutherian and marsupial mammals. Although there have been many hypotheses to explain why genomic imprinting evolved in mammals, few have examined how it arose. The host defence hypothesis suggests that imprinting evolved from existing mechanisms within the cell that act to silence foreign DNA elements that insert into the genome. However, the changes to the mammalian genome that accompanied the evolution of imprinting have been hard to define due to the absence of large-scale genomic resources from all extant classes. The recent release of the platypus genome sequence has provided the first opportunity to make comparisons between prototherian (monotreme, which show no signs of imprinting) and therian (marsupial and eutherian, which have imprinting) mammals. We compared the distribution of repeat elements known to attract epigenetic silencing across the genome from monotremes and therian mammals, particularly focusing on the orthologous imprinted regions. Our analyses show that the platypus has significantly fewer repeats of certain classes in the regions of the genome that have become imprinted in therian mammals. The accumulation of repeats, especially long-terminal repeats and DNA elements, in therian imprinted genes and gene clusters therefore appears to be coincident with, and may have been a potential driving force in, the development of mammalian genomic imprinting. Comparative platypus genome analyses of orthologous imprinted regions have provided strong support for the host defence hypothesis to explain the origin of imprinting.
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87
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Wu S, Zhu J, Li Y, Lin T, Gan L, Yuan X, Xiong J, Liu X, Xu M, Zhao D, Ma C, Li X, Wei G. Dynamic Epigenetic Changes Involved in Testicular Toxicity Induced by Di-2-(Ethylhexyl) Phthalate in Mice. Basic Clin Pharmacol Toxicol 2010; 106:118-23. [DOI: 10.1111/j.1742-7843.2009.00483.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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88
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Köhler C, Mittelsten Scheid O, Erilova A. The impact of the triploid block on the origin and evolution of polyploid plants. Trends Genet 2010; 26:142-8. [PMID: 20089326 DOI: 10.1016/j.tig.2009.12.006] [Citation(s) in RCA: 131] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Revised: 12/11/2009] [Accepted: 12/14/2009] [Indexed: 12/12/2022]
Abstract
Polyploidization, a widespread phenomenon among plants, is considered a major speciation mechanism. Polyploid plants have a high degree of immediate post-zygotic reproductive isolation from their progenitors, as backcrossing to either parent will produce mainly nonviable progeny. This reproductive barrier is called triploid block and it is caused by malfunction of the endosperm. Nevertheless, the main route to polyploid formation is via unreduced gametes and unstable triploid progeny, suggesting that there are ways to overcome the triploid block. Until recently, the mechanistic basis for unreduced gamete formation and the triploid block were completely unknown. Recent developments have revealed genetic pathways leading to unreduced gamete formation as well as the underlying genetic basis for the triploid block in Arabidopsis. These novel findings will provide the basis for a genetic understanding of polyploid formation and subsequent speciation in plants.
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Affiliation(s)
- Claudia Köhler
- Department of Biology and Zurich-Basel Plant Science Center, Swiss Federal Institute of Technology, ETH Centre, CH-8092 Zurich, Switzerland.
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89
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Kanber D, Berulava T, Ammerpohl O, Mitter D, Richter J, Siebert R, Horsthemke B, Lohmann D, Buiting K. The human retinoblastoma gene is imprinted. PLoS Genet 2009; 5:e1000790. [PMID: 20041224 PMCID: PMC2791201 DOI: 10.1371/journal.pgen.1000790] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2009] [Accepted: 11/25/2009] [Indexed: 11/18/2022] Open
Abstract
Genomic imprinting is an epigenetic process leading to parent-of-origin–specific DNA methylation and gene expression. To date, ∼60 imprinted human genes are known. Based on genome-wide methylation analysis of a patient with multiple imprinting defects, we have identified a differentially methylated CpG island in intron 2 of the retinoblastoma (RB1) gene on chromosome 13. The CpG island is part of a 5′-truncated, processed pseudogene derived from the KIAA0649 gene on chromosome 9 and corresponds to two small CpG islands in the open reading frame of the ancestral gene. It is methylated on the maternal chromosome 13 and acts as a weak promoter for an alternative RB1 transcript on the paternal chromosome 13. In four other KIAA0649 pseudogene copies, which are located on chromosome 22, the two CpG islands have deteriorated and the CpG dinucleotides are fully methylated. By analysing allelic RB1 transcript levels in blood cells, as well as in hypermethylated and 5-aza-2′-deoxycytidine–treated lymphoblastoid cells, we have found that differential methylation of the CpG island skews RB1 gene expression in favor of the maternal allele. Thus, RB1 is imprinted in the same direction as CDKN1C, which operates upstream of RB1. The imprinting of two components of the same pathway indicates that there has been strong evolutionary selection for maternal inhibition of cell proliferation. Genomic imprinting is an epigenetic process leading to parent-of-origin–specific DNA methylation and gene expression. Defects in this process lead to abnormal development, growth, or behavior. It is still unclear why and how imprinting evolved and how many human genes are imprinted. Based on genome-wide DNA methylation analysis in a patient with a generalized imprinting defect, we have found that the paradigmatic retinoblastoma 1 (RB1) gene on chromosome 13 is imprinted. Imprinting of RB1 is linked to the insertion of a DNA sequence derived by retrotransposition from a gene on chromosome 9. Part of the inserted DNA sequence has evolved into a differentially methylated alternative RB1 promoter. Differential methylation of this sequence skews expression of the RB1 gene in favour of the maternal allele. The direction of the imprint imposed on the RB1 gene is the same as of the maternally expressed CDKN1C gene, which operates upstream of RB1. The imprinting of two components of the same pathway indicates that there has been strong evolutionary selection for maternal inhibition of cell proliferation.
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Affiliation(s)
- Deniz Kanber
- Institut für Humangenetik, Universitätsklinikum Essen, Essen, Germany
| | - Tea Berulava
- Institut für Humangenetik, Universitätsklinikum Essen, Essen, Germany
| | - Ole Ammerpohl
- Institut für Humangenetik, Christian-Albrechts Universität zu Kiel, Universitätsklinikum Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Diana Mitter
- Institut für Humangenetik, Universitätsklinikum Essen, Essen, Germany
| | - Julia Richter
- Institut für Humangenetik, Christian-Albrechts Universität zu Kiel, Universitätsklinikum Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Reiner Siebert
- Institut für Humangenetik, Christian-Albrechts Universität zu Kiel, Universitätsklinikum Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Bernhard Horsthemke
- Institut für Humangenetik, Universitätsklinikum Essen, Essen, Germany
- * E-mail:
| | - Dietmar Lohmann
- Institut für Humangenetik, Universitätsklinikum Essen, Essen, Germany
| | - Karin Buiting
- Institut für Humangenetik, Universitätsklinikum Essen, Essen, Germany
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90
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Abstract
Genomic imprinting, the allele-specific expression of a gene dependent on its parent-of-origin, has independently evolved in flowering plants and mammals. In mammals and flowering plants, imprinting occurs in the embryo as well as in embryo-nourishing tissues, the placenta and the endosperm, respectively, and it has been suggested that imprinted genes control the nutrient flow from the mother to the offspring ('kinship theory'). Alternatively, imprinting might have evolved as a by-product of a defense mechanism destined to control transposon activity in gametes ('defense hypothesis'). Recent studies provide substantial evidence for the 'defense hypothesis' by showing that imprinted genes in plants are located in the vicinity of transposon or repeat sequences, suggesting that the insertion of transposon or repeat sequences was a prerequisite for imprinting evolution. Transposons or repeat sequences are silenced by DNA methylation, causing silencing of neighboring genes in vegetative tissues. However, because of genome-wide DNA demethylation in the central cell, genes located in the vicinity of transposon or repeat sequences will be active in the central cell and the maternal alleles will remain unmethylated and active in the descendent endosperm, assuming an imprinted expression. Consequently, many imprinted genes are likely to have an endosperm-restricted function, or, alternatively, they have no functional role in the endosperm and are on the trajectory to convert to pseudogenes. Thus, the 'defense hypothesis' as well as 'kinship theory' together can explain the origin of genomic imprinting; whereas the first hypothesis explains how imprinting originates, the latter explains how imprinting is manifested and maintained.
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91
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Imprinting evolution and human health. Mamm Genome 2009; 20:563-72. [PMID: 19830403 DOI: 10.1007/s00335-009-9229-y] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Accepted: 09/16/2009] [Indexed: 01/06/2023]
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92
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Renfree MB, Hore TA, Shaw G, Graves JAM, Pask AJ. Evolution of genomic imprinting: insights from marsupials and monotremes. Annu Rev Genomics Hum Genet 2009; 10:241-62. [PMID: 19630559 DOI: 10.1146/annurev-genom-082908-150026] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Parent-of-origin gene expression (genomic imprinting) is widespread among eutherian mammals and also occurs in marsupials. Most imprinted genes are expressed in the placenta, but the brain is also a favored site. Although imprinting evolved in therian mammals before the marsupial-eutherian split, the mechanisms have continued to evolve in each lineage to produce differences between the two groups in terms of the number and regulation of imprinted genes. As yet there is no evidence for genomic imprinting in the egg-laying monotreme mammals, although these mammals also form a placenta (albeit short-lived) and transfer nutrients from mother to embryo. Therefore, imprinting was not essential for the evolution of the placenta and its importance in nutrient transfer but the elaboration of imprinted genes in marsupials and eutherians is associated with viviparity. Here we review the recent analyses of imprinted gene clusters in marsupials and monotremes, which have served to shed light on the origin and evolution of imprinting mechanisms in mammals.
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Affiliation(s)
- Marilyn B Renfree
- ARC Center of Excellence for Kangaroo Genomics, Melbourne, Victoria 3010, Australia.
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93
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Villar CBR, Erilova A, Makarevich G, Trösch R, Köhler C. Control of PHERES1 imprinting in Arabidopsis by direct tandem repeats. MOLECULAR PLANT 2009; 2:654-660. [PMID: 19825646 DOI: 10.1093/mp/ssp014] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Genomic imprinting is an epigenetic phenomenon that causes monoallelic expression of specific genes dependent on the parent-of-origin. Imprinting of the Arabidopsis gene PHERES1 requires the function of the FERTILIZATION INDEPENDENT SEED (FIS) Polycomb group complex as well as a distally located methylated region containing a tandem triple repeat sequence. In this study, we investigated the regulation of the close PHERES1 homolog PHERES2. We found that PHERES2 is also a direct target gene of the FIS Polycomb group complex, but, in contrast to PHERES1, PHERES2 is equally expressed from maternal and paternal alleles. Thus, PHERES2 is not regulated by genomic imprinting, correlating with the lack of tandem repeats at PHERES2. Eliminating tandem repeats from the PHERES1 locus abolishes PHERES1 imprinting, demonstrating that tandem repeats are essential for PHERES1 imprinting. Taking these results together, our study shows that the recently duplicated genes PHERES1 and PHERES2 are both target genes of the FIS Polycomb group complex but only PHERES1 is regulated by genomic imprinting, which is likely caused by the presence of repeat sequences in the proximity of the PHERES1 locus.
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Affiliation(s)
- Corina Belle R Villar
- Department of Biology and Zurich-Basel Plant Science Center, Swiss Federal Institute of Technology, ETH Centre, CH-8092 Zurich, Switzerland
| | - Aleksandra Erilova
- Department of Biology and Zurich-Basel Plant Science Center, Swiss Federal Institute of Technology, ETH Centre, CH-8092 Zurich, Switzerland
| | - Grigory Makarevich
- Department of Biology and Zurich-Basel Plant Science Center, Swiss Federal Institute of Technology, ETH Centre, CH-8092 Zurich, Switzerland
| | - Raphael Trösch
- Department of Biology and Zurich-Basel Plant Science Center, Swiss Federal Institute of Technology, ETH Centre, CH-8092 Zurich, Switzerland
| | - Claudia Köhler
- Department of Biology and Zurich-Basel Plant Science Center, Swiss Federal Institute of Technology, ETH Centre, CH-8092 Zurich, Switzerland.
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94
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Gehring M, Bubb KL, Henikoff S. Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science 2009; 324:1447-51. [PMID: 19520961 PMCID: PMC2886585 DOI: 10.1126/science.1171609] [Citation(s) in RCA: 401] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
DNA methylation is an epigenetic mark associated with transposable element silencing and gene imprinting in flowering plants and mammals. In plants, imprinting occurs in the endosperm, which nourishes the embryo during seed development. We have profiled Arabidopsis DNA methylation genome-wide in the embryo and endosperm and found that large-scale methylation changes accompany endosperm development and endosperm-specific gene expression. Transposable element fragments are extensively demethylated in the endosperm. We discovered new imprinted genes by the identification of candidates associated with regions of reduced endosperm methylation and preferential expression in endosperm relative to other parts of the plant. These data suggest that imprinting in plants evolved from targeted methylation of transposable element insertions near genic regulatory elements followed by positive selection when the resulting expression change was advantageous.
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Affiliation(s)
- Mary Gehring
- Howard Hughes Medical Institute (HHMI), Fred Hutchinson Cancer Research Center (FHCRC), 1100 Fairview Avenue North, Seattle, WA 98109, USA
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95
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Fertilization and embryonic developmental capacity of epididymal and testicular sperm and immature spermatids and spermatocytes. ACTA ACUST UNITED AC 2009. [DOI: 10.1017/s096227990000140x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Spermatogenesis in mammalian species begins after birth. The gonocytes, arrested at G2 of the cell cycle in the foetus, resume mitotic proliferation after birth. As identified in the mouse, the gonocytes migrate towards the periphery of the seminiferous cords at day 4 to day 6 after birth and are located in close contact with the basal lamina. From this stage the gonocytes are referred to as primitive type A spermatogonia. These cells continue mitotic proliferation and differentiate to form type B spermatogonia. By day 10 after birth, many of the type B spermatogonia have formed preleptotene primary spermatocytes which undergo a final phase of DNA synthesis (leptotene) prior to entering meiotic prophase (zygotene).
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96
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Labet V, Morell C, Cadet J, Eriksson LA, Grand A. Hydrolytic Deamination of 5-Methylcytosine in Protic Medium—A Theoretical Study. J Phys Chem A 2009; 113:2524-33. [DOI: 10.1021/jp808902j] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Vanessa Labet
- Laboratoire “Lésions des Acides Nucléiques”, INAC/SCIB—UMR-E n°3 CEA-UJF, CEA Grenoble, 17 rue des Martyrs, F-38 054 Grenoble cedex 9, France, and School of Science and Technology, and Örebro Life Science Center, Örebro University, 701 82 Örebro, Sweden
| | - Christophe Morell
- Laboratoire “Lésions des Acides Nucléiques”, INAC/SCIB—UMR-E n°3 CEA-UJF, CEA Grenoble, 17 rue des Martyrs, F-38 054 Grenoble cedex 9, France, and School of Science and Technology, and Örebro Life Science Center, Örebro University, 701 82 Örebro, Sweden
| | - Jean Cadet
- Laboratoire “Lésions des Acides Nucléiques”, INAC/SCIB—UMR-E n°3 CEA-UJF, CEA Grenoble, 17 rue des Martyrs, F-38 054 Grenoble cedex 9, France, and School of Science and Technology, and Örebro Life Science Center, Örebro University, 701 82 Örebro, Sweden
| | - Leif A. Eriksson
- Laboratoire “Lésions des Acides Nucléiques”, INAC/SCIB—UMR-E n°3 CEA-UJF, CEA Grenoble, 17 rue des Martyrs, F-38 054 Grenoble cedex 9, France, and School of Science and Technology, and Örebro Life Science Center, Örebro University, 701 82 Örebro, Sweden
| | - André Grand
- Laboratoire “Lésions des Acides Nucléiques”, INAC/SCIB—UMR-E n°3 CEA-UJF, CEA Grenoble, 17 rue des Martyrs, F-38 054 Grenoble cedex 9, France, and School of Science and Technology, and Örebro Life Science Center, Örebro University, 701 82 Örebro, Sweden
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97
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Pask AJ, Papenfuss AT, Ager EI, McColl KA, Speed TP, Renfree MB. Analysis of the platypus genome suggests a transposon origin for mammalian imprinting. Genome Biol 2009; 10:R1. [PMID: 19121219 PMCID: PMC2687786 DOI: 10.1186/gb-2009-10-1-r1] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2008] [Accepted: 01/02/2009] [Indexed: 12/23/2022] Open
Abstract
Comparisons between the platypus and eutherian mammalian genomes provides new insights into how epigenetic imprinting may have evolved in mammalian genomes. Background Genomic imprinting is an epigenetic phenomenon that results in monoallelic gene expression. Many hypotheses have been advanced to explain why genomic imprinting evolved in mammals, but few have examined how it arose. The host defence hypothesis suggests that imprinting evolved from existing mechanisms within the cell that act to silence foreign DNA elements that insert into the genome. However, the changes to the mammalian genome that accompanied the evolution of imprinting have been hard to define due to the absence of large scale genomic resources between all extant classes. The recent release of the platypus genome has provided the first opportunity to perform comparisons between prototherian (monotreme; which appear to lack imprinting) and therian (marsupial and eutherian; which have imprinting) mammals. Results We compared the distribution of repeat elements known to attract epigenetic silencing across the entire genome from monotremes and therian mammals, particularly focusing on the orthologous imprinted regions. There is a significant accumulation of certain repeat elements within imprinted regions of therian mammals compared to the platypus. Conclusions Our analyses show that the platypus has significantly fewer repeats of certain classes in the regions of the genome that have become imprinted in therian mammals. The accumulation of repeats, especially long terminal repeats and DNA elements, in therian imprinted genes and gene clusters is coincident with, and may have been a potential driving force in, the development of mammalian genomic imprinting. These data provide strong support for the host defence hypothesis.
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Affiliation(s)
- Andrew J Pask
- Department of Zoology, The University of Melbourne, Melbourne, Victoria, Australia.
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98
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Abstract
Genomic imprinting is a widespread epigenetic phenomenon in eutherian mammals, which regulates many aspects of growth and development. Parental conflict over the degree of maternal nutrient transfer is the favoured hypothesis for the evolution of imprinting. Marsupials, like eutherian mammals, are viviparous but deliver an altricial young after a short gestation supported by a fully functional placenta, so can shed light on the evolution and time of acquisition of genomic imprinting. All orthologues of eutherian imprinted genes examined have a conserved expression in the marsupial placenta regardless of their imprint status. Differentially methylated regions (DMRs) are the most common mechanism controlling genomic imprinting in eutherian mammals, but none were found in the marsupial imprinted orthologues of IGF2 receptor (IGF2R), INS or mesoderm-specific transcript (MEST). Instead, histone modification appears to be the mechanism used to silence these genes. At least three genes in marsupials have DMRs: H19, IGF2 and PEG10. PEG10 is particularly interesting as it is derived from a retrotransposon, providing the first direct evidence that retrotransposon insertion can drive the evolution of an imprinted region and of a DMR in mammals. The insertion occurred after the prototherian–therian mammal divergence, suggesting that there may have been strong selection for the retention of imprinted regions that arose during the evolution of placentation. There is currently no evidence for genomic imprinting in the egg-laying monotreme mammals. However, since these mammals do have a short-lived placenta, imprinting appears to be correlated with viviparity but not placentation.
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Affiliation(s)
- Marilyn B Renfree
- Department of Zoology, ARC Centre of Excellence for Kangaroo Genomics, The University of Melbourne, Melbourne, Victoria 3010, Australia.
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99
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Kuriyama M, Udagawa A, Yoshimoto S, Ichinose M, Sato K, Yamazaki K, Matsuno Y, Shiota K, Mori C. DNA Methylation Changes during Cleft Palate Formation Induced by Retinoic Acid in Mice. Cleft Palate Craniofac J 2008; 45:545-51. [DOI: 10.1597/07-134.1] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Objectives:The aim of this study was to analyze epigenetic (specifically, DNA methylation) participation in the mechanisms of cleft palate only induced by maternal exposure to all-trans retinoic acid in mice.Design:Cleft palate only was induced in fetuses by maternal exposure to all-trans retinoic acid. Their secondary palates were excised for analysis. Cytosine extension assay and restriction landmark genomic scanning were performed to analyze DNA methylation status. The expression levels of the DNA methyltransferases were examined by real-time reverse transcriptase–polymerase chain reaction.Results:Using cytosine extension assay, on gestation day 14.5, the status of DNA methylation within CpG islands and in global DNA was decreased significantly in all-trans retinoic acid–treated groups compared with the controls (p < .01 and p < .05). In the controls, the status within CpG islands on gestation day 14.5 was significantly increased compared with gestation days 13.5 and 18.5 (p < .01). Using real-time reverse transcriptase–polymerase chain reaction, there was no significant change in the expression of DNA methyltransferases, except on gestation day 18.5. Using restriction landmark genomic scanning on gestation day 18.5, five spots (0.49%) in the controls and one spot (0.1%) in all-trans retinoic acid–treated groups were specifically detected.Conclusions:These results indicate that changes in DNA methylation may play an important role in the manifestation of cleft palate only caused by environmental factors such as maternal exposure to all-trans retinoic acid.
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Affiliation(s)
- Motone Kuriyama
- Department of Plastic and Reconstructive Surgery, Graduate School of Medicine, Chiba University, Japan
| | - Akikazu Udagawa
- Department of Plastic, Reconstructive and Aesthetic Surgery, Chiba University Hospital, Japan
| | - Shinya Yoshimoto
- Department of Plastic and Reconstructive Surgery, Graduate School of Medicine, Chiba University, Japan
| | - Masaharu Ichinose
- Department of Plastic and Reconstructive Surgery, Graduate School of Medicine, Chiba University, Japan
| | - Koji Sato
- Department of Bioenvironmental Medicine, Graduate School of Medicine, Chiba University, Japan
| | - Koji Yamazaki
- Department of Bioenvironmental Medicine, Graduate School of Medicine, Chiba University, Japan
| | - Yoshiharu Matsuno
- Department of Bioenvironmental Medicine, Graduate School of Medicine, Chiba University, Japan
| | - Kunio Shiota
- Graduate School of Agriculture and Life Science, the University of Tokyo, Japan
| | - Chisato Mori
- Department of Bioenvironmental Medicine, Graduate School of Medicine, Chiba University, Japan
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100
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Abstract
Germline genomic methylation is essential for gamete identity and integrity in mammals. The study by Kuramochi-Miyagawa and colleagues (908-917) in the previous issue of Genes & Development links the process of DNA methylation-dependent repression of retrotranspons with the presence of piwi-interacting RNAs (piRNAs) in fetal male germ cells undergoing de novo methylation.
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