title: Influence of the Prader-Willi syndrome imprinting center on the DNA methylation landscape in the mouse brain.
abstract: Reduced representation bisulfite sequencing (RRBS) was used to analyze DNA methylation patterns across the mouse brain genome in mice carrying a deletion of the Prader-Willi syndrome imprinting center (PWS-IC) on either the maternally- or paternally-inherited chromosome. Within the ~3.7 Mb imprinted Angelman/Prader-Willi syndrome (AS/PWS) domain, 254 CpG sites were interrogated for changes in methylation due to PWS-IC deletion. Paternally-inherited deletion of the PWS-IC increased methylation levels ~2-fold at each CpG site (compared to wild-type controls) at differentially methylated regions (DMRs) associated with 5' CpG island promoters of paternally-expressed genes; these methylation changes extended, to a variable degree, into the adjacent CpG island shores. Maternal PWS-IC deletion yielded little or no changes in methylation at these DMRs, and methylation of CpG sites outside of promoter DMRs also was unchanged upon maternal or paternal PWS-IC deletion. Using stringent ascertainment criteria, ~750,000 additional CpG sites were also interrogated across the entire mouse genome. This analysis identified 26 loci outside of the imprinted AS/PWS domain showing altered DNA methylation levels of ≥25% upon PWS-IC deletion. Curiously, altered methylation at 9 of these loci was a consequence of maternal PWS-IC deletion (maternal PWS-IC deletion by itself is not known to be associated with a phenotype in either humans or mice), and 10 of these loci exhibited the same changes in methylation irrespective of the parental origin of the PWS-IC deletion. These results suggest that the PWS-IC may affect DNA methylation at these loci by directly interacting with them, or may affect methylation at these loci through indirect downstream effects due to PWS-IC deletion. They further suggest the PWS-IC may have a previously uncharacterized function outside of the imprinted AS/PWS domain.
authors.affiliation: a Department of Biochemistry and Molecular Biology ; University of Florida ; Gainesville , FL USA.
authors.forename: Jason O
authors.initials: JO
authors.lastname: Brant
authors.forename: Alberto
authors.initials: A
authors.lastname: Riva
authors.forename: James L
authors.initials: JL
authors.lastname: Resnick
authors.forename: Thomas P
authors.initials: TP
authors.lastname: Yang
mesh_terms: D017204:Angelman Syndrome / Q000235:genetics; D000818:Animals; D000951:Antigens, Neoplasm / Q000235:genetics; D001921:Brain / Q000502:physiology*; D002352:Carrier Proteins / Q000235:genetics; D018899:CpG Islands; D019175:DNA Methylation; D005260:Female; D018392:Genomic Imprinting; D059014:High-Throughput Nucleotide Sequencing; D008297:Male; D008810:Mice, Inbred C57BL; D008817:Mice, Mutant Strains; D009363:Neoplasm Proteins / Q000235:genetics; D011218:Prader-Willi Syndrome / Q000235:genetics*; D011401:Promoter Regions, Genetic; D011506:Proteins / Q000235:genetics; D012261:Ribonucleoproteins / Q000235:genetics; D017384:Sequence Deletion; D044767:Ubiquitin-Protein Ligases; D047908:Intracellular Signaling Peptides and Proteins; D064267:Intrinsically Disordered Proteins
chemical_list: D000951:Antigens, Neoplasm; D002352:Carrier Proteins; D009363:Neoplasm Proteins; D011506:Proteins; D012261:Ribonucleoproteins; D044767:Ubiquitin-Protein Ligases; C403091:Magel2 protein, mouse; D047908:Intracellular Signaling Peptides and Proteins; D064267:Intrinsically Disordered Proteins; C491814:Peg12 protein, mouse; C119432:Mkrn3 protein, mouse
keywords: AS, Angelman Syndrome; AS-IC, Angelman Syndrome Imprinting Center; AS-SRO, Angelman Syndrome Shortest Region of deletion Overlap; BGS, Sodium Bisulfite Genomic Sequencing; BISSCA, Bisulfite Sequencing Comparative Analysis; CGI, CpG Island; DH, DNase I Hypersensitive; DMR, Differentially Methylated Region; DNA methylation; EtOH, Ethanol; GO, gene ontology; IC, Imprinting Center; ICR, Imprinting Control Region; IPA, Ingenuity Pathway Analysis ®; PWS, Prader-Willi Syndrome; PWS-IC, Prader-Willi Syndrome Imprinting Center; PWS-SRO, Prader-Willi Syndrome Shortest Region of deletion Overlap; RRBS, Reduced Representation Bisulfite Sequencing; SDS, Sodium Dodecyl Sulfate; SLIM, Sliding Linear Model; TBE, Tris/Borate/EDTA; Tris, Trisaminomethane; UTR, untranslated region; angelman syndrome; genomic imprinting; imprinting center; lncRNA, long non-coding RNA; mat, maternally-inherited allele; pat, paternally-inherited allele; prader-Willi syndrome; reduced representation bisulfite sequencing