A novel approach identifies new differentially methylated regions (DMRs) associated with imprinted genes.

Imprinted genes are critical for normal human growth and neurodevelopment. They are characterized by differentially methylated regions (DMRs) of DNA that confer parent of origin-specific transcription. We developed a new strategy to identify imprinted gene-associated DMRs. Using genome-wide methylation profiling of sodium bisulfite modified DNA from normal human tissues of biparental origin, candidate DMRs were identified by selecting CpGs with methylation levels consistent with putative allelic differential methylation. In parallel, the methylation profiles of tissues of uniparental origin, i.e., paternally-derived androgenetic complete hydatidiform moles (AnCHMs), and maternally-derived mature cystic ovarian teratoma (MCT), were examined and then used to identify CpGs with parent of origin-specific DNA methylation. With this approach, we found known DMRs associated with imprinted genomic regions as well as new DMRs for known imprinted genes, NAP1L5 and ZNF597, and novel candidate imprinted genes. The paternally methylated DMR for one candidate, AXL, a receptor tyrosine kinase, was also validated in experiments with mouse embryos that demonstrated Axl was expressed preferentially from the maternal allele in a DNA methylation-dependent manner.

[1]  A. Sharp,et al.  Methylation profiling in individuals with uniparental disomy identifies novel differentially methylated regions on chromosome 15. , 2010, Genome research.

[2]  K. Buiting.  Prader–Willi syndrome and Angelman syndrome , 2010, American journal of medical genetics. Part C, Seminars in medical genetics.

[3]  A. Green,et al.  The IG-DMR and the MEG3-DMR at Human Chromosome 14q32.2: Hierarchical Interaction and Distinct Functional Properties as Imprinting Control Centers , 2010, PLoS genetics.

[4]  N. Yaegashi,et al.  A tripartite paternally methylated region within the Gpr1-Zdbf2 imprinted domain on mouse chromosome 1 identified by meDIP-on-chip , 2010, Nucleic acids research.

[5]  T. Liehr.  Cytogenetic contribution to uniparental disomy (UPD) , 2010, Molecular Cytogenetics.

[6]  D. Barlow,et al.  Genomic imprinting mechanisms in embryonic and extraembryonic mouse tissues , 2010, Heredity.

[7]  Chia-Lin Wei,et al.  Dynamic changes in the human methylome during differentiation. , 2010, Genome research.

[8]  S W Scherer,et al.  EBV transformation and cell culturing destabilizes DNA methylation in human lymphoblastoid cell lines. , 2010, Genomics.

[9]  Bjørn Tore Gjertsen,et al.  Axl is an essential epithelial-to-mesenchymal transition-induced regulator of breast cancer metastasis and patient survival , 2009, Proceedings of the National Academy of Sciences.

[10]  Daniel F. Gudbjartsson,et al.  Parental origin of sequence variants associated with complex diseases , 2009, Nature.

[11]  M. Bartolomei,et al.  Imprinting and epigenetic changes in the early embryo , 2009, Mammalian Genome.

[12]  C. Harview,et al.  Differential methylation persists at the mouse Rasgrf1 DMR in tissues displaying monoallelic and biallelic expression , 2009, Epigenetics.

[13]  E. Mardis,et al.  Transcriptome-Wide Identification of Novel Imprinted Genes in Neonatal Mouse Brain , 2008, PloS one.

[14]  S. Vigneau,et al.  Genomic imprinting mechanisms in mammals. , 2008, Mutation research.

[15]  E. Birney,et al.  An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). , 2008, Genome research.

[16]  R. Weksberg,et al.  Altered gene expression and methylation of the human chromosome 11 imprinted region in small for gestational age (SGA) placentae. , 2008, Developmental biology.

[17]  B. Tycko,et al.  Genomic surveys by methylation-sensitive SNP analysis identify sequence-dependent allele-specific DNA methylation , 2008, Nature Genetics.

[18]  Bing Ren,et al.  Genome-wide mapping of allele-specific protein-DNA interactions in human cells , 2008, Nature Methods.

[19]  A. Ferguson-Smith,et al.  Deletions and epimutations affecting the human 14q32.2 imprinted region in individuals with paternal and maternal upd(14)-like phenotypes , 2008, Nature Genetics.

[20]  H. Earp,et al.  TAM receptor tyrosine kinases: biologic functions, signaling, and potential therapeutic targeting in human cancer. , 2008, Advances in cancer research.

[21]  A. Hartemink,et al.  Computational and experimental identification of novel human imprinted genes. , 2007, Genome research.

[22]  A. Wood,et al.  A Screen for Retrotransposed Imprinted Genes Reveals an Association between X Chromosome Homology and Maternal Germ-Line Methylation , 2006, PLoS genetics.

[23]  T. Hudson,et al.  A genome-wide approach to identifying novel-imprinted genes , 2007, Human Genetics.

[24]  S. Apostolidou,et al.  Limited evolutionary conservation of imprinting in the human placenta. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[25]  D. Cox,et al.  Analysis of allelic differential expression in human white blood cells. , 2006, Genome research.

[26]  H. Sasaki,et al.  Bisulfite sequencing and dinucleotide content analysis of 15 imprinted mouse differentially methylated regions (DMRs): paternally methylated DMRs contain less CpGs than maternally methylated DMRs , 2006, Cytogenetic and Genome Research.

[27]  R. Kuick,et al.  Mutations in NALP7 cause recurrent hydatidiform moles and reproductive wastage in humans , 2006, Nature Genetics.

[28]  A. Feinberg,et al.  The epigenetic progenitor origin of human cancer , 2006, Nature Reviews Genetics.

[29]  E. Lander,et al.  Finishing the euchromatic sequence of the human genome , 2004 .

[30]  J. Bonfield,et al.  Finishing the euchromatic sequence of the human genome , 2004, Nature.

[31]  Gavin Kelsey,et al.  Resourceful imprinting : Fertility , 2004 .

[32]  Wolf Reik,et al.  Resourceful imprinting , 2004, Nature.

[33]  M. Bartolomei,et al.  Disruption of Imprinted Gene Methylation and Expression in Cloned Preimplantation Stage Mouse Embryos1 , 2003, Biology of reproduction.

[34]  M. Seoud,et al.  Maternal alleles acquiring paternal methylation patterns in biparental complete hydatidiform moles. , 2003, Human molecular genetics.

[35]  G. Kelsey,et al.  Identification of novel imprinted genes in a genome-wide screen for maternal methylation. , 2003, Genome research.

[36]  S. Tilghman,et al.  A differentially methylated region within the gene Kcnq1 functions as an imprinted promoter and silencer. , 2003, Human molecular genetics.

[37]  D. Bonthron,et al.  A global disorder of imprinting in the human female germ line , 2002, Nature.

[38]  Andrew P Feinberg,et al.  A genome-wide screen for normally methylated human CpG islands that can identify novel imprinted genes. , 2002, Genome research.

[39]  D. Barlow,et al.  Quantitative genetics: Turning up the heat on QTL mapping , 2002, Nature Reviews Genetics.

[40]  John M. Greally,et al.  Short interspersed transposable elements (SINEs) are excluded from imprinted regions in the human genome , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[41]  A. Hoffman,et al.  Divergent evolution in M6P/IGF2R imprinting from the Jurassic to the Quaternary. , 2001, Human molecular genetics.

[42]  D. Bonthron,et al.  Imprinting of the Gsα gene GNAS1 in the pathogenesis of acromegaly , 2001 .

[43]  M. Korbonits,et al.  Imprinting of the G(s)alpha gene GNAS1 in the pathogenesis of acromegaly. , 2001, The Journal of clinical investigation.

[44]  C. Wells,et al.  A cluster of oppositely imprinted transcripts at the Gnas locus in the distal imprinting region of mouse chromosome 2. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[45]  D. Accili,et al.  Variable and tissue-specific hormone resistance in heterotrimeric Gs protein α-subunit (Gsα) knockout mice is due to tissue-specific imprinting of the Gsα gene , 1998 .

[46]  D. Accili,et al.  Variable and tissue-specific hormone resistance in heterotrimeric Gs protein alpha-subunit (Gsalpha) knockout mice is due to tissue-specific imprinting of the gsalpha gene. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[47]  G. Mutter.  Role of imprinting in abnormal human development. , 1997, Mutation research.

[48]  C. Polychronakos,et al.  Polymorphic functional imprinting of the human IGF2 gene among individuals, in blood cells, is associated with H19 expression. , 1996, Biochemical and biophysical research communications.

[49]  T. Moore,et al.  Imprinted genes have few and small introns , 1996, Nature Genetics.

[50]  D. Barlow,et al.  Conservation of a maternal-specific methylation signal at the human IGF2R locus. , 1995, Human molecular genetics.

[51]  M. Surani,et al.  Peg1/Mest imprinted gene on chromosome 6 identified by cDNA subtraction hybridization , 1995, Nature Genetics.

[52]  J. Guénet,et al.  Tissue- and developmental stage-specific imprinting of the mouse proinsulin gene, Ins2. , 1995, Developmental biology.

[53]  Rudolf Jaenisch,et al.  Role for DNA methylation in genomic imprinting , 1993, Nature.

[54]  M. Surani,et al.  The inheritance of germline-specific epigenetic modifications during development. , 1993, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[55]  D. Barlow,et al.  The mouse insulin-like growth factor type-2 receptor is imprinted and closely linked to the Tme locus , 1991, Nature.

[56]  Nan Faion T. Wu,et al.  The Beckwith-Wiedemann Syndrome , 1974, Clinical pediatrics.