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Germline recruitment in mice: a genetic program for epigenetic reprogramming.

Germ cells provide an enduring link between generations and therefore must possess the fundamental ability of reprogramming their genome to generate a totipotent state. We wish to understand the molecular basis of the unique properties of the mammalian germ line. Recently we identified Blimp1, a potent transcriptional repressor of a histone methyltransferase subfamily, as a critical determinant of the germ cell lineage in mice. Surprisingly, Blimp1 expression marks the origin of the germ line in proximal epiblast cells in pregastrulation embryos, substantially earlier than previously thought. Furthermore, we showed that established primordial germ cells undergo extensive erasure of genome-wide histone H3 lysine 9 dimethylation (H3K9me2) and DNA methylation, two major repressive epigenetic modifications, and instead acquire high levels of H3-K27 trimethylation (H3K27me3) in their migration period. We suggest that germline specification is a genetic system for the orderly reprogramming of the cells' epigenome toward a totipotent state, with reacquisition of totipotency-associated transcription factors and continued Blimp1 expression preventing their reversion to an explicit pluripotent state or somatic differentiation.

Animals↗

Paternal dual barrier by Ifg2-H19 and Dlk1-Gtl2 to parthenogenesis in mice.

The functional difference between the maternal and paternal genome, which is characterized by epigenetic modifications during gametogenesis, that is genomic imprinting, prevents mammalian embryos from parthenogenesis. Genomic imprinting leads to nonequivalent expression of imprinted genes from the maternal and paternal alleles. However, our research showed that alteration of maternal imprinting by oocyte reconstruction using nongrowing oocytes together with deletion of the H19 gene, provides appropriate expression of maternally imprinted genes. Here we discuss that further alteration of paternally imprinted gene expressions at chromosomes 7 and 12 allows the ng/fg parthenogenetic embryos to develop to term, suggesting that the paternal contribution is obligatory for the descendant.

Animals↗

Polycomb gene product Bmi-1 regulates stem cell self-renewal.

The Polycomb group (PcG) gene Bmi-1 has recently been implicated in the maintenance of hematopoietic stem cells (HSCs). However, the role of each component of PcG complex in HSCs and the impact of forced expression of PcG genes on stem cell self-renewal remain to be elucidated. To address these issues, we performed both loss-of-function and gain-of-function analysis on various PcG proteins. Expression analysis revealed that not only Bmi-1 but also other PcG genes are predominantly expressed in HSCs. Loss-of-function analyses, however, demonstrated that absence of Bmi-1 is preferentially linked with a profound defect in HSC self-renewal, indicating a central role for Bmi-1, but not the other components, in the maintenance of HSC self-renewal. Over-expression analysis of PcG genes also confirmed an important role of Bmi-1 in HSC self-renewal. Our findings indicate that the expression level of Bmi-1 is the critical determinant for the self-renewal capacity of HSCs. These findings uncover novel aspects of stem cell regulation exerted through epigenetic modifications by the PcG proteins.

Animals↗

How Have Massively Parallel Sequencing Technologies Furthered Our Understanding of Oncogenesis and Cancer Progression?

Massively parallel sequencing technologies have been a boon to many fields of biological science, including oncology. Cancer is an umbrella term for many diseases featuring abnormal cellular growth due to genetic and epigenetic aberrations. Advances in sequencing technology allow for interrogation of the DNA and RNA of cancer cells and other cells in the tumor microenvironment down to a single-base resolution. However, these strides come after a rich history of ground-breaking biological assays, like the discovery of the Philadelphia chromosome in the context of leukemia. Many specific genetic and epigenetic modifications have been implicated in oncogenesis, cancer progression, and response to treatment. Sequencing technologies have also helped to associate populations of bacteria in the microbiome to cancer development and prognosis. However, all this new information, especially when procured via high-throughput methods, comes at the cost of being more computationally and staff-resource intensive. There is also more risk to the privacy of the individuals with sequenced genomes. Notwithstanding, the overall benefit of sequencing technologies can greatly outweigh the risks with careful advancements and continued focus on the goal: helping those affected by cancer via precision medicine. Cancer biology has been and will continue to be elucidated by sequencing innovations in ways unimaginable without it.

Humans↗

Expression of imprinted genes in cloned mice.

Genomic imprinting is a mammalian specific epigenetic modification of the genome. Assessment of the integrity of the imprinting memory in somatic cell cloned animals is important not only for understanding of the "reprogramming" process during cloning by nuclear transfer, but also for the applications of this technique for therapeutic cloning in the future. In this chapter, we summarize the analytical methods for assessment of monoallelic expression of imprinting genes and expression analysis. From a practical point of view, the authors suggest the use of intersubspecific F1 hybrids between the laboratory mouse (Mus musculus musculus) and the JF1 strain (Mus musculus molossinus). We also list the sequence for PCR primers to detect the polymorphism of imprinted genes between musculus and molossinus.

Animals↗

Gene expression and methylation patterns in cloned embryos.

A considerable proportion of the offspring, in particular in ruminants and mouse, born from nuclear transfer (NT)-derived and in vitro-produced (IVP) embryos are affected by multiple abnormalities, of which a high birthweight and an extended gestation length are the predominant features; a phenomenon that has been termed "Large Offspring syndrome" (LOS). According to a current hypothesis, LOS is caused by persistent aberrations of expression patterns of developmentally important genes starting as early as at the preimplantation stages. The underlying mechanisms are widely unknown at present, but epigenetic modifications of embryonic and fetal gene expression patterns, primarily caused by alterations in DNA methylation are thought to be involved in this syndrome. Appropriate DNA methylation is essential for regular transcription during mammalian development and differentiation. Sensitive reverse transcription polymerase chain reaction assays allow the study of messenger RNA (mRNA) expression levels of specific genes in single embryos. The methylation status of a specific gene can be assessed by bisulfite sequencing. Studies to unravel mRNA expression patterns from IVP- and NT-derived embryos have revealed numerous aberrations ranging from suppression of expression to de novo overexpression or more frequently to a significant upregulation or downregulation of a specific gene. mRNA expression patterns from in vivo-derived embryos are essential as the "physiological standard" against which the findings for IVP and NT-derived embryos are to be compared. Unraveling the underlying molecular mechanisms will contribute to the production of viable embryos and aid to improve biotechnologies applied to early mammalian embryos.

Animals↗

Genetic control and development expression of malate dehydrogenase in Apis mellifera.

Starch gel electrophoresis of extracts of Apis mellifera indicates that genetic variability exists for the enzyme cytoplasmic malate dehydrogenase (E.C. 1.1.1.37). Analysis of individuals throughout development indicates that the isozyme patterns are identical for larvae and adults and suggests a dimeric structure for the molecule. The isozyme pattern observed in pupae is more complex than that of larvae and adults may be due to an additional pupal-specific MDH gene being expressed or to an epigenetic modification of the isozymes. Forty-three colonies with artificially inseminated queens were used to study the Mendelian pattern of inheritance. The data revealed that the MDH isozymes are encoded by three alleles, Mdh-1A, Mdh-1B, and Mdh-1C. The frequency of the Mdh-1 alleles is different in two analyzed subspecies, A. m. adansonii (African bees) and A. m. ligustica (Italian bees), with Mdh-1A and Mdh-1B in the African bees being 0-768 and 0.202, respectively. For the Italian bees, these frequencies are 0.136 and 0:154, respectively.

Alleles↗

Origin of alpha-glycerophosphate dehydrogenase isozymes in Drosophila melanogaster and their functional relationship in the alpha-glycerophosphate cycle.

The basis for the differentiation of L-glycerol-3-phosphate dehydrogenase (alpha-GPDH) into larval and adult isozymes in Drosophila melanogaster was investigated by the correlation of a lack of appearance of each isozyme during development within Drosophila bearing alpha-GPDH "null" alleles and by the study of a putative conversion factor. Conversion studies indicate the presence of a heat-labile RNase-resistant conversion factor present in crude larval extracts with the ability to convert GPDH-1 to GPDH-2 and GPDH-3 but not vice versa. In addition, "null" mutations at the Gpdh locus obliterate all isozymatic species of alpha-GPDH in all developmental stages. These observations suggest that all alpha-GPDH isozymes are the product of a single structural gene and that the multiple forms of this enzyme arise during successive developmental stages through an epigenetic modification of the primary Gpdh+ polypeptide. Finally, observations are reported which bear on the functional divergence of the alpha-glycerophosphate cycle in the adult and larval stage of development.

Alleles↗

Genetics of cat hemoglobins: a quantitative polymorphism.

Blood samples from domestic cats, representing the parents (26) and offspring (91) from 33 matings, were analyzed to determine the proportions of hemoglobins A and B. Evidence is presented that the proportions of the two hemoglobins are genetically determined and that cats may be divided into three groups on the basis of this characteristic. Family data and Hardy-Weinberg analysis support the hypothesis that the three groups represent the possible combinations of an allelic gene pair. In an attempt to explain the observed phenotypic differences, possible points of action of this gene pair are discussed, including effects on rates of synthesis or epigenetic modification of globin chains.

Alleles↗

Epigenetic diagnostics of cancer--the application of DNA methylation markers.

In recent years it has become apparent that epigenetic events are potentially equally responsible for cancer initiation and progression as genetic abnormalities. DNA methylation is the main epigenetic modification in humans. Two DNA methylation lesions coexist in human neoplasms: hypermethylation of promoter regions of specific genes within a context of genomic hypomethylation. Aberrant methylation is found at early stages of carcinogenesis and distinct types of cancer exhibit specific patterns of methylation changes. Tumor specific DNA is readily obtainable from different clinical samples and methylation status analysis often permits sensitive disease detection. Methylation markers may also serve for prognostic and predictive purposes as they often reflect the metastatic potential and sensitivity to therapy. As current findings show a great potential of recently characterised methylation markers, more studies in the field are needed in the future. Large clinical studies of newly developed markers are especially needed. The review describes the diagnostic potential of DNA methylation markers.

Biomarkers, Tumor↗

siRNA-mediated transcriptional gene silencing: the potential mechanism and a possible role in the histone code.

Epigenetics is the study of meiotically and mitotically heritable changes in gene expression which are not coded for in the DNA. Three distinct mechanisms appear intricately related in initiating and sustaining epigenetic modifications: RNA-associated silencing, DNA methylation and histone modification. Recently, in human cells small-interfering RNAs (siRNAs) have been shown to mediate transcriptional gene silencing (TGS). The observation that siRNAs can function to suppress gene expression at the level of transcription has created a major paradigm shift in mammalian RNA interference. The putative mechanism(s) of siRNA-mediated TGS in both yeast and human cells will be discussed. Undoubtedly, the ramifications from this paradigm shift in which RNA has demonstrated a potent and specific capability to regulate the expression of the gene are immeasurable both therapeutically (i. e. directed control of gene expression) and biologically in understanding the evolution of the cell.

Animals↗

Epigenetic control of nuclear architecture.

The cell nucleus is a highly structured compartment where nuclear components are thought to localize in non-random positions. Correct positioning of large chromatin domains may have a direct impact on the localization of other nuclear components, and can therefore influence the global functionality of the nuclear compartment. DNA methylation of cytosine residues in CpG dinucleotides is a prominent epigenetic modification of the chromatin fiber. DNA methylation, in conjunction with the biochemical modification pattern of histone tails, is known to lock chromatin in a close and transcriptionally inactive conformation. The relationship between DNA methylation and large-scale organization of nuclear architecture, however, is poorly understood. Here we briefly summarize present concepts of nuclear architecture and current data supporting a link between DNA methylation and the maintenance of large-scale nuclear organization.

Animals↗

High rate of mutation reporter gene inactivation during human T cell proliferation.

Caspase activation and degradation of deoxyribonucleic acid (DNA) damage response factors occur during in vitro T-cell proliferation, and an increased frequency of hypoxanthine-guanine phosphoribosyltransferase (HPRT)-negative variants have been reported in conditions associated with in vivo T-cell proliferation. We have applied two human somatic cell mutation reporter assays, for the HPRT and phosphatidylinositol glycan class A (PIG-A) genes, to human T cells activated in vitro with anti-CD3 and anti-CD28. We demonstrate proliferation throughout 6 weeks of cultivation, and find that the frequency of variant cells phenotypically negative for HPRT and PIG-A, respectively, increases from 10(-5) up to 10(-3) -10(-2). We also report preliminary evidence for low-density CpG methylation in the HPRT promoter suggesting that epigenetic modification may contribute to this markedly heightened rate of gene inactivation.

Base Sequence↗

Butyrates and decitabine cooperate to induce histone acetylation and granulocytic maturation of t(8;21) acute myeloid leukemia blasts.

Core histones are proteins organized in octamers, to which DNA is wrapped more or less tightly, depending on their acetylation status. Gene transcription is regulated by a complex series of epigenetic modifications, i.e., histone modification such as methylation and acetylation, events determined by the enzymatic activity of histone methyltransferases, and histone acetyltransferases, respectively, the latter counterbalanced by histone deacetylases (HDAC). Acetylation of histones facilitates destabilization of DNA-nucleosome interaction and renders DNA more accessible to transcription factors. Methylation of different specific lysine residues of histones is differently linked to euchromatin (transcripted DNA) or heterochromatin (silenced DNA). On the other hand, methylation of the promoter regions of some genes by DNA methyltransferases (DNMT) leads to transcriptional silencing and is a common mechanism to regulate gene expression. In normal eukaryotic cells, DNA methylation and histone acetylation are interdependent and maintain equilibrium, allowing temporal expression of genes. In neoplastic cells, this balance is frequently disrupted. In leukemic cells, hypermethylation of CpG islands in the promoter region of genes critical for cell cycle and maturation is frequent, and DNMTs were found to be overexpressed, findings paralleled by evidence of transcriptional repression of downstream genes. Therefore, the combination of HDAC and DNMT inhibitors has been considered to be a possible therapeutic approach to restore normal gene expression in acute myeloid leukemia (AML) and other diseases. Human AML1/ETO Kasumi cells were exposed to the HDAC inhibitor D1 (O-n-butanoil-2,3-O-isopropylidene-alpha-D: -mannofuranoside) and 5-aza-deoxycytidine (decitabine) alone and in combination. Histone acetylation as measured by flow cytometry was increased following treatment with D1 and the combination of D1 and decitabine. Addition of D1 alone or in combination with decitabine also led to inhibition of cell proliferation and induction of apoptosis. Thus, treatment of AML with HDAC inhibitors such as D1 and DNMT inhibitors such as decitabine might have clinical benefit for patients, especially these presenting subtypes of AML, like AML1/ETO, in which the leukemogenic mechanism involves corepressor protein complexes containing HDAC and DNMT.

Antineoplastic Combined Chemotherapy Protocols↗

QTLs for pre- and postweaning body weight and body composition in selected mice.

In an intercross between the high-body-weight-selected mouse line NMRI8 and the inbred line DBA/2, we analyzed genetic effects on growth during the suckling period and after weaning during the juvenile phase of development. QTL mapping results indicated that a switch of gene activation might occur at the age of three weeks when animals are weaned. We found QTLs for body weight with major effects at the age of two and three weeks when animals are fed by their mothers, and QTLs with highest effects after weaning when animals have to live on their own under ad libitum access to food. Specific epistatic effects on body weight at two and three weeks and epistatic interaction influencing growth after weaning support this finding. QTL effects explained the greatest variance during puberty when animals grow fastest and become fertile. In the present study, all except one QTL effect for early body weight had dominance variance components. These might result from direct single-locus-dominant allelic expression, but also from the identified epistatic interaction between different QTLs that we have found for body weight at all ages. Beside body weight, body composition traits (muscle weight, reproductive fat weight, weight of inner organs) were analyzed. Sex-dimorphic QTLs were found for body weight and fat deposition. The identified early-growth QTLs could be the target of epigenetic modifications which might influence body weight at later ages.

Age Factors↗

Scaffold attachment factor A (SAF-A) is concentrated in inactive X chromosome territories through its RGG domain.

Female mammalian cells inactivate transcription from one of their X chromosomes to equalize gene expression of X-linked genes between males and females. Inactivation is a multistep process that involves a large non-coding RNA termed XIST, a variety of epigenetic modifications of chromatin, and alterations in protein composition such as enrichment of the histone variant macroH2A. We show here that inactive X chromosomes are also enriched in a well-characterized protein component of the nuclear scaffold, SAF-A. This protein has been implicated in chromatin organization, owing to its high specificity for scaffold-associated region (SAR)-DNA, in transcriptional regulation, e.g. of hormone-regulated genes, owing to its functional interaction with steroid receptors, and in RNA processing, owing to its interaction with RNA and heterogeneous nuclear ribonucleoprotein (hnRNP) particles. After near complete removal of DNA and associated chromatin proteins such as macroH2A, SAF-A remains with the "nuclear matrix", still highlighting the former position of inactive X chromosomes. Interestingly, the enrichment of SAF-A in the inactive X chromosome depends on the RNA binding domain of the protein, the RGG box, raising the possibility that interaction of SAF-A with XIST RNA may contribute to the silencing of X-linked genes by local changes in nuclear architecture.

Cells, Cultured↗

A maternal hypomethylation syndrome presenting as transient neonatal diabetes mellitus.

The expression of imprinted genes is mediated by allele-specific epigenetic modification of genomic DNA and chromatin, including parent of origin-specific DNA methylation. Dysregulation of these genes causes a range of disorders affecting pre- and post-natal growth and neurological function. We investigated a cohort of 12 patients with transient neonatal diabetes whose disease was caused by loss of maternal methylation at the TNDM locus. We found that six of these patients showed a spectrum of methylation loss, mosaic with respect to the extent of the methylation loss, the tissues affected and the genetic loci involved. Five maternally methylated loci were affected, while one maternally methylated and two paternally methylated loci were spared. These patients had higher birth weight and were more phenotypically diverse than other TNDM patients with different aetiologies, presumably reflecting the influence of dysregulation of multiple imprinted genes. We propose the existence of a maternal hypomethylation syndrome, and therefore suggest that any patient with methylation loss at one maternally-methylated locus may also manifest methylation loss at other loci, potentially complicating or even confounding the clinical presentation.

Birth Weight↗

Folic acid, polymorphism of methyl-group metabolism genes, and DNA methylation in relation to GI carcinogenesis.

DNA methylation is the main epigenetic modification after replication in humans. DNA (cytosine-5)-methyltransferase (DNMT) catalyzes the transfer of a methyl group from S-adenosyl-L-methionine (SAM) to C5 of cytosine within CpG dinucleotide sequences in the genomic DNA of higher eukaryotes. There is considerable evidence that aberrant DNA methylation plays an integral role in carcinogenesis. Folic acid or folate is crucial for normal DNA synthesis and can regulate DNA methylation, and through this, it affects cellular SAM levels. Folate deficiency results in DNA hypomethylation. Epidemiological studies have indicated that folic acid protects against gastrointestinal (GI) cancers. Methylene-tetrahydrofolate reductase (MTHFR) and methionine synthase (MS) are the enzymes involved in folate metabolism and are thought to influence DNA methylation. MTHFR is highly polymorphic, and the variant genotypes result in decreased MTHFR enzyme activity and lower plasma folate level. Two common MTHFR polymorphisms, 677CT (or 677TT) and A1298C, and an MS polymorphism, A-->G at 2756, have been identified. Most studies support an inverse association between folate status and the rate of colorectal adenomas and carcinomas. During human GI carcinogenesis, MTHFR is highly polymorphic, and the variant genotypes result in decreased MTHFR enzyme activity and lower plasma folate level, as well as aberrant methylation.

DNA Methylation↗