Identification of novel imprinted genes in a genome-wide screen for maternal methylation.
A characteristic of imprinted genes is that the maternal and paternal alleles show differences in methylation. To perform a genome-wide screen for novel imprinted loci, we applied methylation-sensitive representational difference analysis (Me-RDA) to parthenogenetic mouse embryos, to identify differentially methylated regions (DMRs) methylated specifically on the maternal allele. We isolated a total of 26 distinct clones from known and novel DMRs and identified three novel imprinted genes. Nap1l5 is located on proximal chromosome 6 and encodes a protein with homology with nucleosome assembly proteins (NAPs); it has tissue-specific imprinting with expression from the paternal allele. We identified two DMRs on chromosome 15, a chromosome that was not thought to contain imprinted loci, and demonstrated that each is associated with a paternally expressed transcript. Peg13 gives rise to a noncoding RNA that is highly expressed in the brain and imprinted in all tissues examined. A DMR was also identified at the chromosome 15 Slc38a4 gene, which encodes a system A amino acid transporter; we show that Slc38a4 is imprinted in a tissue-specific manner. Interestingly, two of the three novel genes identified in this screen are located within the introns of other genes; their identification indicates that such "microimprinted" domains may be more common than previously thought.
Smith
Rachel J
RJ
Developmental Genetics Program, The Babraham Institute, Cambridge CB2 4AT, UK.
Dean
Wendy
W
Konfortova
Galia
G
Kelsey
Gavin
G
D000483:Alleles; D026924:Amino Acid Transport System A / Q000235:genetics; D000818:Animals; D018797:Cell Cycle Proteins; D002874:Chromosome Mapping / Q000379:methods; D018899:CpG Islands / Q000235:genetics; D019175:DNA Methylation; D004622:Embryo, Mammalian; D005260:Female; D018507:Gene Expression Regulation, Developmental / Q000235:genetics; D005820:Genetic Testing / Q000379:methods*; D016678:Genome; D018392:Genomic Imprinting / Q000235:genetics*; D006801:Humans; D051379:Mice; D008810:Mice, Inbred C57BL; D008808:Mice, Inbred CBA; D008969:Molecular Sequence Data; D009687:Nuclear Proteins; D056490:Nucleosome Assembly Protein 1; D009707:Nucleosomes / Q000235:genetics; D011506:Proteins / Q000235:genetics; D023121:RNA, Messenger, Stored / Q000235:genetics; D051381:Rats; D012689:Sequence Homology, Nucleic Acid
D026924:Amino Acid Transport System A; D018797:Cell Cycle Proteins; C533557:NAP1L1 protein, human; C533558:Nap1l1 protein, mouse; C533555:Nap1l1 protein, rat; D009687:Nuclear Proteins; D056490:Nucleosome Assembly Protein 1; D009707:Nucleosomes; D011506:Proteins; D023121:RNA, Messenger, Stored; C420522:Slc38a4 protein, mouse; C486010:Slc38a4 protein, rat