Article

Lopes, S. et al. Epigenetic modifications in an imprinting cluster are controlled by a hierarchy of DMRs suggesting long-range chromatin interactions. Hum. Mol. Genet. 12, 295-305

Laboratory of Developmental Genetics and Imprinting, Developmental Genetics Programme, The Babraham Institute, Cambridge CB2 4AT, UK.
Human Molecular Genetics (Impact Factor: 6.68). 03/2003; 12(3):295-305. DOI: 10.1093/hmg/ddg022
Source: PubMed

ABSTRACT Imprinted genes and their control elements occur in clusters in the mammalian genome and carry epigenetic modifications. Observations from imprinting disorders suggest that epigenetic modifications throughout the clusters could be under regional control. However, neither the elements that are responsible for regional control, nor its developmental timing, particularly whether it occurs in the germline or postzygotically, are known. Here we examine regional control of DNA methylation in the imprinted Igf2-H19 region in the mouse. Paternal germline specific methylation was reprogrammed after fertilization in two differentially methylated regions (DMRs) in Igf2, and was reestablished after implantation. Using a number of knockout strains in the region, we found that the DMRs themselves are involved in regional coordination in a hierarchical fashion. Thus the H19 DMR was needed on the maternal allele to protect the Igf2 DMRs 1 and 2 from methylation, and Igf2 DMR1 was needed to protect DMR2 from methylation. This regional coordination occurred exclusively after fertilization during somatic development, and did not involve linear spreading of DNA methylation, suggesting a model in which long-range chromatin interactions are involved in regional epigenetic coordination. These observations are likely to be relevant to other gene clusters in which epigenetic regulation plays a role, and in pathological situations in which epigenetic regulation is disrupted.

Download full-text

Full-text

Available from: Adele Murrell, Aug 29, 2015
0 Followers
 · 
88 Views
  • Source
    • "Furthermore, biallelic methylation at the Zdbf2 DMR in offspring derived from Dnmt3L mat-/- mothers correlated with biallelic expression of Zdbf2. While the exact mechanism responsible for the parental allele-specific acquisition of DNA methylation at secondary DMRs has not yet been determined, it is clear that there is a relationship between the epigenetic states at primary and secondary DMRs [9,10]. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Background Differential distribution of DNA methylation on the parental alleles of imprinted genes distinguishes the alleles from each other and dictates their parent of origin-specific expression patterns. While differential DNA methylation at primary imprinting control regions is inherited via the gametes, additional allele-specific DNA methylation is acquired at secondary sites during embryonic development and plays a role in the maintenance of genomic imprinting. The precise mechanisms by which this somatic DNA methylation is established at secondary sites are not well defined and may vary as methylation acquisition at these sites occurs at different times for genes in different imprinting clusters. Results In this study, we show that there is also variability in the timing of somatic DNA methylation acquisition at multiple sites within a single imprinting cluster. Paternal allele-specific DNA methylation is initially acquired at similar stages of post-implantation development at the linked Dlk1 and Gtl2 differentially methylated regions (DMRs). In contrast, unlike the Gtl2-DMR, the maternal Dlk1-DMR acquires DNA methylation in adult tissues. Conclusions These data suggest that the acquisition of DNA methylation across the Dlk1/Gtl2 imprinting cluster is variable. We further found that the Dlk1 differentially methylated region displays low DNA methylation fidelity, as evidenced by the presence of hemimethylation at approximately one-third of the methylated CpG dyads. We hypothesize that the maintenance of DNA methylation may be less efficient at secondary differentially methylated sites than at primary imprinting control regions.
    Epigenetics & Chromatin 05/2014; 7:9. DOI:10.1186/1756-8935-7-9 · 4.46 Impact Factor
  • Source
    • "However, the germline status of most human imprinted DMRs is currently unknown. Several germline DMRs have been shown to govern postzygotic secondary DMRs that are regulated in a hierarchical fashion [Coombes et al., 2003; Kagami et al., 2010; Lopes et al., 2003]. In all cases to date, the imprinted methylation profile is maintained irrespective of gene expression levels, with some imprinted transcripts being highly expressed during embryonic development and showing a temporal decrease after birth [Iglesias-Platas et al., 2012]. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Genomic imprinting is the parent-of-origin specific allelic transcriptional silencing observed in mammals, which is governed by DNA methylation established in the gametes and maintained throughout development. The frequency and extent of epimutations associated with the nine reported imprinting syndromes varies, since it is evident that aberrant pre-implantation maintenance of imprinted differentially methylated regions (DMRs) may affect multiple loci. Using a custom Illumina Goldengate array targeting 27 imprinted-DMRs we profiled allelic methylation in 65 imprinting defect patients. We identify multi-locus hypomethyaltion in numerous BWS, TNDM and PHP-1B patients, and an individual with SRS. Our data reveals a broad range of epimutations exist in certain imprinting syndromes, with the exception of PWS and AS patients that are associated with solitary SNRPN-DMR defects. A mutation analysis identified a 1 bp deletion in the ZFP57 gene in a TNDM patient with methylation defects at multiple maternal DMRs. In addition we observe missense variants in ZFP57, NLRP2, and NLRP7 that are not consistent with maternal effect and aberrant establishment or methylation maintenance, and are likely benign. This work illustrates that further extensive molecular characterization of these rare patients is required to fully understand the mechanism underlying the aetiology of imprint establishment and maintenance.
    Human Mutation 02/2013; 34(4). DOI:10.1002/humu.22276 · 5.05 Impact Factor
  • Source
    • "In support of this idea, binding sites for Oct4 and Klf4 were identified in the Dlk1-Dio3 region, and Chip-qPCR analysis revealed increased recruitment of Klf4 near the TSS of Gtl2 in transgene-carrying iPSCs. Our findings imply an active role of Klf4 (and possibly Oct4) in establishing the methylation status of Gtl2 and suggest that, when present at supraphysiological levels, Klf4 may protect this region from cytosine methylation through a mechanism similar to that described for the imprinted Igf2 gene [44]. These results are in concordance with recent studies emphasizing the role of Klf4 in establishing appropriate Gtl2 imprinting [45]. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Delivery of the transcription factors Oct4, Klf4, Sox2 and c-Myc via integrating viral vectors has been widely employed to generate induced pluripotent stem cell (iPSC) lines from both normal and disease-specific somatic tissues, providing an invaluable resource for medical research and drug development. Residual reprogramming transgene expression from integrated viruses nevertheless alters the biological properties of iPSCs and has been associated with a reduced developmental competence both in vivo and in vitro. We performed transcriptional profiling of mouse iPSC lines before and after excision of a polycistronic lentiviral reprogramming vector to systematically define the overall impact of persistent transgene expression on the molecular features of iPSCs. We demonstrate that residual expression of the Yamanaka factors prevents iPSCs from acquiring the transcriptional program exhibited by embryonic stem cells (ESCs) and that the expression profiles of iPSCs generated with and without c-Myc are indistinguishable. After vector excision, we find 36% of iPSC clones show normal methylation of the Gtl2 region, an imprinted locus that marks ESC-equivalent iPSC lines. Furthermore, we show that the reprogramming factor Klf4 binds to the promoter region of Gtl2. Regardless of Gtl2 methylation status, we find similar endodermal and hepatocyte differentiation potential comparing syngeneic Gtl2(ON) vs Gtl2(OFF) iPSC clones. Our findings provide new insights into the reprogramming process and emphasize the importance of generating iPSCs free of any residual transgene expression.
    PLoS ONE 12/2012; 7(12):e51711. DOI:10.1371/journal.pone.0051711 · 3.23 Impact Factor
Show more

Similar Publications