title: Genome-wide DNA methylation analysis of transient neonatal diabetes type 1 patients with mutations in ZFP57.
abstract: BACKGROUND
  Transient neonatal diabetes mellitus 1 (TNDM1) is a rare imprinting disorder characterized by intrautering growth retardation and diabetes mellitus usually presenting within the first six weeks of life and resolves by the age of 18 months. However, patients have an increased risk of developing diabetes mellitus type 2 later in life. Transient neonatal diabetes mellitus 1 is caused by overexpression of the maternally imprinted genes PLAGL1 and HYMAI on chromosome 6q24. One of the mechanisms leading to overexpression of the locus is hypomethylation of the maternal allele of PLAGL1 and HYMAI. A subset of patients with maternal hypomethylation at PLAGL1 have hypomethylation at additional imprinted loci throughout the genome, including GRB10, ZIM2 (PEG3), MEST (PEG1), KCNQ1OT1 and NESPAS (GNAS-AS1). About half of the TNDM1 patients carry mutations in ZFP57, a transcription factor involved in establishment and maintenance of methylation of imprinted loci. Our objective was to investigate whether additional regions are aberrantly methylated in ZFP57 mutation carriers.
  
  
  METHODS
  Genome-wide DNA methylation analysis was performed on four individuals with homozygous or compound heterozygous ZFP57 mutations, three relatives with heterozygous ZFP57 mutations and five controls. Methylation status of selected regions showing aberrant methylation in the patients was verified using bisulfite-sequencing.
  
  
  RESULTS
  We found large variability among the patients concerning the number and identity of the differentially methylated regions, but more than 60 regions were aberrantly methylated in two or more patients and a novel region within PPP1R13L was found to be hypomethylated in all the patients. The hypomethylated regions in common between the patients are enriched for the ZFP57 DNA binding motif.
  
  
  CONCLUSIONS
  We have expanded the epimutational spectrum of TNDM1 associated with ZFP57 mutations and found one novel region within PPP1R13L which is hypomethylated in all TNDM1 patients included in this study. Functional studies of the locus might provide further insight into the etiology of the disease.
authors.affiliation: Wilhelm Johannsen Center for Functional Genome Research, Institute of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, DK-2200, Copenhagen N, Denmark. madsba@sund.ku.dk.
authors.forename: Mads
authors.initials: M
authors.lastname: Bak
authors.affiliation: Wilhelm Johannsen Center for Functional Genome Research, Institute of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, DK-2200, Copenhagen N, Denmark.|Center for Applied Human Molecular Genetics, Kennedy Center, DK-2600, Glostrup, Denmark.
authors.forename: Susanne E
authors.initials: SE
authors.lastname: Boonen
authors.affiliation: Institute of Cancer Biology, Danish Cancer Society, DK-2100, Copenhagen Ø, Denmark.
authors.forename: Christina
authors.initials: C
authors.lastname: Dahl
authors.affiliation: Center for Applied Human Molecular Genetics, Kennedy Center, DK-2600, Glostrup, Denmark.
authors.forename: Johanne M D
authors.initials: JM
authors.lastname: Hahnemann
authors.affiliation: Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK.|Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury NHS Foundation Trust, SP2 8BJ, Salisbury, UK.
authors.forename: Deborah J D G
authors.initials: DJ
authors.lastname: Mackay
authors.affiliation: Center for Applied Human Molecular Genetics, Kennedy Center, DK-2600, Glostrup, Denmark.|Institute of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, DK-2200N, Copenhagen, Denmark.
authors.forename: Zeynep
authors.initials: Z
authors.lastname: Tümer
authors.affiliation: Center for Applied Human Molecular Genetics, Kennedy Center, DK-2600, Glostrup, Denmark.
authors.forename: Karen
authors.initials: K
authors.lastname: Grønskov
authors.affiliation: Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK.|Wessex Clinical Genetics Service, Southampton University Hospitals Trust, Southampton, SO16 5YA, UK.
authors.forename: I Karen
authors.initials: IK
authors.lastname: Temple
authors.affiliation: Institute of Cancer Biology, Danish Cancer Society, DK-2100, Copenhagen Ø, Denmark.
authors.forename: Per
authors.initials: P
authors.lastname: Guldberg
authors.affiliation: Wilhelm Johannsen Center for Functional Genome Research, Institute of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, DK-2200, Copenhagen N, Denmark.
authors.forename: Niels
authors.initials: N
authors.lastname: Tommerup
mesh_terms: D000483:Alleles; D016022:Case-Control Studies; D019175:DNA Methylation; D004268:DNA-Binding Proteins / Q000235:genetics*; D003920:Diabetes Mellitus / Q000175:diagnosis / Q000235:genetics*; D056426:Genetic Loci; D018392:Genomic Imprinting; D006720:Homozygote; D006801:Humans; D007223:Infant; D007232:Infant, Newborn, Diseases / Q000175:diagnosis / Q000235:genetics*; D047908:Intracellular Signaling Peptides and Proteins / Q000235:genetics; D012097:Repressor Proteins / Q000235:genetics; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D004268:DNA-Binding Proteins; D047908:Intracellular Signaling Peptides and Proteins; C119612:PPP1R13L protein, human; D012097:Repressor Proteins; D014157:Transcription Factors; C531063:ZFP57 protein, human
keywords: DNA methylation; Imprinting disorder; Next-generation sequencing; Transient neonatal diabetes