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PubMed2002

Epigenetic mechanisms for primary differentiation in mammalian embryos.

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.

Animals↗
PubMed1996

Chromosomal inheritance of epigenetic states in fission yeast during mitosis and meiosis.

Inheritance of the active and inactive states of gene expression by individual cells is crucial for development. In fission yeast, mating-type region consists of three loci called mat1, mat2, and mat3. Transcriptionally silent mat2 and mat3 loci are separated by a 15 kb interval, designated the K-region, and serve as donors of information for transcriptionally active mat1 interconversion. In a strain carrying replacement of 7.5 kb of the K-region with the ura4 gene, we discovered that ura4 silencing and efficiency of mating-type switching were covariegated and were regulated by an epigenetic mechanism. Genetic analyses demonstrated that epigenetic states were remarkably stable not only in mitosis but also in meiosis and were linked to the mating-type region. This study indicates that different epigenetic states are heritable forms of chromatin organization at the mat region.

Blotting, Southern↗
PubMed2004

Genetic and epigenetic regulation of the FLO gene family generates cell-surface variation in yeast.

The FLO gene family of Saccharomyces cerevisiae includes an expressed gene, FLO11, and a set of silent, telomere-adjacent FLO genes. This gene family encodes cell-wall glycoproteins that regulate cell-cell and cell-surface adhesion. Epigenetic silencing of FLO11 regulates a key developmental switch: when FLO11 is expressed, diploid cells form pseudohyphal filaments; when FLO11 is silent, the cells grow in yeast form. The epigenetic state of FLO11 is heritable for many generations and regulated by the histone deacetylase (HDAC) Hda1p. The silent FLO10 gene is activated by high-frequency loss-of-function mutations at either IRA1 or IRA2. FLO10 is regulated by the same transcription factors that control FLO11: Sfl1p and Flo8p, but is silenced by a distinct set of HDACs: Hst1p and Hst2p. These sources of epigenetic and genetic variation explain the observed heterogeneity of cell-surface protein expression within a population of cells derived from a single clone.

Cell Differentiation↗
PubMed2002

Recent advances in the study of epigenetic effects induced by the phycotoxin okadaic acid.

Okadaic acid (OA) is a phycotoxin produced by dinoflagellates. It accumulates in the digestive tracts of shellfish causing diarrhetic shellfish poisoning (DSP) in consumers. OA is a tumour promoter, and an inhibitor of both protein phosphatases and protein synthesis. OA induces DNA adducts, suggesting it may be carcinogenic. Since the Ames test without S(9) was negative, but a mutagenesis test was positive in mammalian cells, the question as to whether its molecular mechanism is genotoxic or epigenetic became unavoidable. Therefore, experiments were performed to search for epigenetic effects, since evidence for DNA-adduct formation using the gamma-(32)P-ATP post-labelling method was not obtained. We found that OA is a potent inducer of lipid peroxidation in human intestinal cells (Caco-2) at low concentrations (0.75-7.5 ng/ml versus IC50 of 15 ng/ml) with increased rates of 8-OH-dG and m(5)dC formation causing CG to AT transversion mutations and gene deregulation, respectively. The transcription and translation of connexin 43-specific mRNA were inhibited, and 3H-uridine incorporation in RNA was concomitantly increased. Consequently gap junction intracellular communication (GJIC) was inhibited, making possible cellular anarchic proliferation. Higher OA concentrations also disorganized the cellular cytoskeleton, since both actin and tubulin formations were impaired. Our results suggest that OA may induce tumours via an epigenetic mechanism.

Caco-2 Cells↗
PubMed2003

Polycomb group genes as epigenetic regulators of normal and leukemic hemopoiesis.

Epigenetic modification of chromatin structure underlies the differentiation of pluripotent hemopoietic stem cells (HSCs) into their committed/differentiated progeny. Compelling evidence indicates that Polycomb group (PcG) genes play a key role in normal and leukemic hemopoiesis through epigenetic regulation of HSC self-renewal/proliferation and commitment. The PcG proteins are constituents of evolutionary highly conserved molecular pathways regulating cell fate in several other tissues through diverse mechanisms, including 1) regulation of self-renewal/proliferation, 2) regulation of senescence/immortalization, 3) interaction with the initiation transcription machinery, 4) interaction with chromatin-condensation proteins, 5) modification of histones, 6) inactivation of paternal X chromosome, and 7) regulation of cell death. It is therefore not surprising that PcG genes lead to pleiotropic phenotypes when mutated and have been associated with malignancies in several systems in both mice and humans. Although much remains to be learned regarding the PcG mechanism(s) of action, advances in identifying the functional domains and enzymatic activities of these multimeric protein complexes have provided insights into how PcG proteins accomplish such processes. Some of the new insights into a role for the PcG cellular memory system in regulating normal and leukemic hemopoiesis are reviewed here, with special emphasis on their potential involvement in epigenetic regulation of gene expression through modification of chromatin structure.

Animals↗
PubMed2003

Epigenetic gene silencing in cancer initiation and progression.

Hypermethylation of CpG islands, an epigenetic event that is not accompanied by changes in DNA sequence, represents an alternative mechanism to deletions or mutations to inactivate tumor suppressor genes. Recent evidence supports the notion that CpG island hypermethylation, by silencing key cancer-related genes, plays a major causal role in cancer. However, a long-standing issue in the field is the sequence of molecular events leading to epigenetic gene silencing. A new model has been proposed that chromatin remodeling, as a result of histone deacetylation and methylation, is the primary event in abrogating transcriptional initiation; subsequently, CpG island hypermethylation establishes a permanent state of gene silencing. Accumulating evidence indicates that CpG island hypermethylation is an early event in cancer development and, in some cases, may precede the neoplastic process. Because of their heritable nature, hypermethylated CpG islands leave 'molecular footprints' in evolving cancer cells and can be used as molecular markers to reconstruct epigenetic progression during tumorigenesis. Furthermore, hypermethylated CpG islands are proving to be useful for molecular classification of different cancer types.

CpG Islands↗
PubMed2001

Epigenetics: interaction of DNA methylation and chromatin.

Epigenetic regulation is the mechanism by which gene function is selectively activated or inactivated in the cells. It provides higher-ordered and more specified genetic information, compared with the whole genome itself. Recently, a variety of regulatory proteins including DNA methyltransferases, methyl-CpG binding proteins, histone-modifying enzymes, chromatin remodeling factors, and their multimolecular complexes have been identified. These facilitate our understanding of the molecular basis for transcription, DNA replication, mutation and repair, DNA recombination, and chromosome dynamics, which are crucial for normal cell regulation. Abnormalities in the epigenetic states represent human disease phenotypes, especially developmental defects and tumorigenesis. Therefore, epigenetics will become the focus and a major target for emerging biological and medical discoveries.

Acetylation↗
PubMed1997

The functional matrix hypothesis revisited. 4. The epigenetic antithesis and the resolving synthesis.

In two interrelated articles, the current revision of the functional matrix hypothesis extends to a reconsideration of the relative roles of genomic and of epigenetic processes and mechanisms in the regulation (control, causation) of craniofacial growth and development. The dialectical method was chosen to analyze this matter, because it explicitly provides for the fuller presentation of a genomic thesis, an epigenetic antithesis, and a resolving synthesis. The later two are presented here, where the synthesis suggests that both genomic and epigenetic factors are necessary causes, that neither alone is also a sufficient cause, and that only the two, interacting together, furnish both the necessary and sufficient cause(s) of ontogenesis. This article also provides a comprehensive bibliography that introduces the several new, and still evolving, disciplines that may provide alternative viewpoints capable of resolving this continuing controversy; repetition of the present theoretical bases for the arguments on both sides of these questions seems nonproductive. In their place, it is suggested that the group of disciplines, broadly termed Complexity, would most likely amply repay deeper consideration and application in the study of ontogenesis.

Biomechanical Phenomena↗
PubMed1996

Epigenetic carcinogens: evaluation and risk assessment.

Regulatory policies in the U.S. have been developed based upon a single model of cancer causation, which assumes chemical-induced genetic alterations. Such a model predicts some degree of cancer risk even at extremely low exposure levels. Many chemicals that produce tumors in experimental animals have been shown to act by epigenetic mechanisms that do not involve an attack by the chemical on DNA leading to subsequent genetic alteration. Such indirect mechanisms require prolonged exposures to high levels of chemicals for the production of tumors. For chemicals that are carcinogenic in this manner, the cancer mechanism would not be operative at exposures below a threshold at which the relevant cellular effect does not occur. Also, in contrast to DNA-reactive mechanisms, epigenetic effects may be unique to the rodent species used for testing. Certain chemical tumorigens have been well studied and provide examples for the use of mechanistic information in risk assessment. Butylated hydroxyanisole and saccharin are nongenotoxic food additives for which no risk to humans is predicted based upon low exposure levels and the likelihood that humans are either insensitive or much less sensitive to the tumorigenic effects found in rodent test species. For another non-genotoxic food additive d-limonene, the mechanism that underlies kidney tumor development in male rats is not expected to be operative in humans at all. The pharmaceutical phenobarbital represents a large group of non-genotoxic liver microsome enzyme inducers, which produce liver cancer in mice at levels that are near to therapeutic doses in humans. Epidemiology studies have not shown phenobarbital-related tumors in humans, indicating that humans may be less sensitive to the effects of phenobarbital. The mechanistic considerations involved in the risk assessment of these agents demonstrate that humans are not at risk from current exposure levels of many epigenetic carcinogens.

Animals↗
PubMed2002

The novel BORIS + CTCF gene family is uniquely involved in the epigenetics of normal biology and cancer.

CTCF is a ubiquitous 11 zinc finger (ZF) protein with highly versatile functions: in addition to transcriptional silencing or activating in a context-dependent fashion, it organizes epigenetically controlled chromatin insulators that regulate imprinted genes in soma. Recently, we have identified a CTCF paralogue, termed BORIS for Brother of the Regulator of Imprinted Sites, that is expressed only in the testis. BORIS has the same exons encoding the 11 ZF domain as mammalian CTCF genes, and hence interacts with similar cis elements, but encodes amino and carboxy termini distinct from those in CTCF. Normally, CTCF and BORIS are expressed in a mutually exclusive pattern that correlates with re-setting of methylation marks during male germ cell differentiation. The antagonistic features of these two gene siblings are underscored by showing that while CTCF overexpression blocks cell proliferation, expression of BORIS in normally BORIS-negative cells promotes cell growth which can lead to transformation. The suggestion that BORIS directs epigenetic reprogramming at CTCF target sites impinges on the observations that human BORIS is not only abnormally activated in a wide range of human cancers, but also maps to the cancer-associated amplification region at 20q13. The sibling rivalry occasioned by aberrant expression of BORIS in cancer may interfere with normal functions of CTCF including growth suppression, and contribute to epigenetic dysregulation which is a common feature in human cancer.

Animals↗
PubMed2006

Analysis of an epigenetic argument against human reproductive cloning.

Human reproductive cloning is a much disputed ethical issue. This technology is often condemned as being contrary to human dignity. However, there are also risk arguments. An ethical argument that is often put forward by scientists but seldom developed in more detail focuses on health risks in animal cloning. There is a high risk that animal clones exhibit abnormalities and these are increasingly believed to be due to errors in epigenetic reprogramming. The argument is that human reproductive cloning should not be carried out because human clones are also likely to exhibit abnormalities due to inappropriate epigenetic reprogramming. Different versions of this epigenetic argument are analysed, a categorical version and a non-categorical. The non-categorical version is suggested to be more well-considered. With regard to policy making on human reproductive cloning, the categorical version can be used to prescribe a permanent ban, while the non-categorical version can be used to prescribe a temporary ban. The implications of the precautionary principle--as interpreted in the European Union--are investigated. The conclusion is that it seems possible to support a temporary ban by reference to this principle.

Animals↗
PubMed2004

Reprogramming of epigenetic inheritance by somatic cell nuclear transfer.

Somatic cloning by nuclear transfer returns a differentiated cell to a totipotent stage, a process termed nuclear reprogramming. During this de-differentiation process, genes inactivated during tissue differentiation are re-activated in a temporal and spatial special manner. It is believed that tissue differentiation occurs through epigenetic mechanisms, genetic inheritance that does not involve changes in DNA sequences. Developmental abnormalities and a high mortality rate in cloned offspring have frequently been observed and probably result from incomplete nuclear reprogramming. In this review, the reprogramming of two epigenetic mechanisms, imprinting and X chromosome inactivation, as well as recent attempts to modify pre-existing epigenetic marks in donor cells to improve nuclear transfer efficacy, are discussed.

Animals↗
PubMed2005

The problematic in-vitro embryo in the age of epigenetics.

During use of many assisted reproductive technologies, the embryo spends time in vitro. The immediate and long-term epigenetic impacts of this exposure to an in-vitro environment are discussed in the context of the health of the offspring. Three exemplary types of possible epigenetic impact are discussed: embryonic cell numbers, mitochondria, and genomic imprints. There is evidence that all of these can be affected in the short term and that these short-term impacts can have heritable consequences across developmental cell generations into maturity. There is also evidence of association between the observed impact and pathology, but as yet no unequivocal evidence of causality for humans and mice. The problematic in-vitro embryo is considered paradigmatic for a central question facing biology: how does the environment interact epigenetically with the genome to produce variable phenotypic outcomes?

Adaptation, Biological↗
PubMed2001

Imprinting of R-r, paramutation of B-I and Pl, and epigenetic silencing of MuDR/Mu transposons in Zea mays L. are coordinately affected by inbred background.

The extent of imprinting at R-r, frequency of paramutation at B-Intense and Pl, and epigenetic silencing of Mu transposons were evaluated in the W23 and A188 inbred lines of maize. All types of epigenetic phenomena affecting these loci of the anthocyanin pathway occurred more frequently in the W23 inbred line. Absence of down-regulation was dominant in F1 hybrid progeny. Identical alleles programme lower anthocyanin accumulation in A188 than in W23, and A188 plants develop more rapidly than W23. The possibilities that specific genetic factors, intrinsic gene expression levels and/or the rapidity of the life cycle modulate epigenetic gene controls are discussed.

Anthocyanins↗
PubMed2002

Major psychosis and chromosome 22: genetics meets epigenetics.

Elucidation of genetic factors in schizophrenia and bipolar disorder remains a challenging task to psychiatric researchers. As a rule, data from genetic linkage and association studies are quite controversial. In this article, we further explore the possibility that in addition to DNA sequences variation, a putative epigenetic dysregulation of brain genes plays an important role in the etiopathogenesis of major psychosis. We provide an epigenetic interpretation of unclear genetic findings specifically pertaining to chromosome 22 in schizophrenia and bipolar disorder. It is suggested that epigenetic strategies, when applied in conjunction with traditional genetic ones, may significantly expedite the uncovering of the molecular causes of major psychosis.

Journal Article↗
PubMed2001

Epigenetic changes accompanying human mammary epithelial cell immortalization.

Acquisition of immortality may be an early and crucial step in malignant progression. We hypothesize that acquisition of unlimited growth potential in individual human mammary epithelial cells (HMEC) requires inactivation of several distinct negative growth constraints as well as reactivation of a mechanism to maintain telomeres on chromosomes. Some of the heritable changes that occur during HMEC immortalization, i.e., loss of expression of cyclin dependent kinase inhibitors p16INK4a and p57KIP2, loss of TGFbeta-mediated growth inhibition, and derepression of telomerase, appear to occur without identifiable mutations in the genes and pathways involved. The absence of mutations, combined with the fact that the changes are often incremental over several cell generations even in clonal populations indicates that some changes associated with immortalization can be epigenetic. We have used the term "conversion" to describe the gradual epigenetic process in chemical carcinogen-immortalized HMEC that leads to activation of telomerase, stabilization of telomere length, and ability to grow uniformly well in the presence or absence of TGFbeta. Characterization of the epigenetic mechanisms involved in immortalization may uncover additional factors that drive tumor progression, and that may be responsive to novel forms of intervention.

Breast↗
PubMed2004

An engineered epigenetic transgene switch in mammalian cells.

In multicellular systems cell identity is imprinted by epigenetic regulation circuits, which determine the global transcriptome of adult cells in a cell phenotype-specific manner. By combining two repressors, which control each other's expression, we have developed a mammalian epigenetic circuitry able to switch between two stable transgene expression states after transient administration of two alternate drugs. Engineered Chinese hamster ovary cells (CHO-K1) showed toggle switch-specific expression profiles of a human glycoprotein in culture, as well as after microencapsulation and implantation into mice. Switch dynamics and expression stability could be predicted with mathematical models. Epigenetic transgene control through toggle switches is an important tool for engineering artificial gene networks in mammalian cells.

Alkaline Phosphatase↗
PubMed2002

Evidence for an epigenetic mechanism by which Hsp90 acts as a capacitor for morphological evolution.

Morphological alterations have been shown to occur in Drosophila melanogaster when function of Hsp90 (heat shock 90-kDa protein 1alpha, encoded by Hsp83) is compromised during development. Genetic selection maintains the altered phenotypes in subsequent generations. Recent experiments have shown, however, that phenotypic variation still occurs in nearly isogenic recombinant inbred strains of Arabidopsis thaliana. Using a sensitized isogenic D. melanogaster strain, iso-Kr(If-1), we confirm this finding and present evidence supporting an epigenetic mechanism for Hsp90's capacitor function, whereby reduced activity of Hsp90 induces a heritably altered chromatin state. The altered chromatin state is evidenced by ectopic expression of the morphogen wingless in eye imaginal discs and a corresponding abnormal eye phenotype, both of which are epigenetically heritable in subsequent generations, even when function of Hsp90 is restored. Mutations in nine different genes of the trithorax group that encode chromatin-remodeling proteins also induce the abnormal phenotype. These findings suggest that Hsp90 acts as a capacitor for morphological evolution through epigenetic and genetic mechanisms.

Animals↗