Identifying clinically relevant imprinted gDMRs sensitive to a transient loss of DNA methylation in human differentiated cells

Sarah-Jayne Mackin, Karla M O'Neill, Rachelle E Irwin, Colum P Walsh

Research output: Contribution to journalArticle

Abstract

Background: Imprinted genes are autosomal, but only expressed from one parental allele and are often clustered in small groups. They play an important role in the regulation of normal mammalian each allele are important in regulating the genes, with marks being characterised as primary or secondary DMRs, depending on whether they are inherited from the germ cells or arise later, respectively. Imprinting disorders such as Prader-Willi Syndome (PWS) and Beckwith-Weidemann Syndrome (BWS) arise either from uniparental disomy or faulty DNA methylation. We wished to determine 1) which of the loci are most sensitive to loss of methylation 2) to more precisely define the sensitive regions and 3) determine what happens at primary versus secondary imprints. Methods: Stable knockdowns of the maintenance methyltransferase DNMT1 were generated in hTERT-immortalised adult fibroblastsusing shRNA. Genome wide methylation levels were assayed using the Illumina 450k BeadChip array and analysed using bioinformatic approaches. Results: We found that 1) the imprinted loci varied extensively in their sensitivity to loss of methylation 2) the extended locus involved in PWS was particularly sensitive 3) that loss of methylation at primary DMR appears to drive gains in methylation at secondary DMR. Conclusion: Our results point to a mechanistic link between primary and secondary DMR which may explain why imprints are difficult to reprogram in somatic tissues.
LanguageEnglish
Pages55-68
JournalThe Ulster Medical Journal
Volume86
Issue number1
Early online date6 Feb 2017
Publication statusE-pub ahead of print - 6 Feb 2017

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DNA Methylation
Methylation
Alleles
Uniparental Disomy
Methyltransferases
Computational Biology
Germ Cells
Small Interfering RNA
Genes
Maintenance
Genome

Keywords

  • Imprints
  • Methylation
  • DMR
  • Reprogram.

Cite this

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title = "Identifying clinically relevant imprinted gDMRs sensitive to a transient loss of DNA methylation in human differentiated cells",
abstract = "Background: Imprinted genes are autosomal, but only expressed from one parental allele and are often clustered in small groups. They play an important role in the regulation of normal mammalian each allele are important in regulating the genes, with marks being characterised as primary or secondary DMRs, depending on whether they are inherited from the germ cells or arise later, respectively. Imprinting disorders such as Prader-Willi Syndome (PWS) and Beckwith-Weidemann Syndrome (BWS) arise either from uniparental disomy or faulty DNA methylation. We wished to determine 1) which of the loci are most sensitive to loss of methylation 2) to more precisely define the sensitive regions and 3) determine what happens at primary versus secondary imprints. Methods: Stable knockdowns of the maintenance methyltransferase DNMT1 were generated in hTERT-immortalised adult fibroblastsusing shRNA. Genome wide methylation levels were assayed using the Illumina 450k BeadChip array and analysed using bioinformatic approaches. Results: We found that 1) the imprinted loci varied extensively in their sensitivity to loss of methylation 2) the extended locus involved in PWS was particularly sensitive 3) that loss of methylation at primary DMR appears to drive gains in methylation at secondary DMR. Conclusion: Our results point to a mechanistic link between primary and secondary DMR which may explain why imprints are difficult to reprogram in somatic tissues.",
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Identifying clinically relevant imprinted gDMRs sensitive to a transient loss of DNA methylation in human differentiated cells. / Mackin, Sarah-Jayne; O'Neill, Karla M; Irwin, Rachelle E; Walsh, Colum P.

In: The Ulster Medical Journal, Vol. 86, No. 1, 06.02.2017, p. 55-68.

Research output: Contribution to journalArticle

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AU - Irwin, Rachelle E

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AB - Background: Imprinted genes are autosomal, but only expressed from one parental allele and are often clustered in small groups. They play an important role in the regulation of normal mammalian each allele are important in regulating the genes, with marks being characterised as primary or secondary DMRs, depending on whether they are inherited from the germ cells or arise later, respectively. Imprinting disorders such as Prader-Willi Syndome (PWS) and Beckwith-Weidemann Syndrome (BWS) arise either from uniparental disomy or faulty DNA methylation. We wished to determine 1) which of the loci are most sensitive to loss of methylation 2) to more precisely define the sensitive regions and 3) determine what happens at primary versus secondary imprints. Methods: Stable knockdowns of the maintenance methyltransferase DNMT1 were generated in hTERT-immortalised adult fibroblastsusing shRNA. Genome wide methylation levels were assayed using the Illumina 450k BeadChip array and analysed using bioinformatic approaches. Results: We found that 1) the imprinted loci varied extensively in their sensitivity to loss of methylation 2) the extended locus involved in PWS was particularly sensitive 3) that loss of methylation at primary DMR appears to drive gains in methylation at secondary DMR. Conclusion: Our results point to a mechanistic link between primary and secondary DMR which may explain why imprints are difficult to reprogram in somatic tissues.

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