Differentially methylated regions in maternal and paternal uniparental disomy for chromosome 7

DNA methylation is a hallmark of genomic imprinting and differentially methylated regions (DMRs) are found near and in imprinted genes. Imprinted genes are expressed only from the maternal or paternal allele and their normal balance can be disrupted by uniparental disomy (UPD), the inheritance of bo...

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Veröffentlicht in:Epigenetics 2014-03, Vol.9 (3), p.351-365
Hauptverfasser: Hannula-Jouppi, Katariina, Muurinen, Mari, Lipsanen-Nyman, Marita, Reinius, Lovisa E, Ezer, Sini, Greco, Dario, Kere, Juha
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container_end_page 365
container_issue 3
container_start_page 351
container_title Epigenetics
container_volume 9
creator Hannula-Jouppi, Katariina
Muurinen, Mari
Lipsanen-Nyman, Marita
Reinius, Lovisa E
Ezer, Sini
Greco, Dario
Kere, Juha
description DNA methylation is a hallmark of genomic imprinting and differentially methylated regions (DMRs) are found near and in imprinted genes. Imprinted genes are expressed only from the maternal or paternal allele and their normal balance can be disrupted by uniparental disomy (UPD), the inheritance of both chromosomes of a chromosome pair exclusively from only either the mother or the father. Maternal UPD for chromosome 7 (matUPD7) results in Silver-Russell syndrome (SRS) with typical features and growth retardation, but no gene has been conclusively implicated in SRS. In order to identify novel DMRs and putative imprinted genes on chromosome 7, we analyzed eight matUPD7 patients, a segmental matUPD7q31-qter, a rare patUPD7 case and ten controls on the Infinium HumanMethylation450K BeadChip with 30 017 CpG methylation probes for chromosome 7. Genome-scale analysis showed highly significant clustering of DMRs only on chromosome 7, including the known imprinted loci GRB10, SGCE/PEG10, and PEG/MEST. We found ten novel DMRs on chromosome 7, two DMRs for the predicted imprinted genes HOXA4 and GLI3 and one for the disputed imprinted gene PON1. Quantitative RT-PCR on blood RNA samples comparing matUPD7, patUPD7, and controls showed differential expression for three genes with novel DMRs, HOXA4, GLI3, and SVOPL. Allele specific expression analysis confirmed maternal only expression of SVOPL and imprinting of HOXA4 was supported by monoallelic expression. These results present the first comprehensive map of parent-of-origin specific DMRs on human chromosome 7, suggesting many new imprinted sites.
doi_str_mv 10.4161/epi.27160
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subjects Alleles
chromosome 7
Chromosomes, Human, Pair 7 - genetics
differentially methylated regions
DNA Methylation
Female
genome-scale analysis
Genomic Imprinting
Homeodomain Proteins - genetics
Humans
imprinting
Kruppel-Like Transcription Factors - genetics
Male
Medicin och hälsovetenskap
methylation
Nerve Tissue Proteins - genetics
Research Paper
Silver-Russell syndrome
Silver-Russell Syndrome - genetics
Uniparental Disomy
Zinc Finger Protein Gli3
title Differentially methylated regions in maternal and paternal uniparental disomy for chromosome 7
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