A methylation-dependent DNA-binding activity recognising the methylated promoter region of the mouse Xist gene

Epigenetic mechanisms of peptidergic regulation of gene expression during aging of human cells

Expression levels of genes encoding specific transcription factors and other functionally important proteins vary upon aging of pancreatic and bronchial epithelium cell cultures. The peptides KEDW and AEDL tissue-specifically affect gene expression in pancreatic and bronchial cell cultures, respectively. It is established in this work that the DNA methylation patterns of the PDX1, PAX6, NGN3, NKX2-1, and SCGB1A1 gene promoter regions change upon aging in pancreatic and bronchial cell cultures in correlation with variations in their expression levels. Thus, stable changes in gene expression upon aging of cell cultures could be caused by changes in their promoter methylation patterns. The methylation patterns of the PAX4 gene in pancreatic cells as well as those of the FOXA1, SCGB3A2, and SFTPA1 genes in bronchial cells do not change upon aging and are unaffected by peptides, whereas their expression levels change in both cases. The promoter region of the FOXA2 gene in pancreatic cells contains a small number of methylated CpG sites, their methylation levels being affected by cell culture aging and KEDW, though without any correlation with gene expression levels. The promoter region of the FOXA2 gene is completely unmethylated in bronchial cells irrespective of cell culture age and AEDL action. Changes in promoter methylation might be the cause of age- and peptide-induced variations in expression levels of the PDX1, PAX6, and NGN3 genes in pancreatic cells and NKX2-1 and SCGB1A1 genes in bronchial cells. Expression levels of the PAX4 and FOXA2 genes in pancreatic cells and FOXA1, FOXA2, SCGB3A2, and SFTPA1 genes in bronchial cells seem to be controlled by some other mechanisms.

Prospects for epigenetic epidemiology

Epigenetic modification can mediate environmental influences on gene expression and can modulate the disease risk associated with genetic variation. Epigenetic analysis therefore holds substantial promise for identifying mechanisms through which genetic and environmental factors jointly contribute to disease risk. The spatial and temporal variance in epigenetic profile is of particular relevance for developmental epidemiology and the study of aging, including the variable age at onset for many common diseases. This review serves as a general introduction to the topic by describing epigenetic mechanisms, with a focus on DNA methylation; genetic and environmental factors that influence DNA methylation; epigenetic influences on development, aging, and disease; and current methodology for measuring epigenetic profile. Methodological considerations for epidemiologic studies that seek to include epigenetic analysis are also discussed.

Conservation of genomic imprinting at the XIST, IGF2, and GTL2 loci in the bovine

Genomic imprinting is theorized to exist in all placental mammals and some marsupials; however, extensive comparative analysis of animals aside from humans and mice remains incomplete. Here we report conservation of genomic imprinting in the bovine at the X chromosome inactivation-specific transcript (XIST), insulin-like growth factor 2 (IGF2), and gene trap locus 2 (GTL2) loci. Coding single nucleotide polymorphisms (SNPs) between Bos gaurus and Bos taurus were detected at the XIST, IGF2, and GTL2 loci, which have previously been identified as imprinted in either humans, mice, or sheep. Expression patterns of parental alleles in F1 hybrids indicated preferential paternal expression at the XIST locus solely in the chorion of females, whereas analysis of the IGF2 and GTL2 loci indicated preferential paternal and maternal expression of alleles, respectively, in both fetal and placental tissues. Comparative sequence analysis of the XIST locus and adjacent regions suggests that repression of the maternal allele in the bovine is controlled by a different mechanism than in mice, further reinforcing the importance of comparative analysis of imprinting.

Mammalian embryonic development--insights from studies on the X chromosome

This paper reviews our early studies on the cycle of changes of X chromosome activity in different lineages of the developing female mouse embryo. The emphasis is placed on the insights gained into key developmental processes such as the temporal and spatial aspects of developmental totipotency, the timing and cell numbers involved in the origin of the germ line, the molecular mechanisms of genetic deprogramming, reprogramming and X chromosome imprinting, and transgenerational epigenetic inheritance. When viewed in this way, it is quite remarkable to see how much was learned about mammalian development from early studies on the X chromosome. Indeed several paradigm shifts occurred as a result of these studies and these are highlighted in this review.

Leptin gene expression in human preadipocytes is switched on by maturation-induced demethylation of distinct CpGs in its proximal promoter

The peptide hormone leptin plays a major role in the regulation of energy intake and expenditure and is predominantly expressed in mature adipocytes but not in preadipocytes. Using bisulfite genomic sequencing, we found that 32 CpGs, distributed within a 317-bp sequence of the proximal leptin promoter, were highly methylated in human preadipocytes (73.4% +/- 9.0%). During maturation toward terminally differentiated adipocytes, this promoter region was extremely demethylated (9.4% +/- 4.4%). CpG methylation-dependent transcriptional activity of the promoter fragment was determined in transfection experiments using a set of 5'-truncated mock-, HhaI-, and SssI-methylated promoter-reporter constructs. Whereas the methylated CpG within the CCAAT/enhancer-binding protein alpha recognition site down-regulated reporter expression, methylated CpGs proximal to the TATA motif and/or in a further upstream region abrogated promoter activity completely. These distinct promoter CpG sequences were found unmethylated in leptin-expressing mature adipocytes. As evidenced by electrophoretic mobility shift assays, nuclear protein complexes were specifically formed on methylated oligonucleotide probes corresponding to the dedicated promoter sequences, indicating that methyl-CpG binding proteins participate in transcriptional repression and regulation of the human leptin gene.

The p120 catenin partner Kaiso is a DNA methylation-dependent transcriptional repressor

We describe a novel mammalian DNA binding activity that requires at least two symmetrically methylated CpG dinucleotides in its recognition sequence, preferably within the sequence 5'CGCG. A key component of the activity is Kaiso, a protein with POZ and zinc-finger domains that is known to associate with p120 catenin. We find that Kaiso behaves as a methylation-dependent transcriptional repressor in transient transfection assays. Kaiso is a constituent of one of two methyl-CpG binding complexes originally designated as MeCP1. The data suggest that zinc-finger motifs are responsible for DNA binding, and may therefore target repression to specific methylated regions of the genome. As Kaiso associates with p120 catenin, Kaiso may link events at the cell surface with DNA methylation-dependent gene silencing.

Methylation in the initiation region of the first exon suppresses collagen pro-alpha2(I) gene transcription

Our previous studies demonstrated that the collagen alpha2(I) gene is hypermethylated in the promoter/first exon region after chemical transformation and the alpha2(I) promoter/first exon is sensitive to methylation in transfection studies. In this paper, we demonstrate that a minimum collagen promoter containing the preinitiation region (-41 to +54) driving luciferase reporter gene was inactivated by DNA methylation as judged by transfection assays. All the methylation sites within the preinitiation region were located in the first exon, not in the promoter. Methylation of the promoter construct inhibited transcription as determined by an in vitro assay, only if proteins were extracted from nuclei using 500 mM NaCl. Gel mobility shift analysis suggested that methylation within the first exon decreased the formation of the largest preinitiation complex while increasing the formation of faster migrating protein-DNA complexes. Competition gel mobility shift analysis indicated that the faster migrating protein-DNA complex could be competed by a smaller initiator probe which did not contain TATA binding region. A protein-DNA complex with increased affinity to methylated sequences was detected using the initiator probe, which contained two methylation sites and no TATA sequence (-25 to 30) suggesting that a separate repressor complex binds to the methylated sequences. Mutations at the methylation sites (+7, +23) in the first exon also increased the protein-DNA complex formation in gel shift analysis and inhibited collagen alpha2(I) transcription as judged by transient transfection and in vitro transcription assays. Therefore, these methylation sites in the preinitiation region are important for transcription of alpha2(I) gene and the protein responsible for the repression of transcription is extractable using high salt nuclear extracts.

Identification and characterization of a family of mammalian methyl-CpG binding proteins

Methylation at the DNA sequence 5'-CpG is required for mouse development. MeCP2 and MBD1 (formerly PCM1) are two known proteins that bind specifically to methylated DNA via a related amino acid motif and that can repress transcription. We describe here three novel human and mouse proteins (MBD2, MBD3, and MBD4) that contain the methyl-CpG binding domain. MBD2 and MBD4 bind specifically to methylated DNA in vitro. Expression of MBD2 and MBD4 tagged with green fluorescent protein in mouse cells shows that both proteins colocalize with foci of heavily methylated satellite DNA. Localization is disrupted in cells that have greatly reduced levels of CpG methylation. MBD3 does not bind methylated DNA in vivo or in vitro. MBD1, MBD2, MBD3, and MBD4 are expressed in somatic tissues, but MBD1 and MBD2 expression is reduced or absent in embryonic stem cells which are known to be deficient in MeCP1 activity. The data demonstrate that MBD2 and MBD4 bind specifically to methyl-CpG in vitro and in vivo and are therefore likely to be mediators of the biological consequences of the methylation signal.

Imprinting mechanisms

A number of recent studies have provided new insights into mechanisms that regulate genomic imprinting in the mammalian genome. Regions of allele-specific differential methylation (DMRs) are present in all imprinted genes examined. Differential methylation is erased in germ cells at an early stage of their development, and germ-line-specific methylation imprints in DMRs are reestablished around the time of birth. After fertilization, differential methylation is retained in core DMRs despite genome-wide demethylation and de novo methylation during preimplantation and early postimplantation stages. Direct repeats near CG-rich DMRs may be involved in the establishment and maintenance of allele-specific methylation patterns. Imprinted genes tend to be clustered; one important component of clustering is enhancer competition, whereby promoters of linked imprinted genes compete for access to enhancers. Regional organization and spreading of the epigenotype during development is also important and depends on DMRs and imprinting centers. The mechanism of cis spreading of DNA methylation is not known, but precedent is provided by the Xist RNA, which results in X chromosome inactivation in cis. Reading of the somatic imprints could be carried out by transcription factors that are sensitive to methylation, or by methyl-cytosine-binding proteins that are involved in transcriptional repression through chromatin remodeling.

Regulation of X-chromosome inactivation in development in mice and humans

Dosage compensation for X-linked genes in mammals is accomplished by inactivating one of the two X chromosomes in females. X-chromosome inactivation (XCI) occurs during development, coupled with cell differentiation. In somatic cells, XCI is random, whereas in extraembryonic tissues, XCI is imprinted in that the paternally inherited X chromosome is preferentially inactivated. Inactivation is initiated from an X-linked locus, the X-inactivation center (Xic), and inactivity spreads along the chromosome toward both ends. XCI is established by complex mechanisms, including DNA methylation, heterochromatinization, and late replication. Once established, inactivity is stably maintained in subsequent cell generations. The function of an X-linked regulatory gene, Xist, is critically involved in XCI. The Xist gene maps to the Xic, it is transcribed only from the inactive X chromosome, and the Xist RNA associates with the inactive X chromosome in the nucleus. Investigations with Xist-containing transgenes and with deletions of the Xist gene have shown that the Xist gene is required in cis for XCI. Regulation of XCI is therefore accomplished through regulation of Xist. Transcription of the Xist gene is itself regulated by DNA methylation. Hence, the differential methylation of the Xist gene observed in sperm and eggs and its recognition by protein binding constitute the most likely mechanism regulating imprinted preferential expression of the paternal allele in preimplantation embryos and imprinted paternal XCI in extraembryonic tissues. This article reviews the mechanisms underlying XCI and recent advances elucidating the functions of the Xist gene in mice and humans.

The role of Xist in X-inactivation

The past year has seen important progress in our understanding of the role of the X inactive specific transcript gene (Xist) in the initiation and propagation of X-inactivation. A 35 kb Xist transgene had been shown to recapitulate the functions of the X-inactivation centre, progress has been made towards indentifying factors controlling the randomness of X-inactivation, and RNA stabilisation has been shown to play a role in Xist regulation at the onset of X-inactivation.

Expression of an Xist promoter-luciferase construct during spermatogenesis and in preimplantation embryos: regulation by DNA methylation

Dosage compensation for X-linked genes in mammals is accomplished by inactivating one of the two X chromosomes in females, a process involving a regulatory gene, Xist (X-inactive specific transcript). Xist maps to the X-inactivation centre and is expressed from the inactive X chromosome in female somatic cells and at the time of X inactivation during spermatogenesis in the male. In female preimplantation embryos, Xist demonstrates imprinting in that the paternal allele inherited from the sperm is preferentially expressed. This preferential paternal Xist expression is correlated with paternal X inactivation in the extraembryonic lineages at the blastocyst stage. We have analysed a 233-bp Xist promoter fragment (nt -220 to +13) for its ability to direct appropriate expression and its regulation by DNA methylation. This minimal promoter sequence directs expression of the luciferase reporter gene following injection of the construct into one-cell embryos. In vitro methylation of the construct before injection represses transcription. In six different transgenic lines, expression of the Xist promoter-luciferase transgene occurs only in the testis of the males (as for the endogenous Xist gene). The testis-specific expression is correlated with hypomethylation of the transgene, although to different extents in different lines. Following paternal transmission, expression of the Xist promoter-luciferase construct in preimplantation embryos is correlated with degree of hypomethylation in the testis and the degree of hypomethylation of the transgene in embryos at the morula stage. It is concluded that the patterns of methylation of the transgene in sperm (and in microinjected transgenes) can regulate the activity of the Xist promoter in the preimplantation embryo and thus support the hypothesis that gametic methylation patterns govern imprinted expression of the endogenous Xist gene in development.