Genome-Wide Methylation Analysis Identifies Novel Cpg Loci For Perimembranous Ventricular Septal Defects In Human

References

• March of Dimes Birth Defects Foundation . Global Report on Birth Defects. The Hidden Toll of Dying and Disabled Children . March of Dimes Birth Defects Foundation , White Plains, NY, USA ( 2006 ).
   Google Scholar
• Penny DJ , VickGW3rd . Ventricular septal defect . Lancet377 ( 9771 ), 1103 – 1112 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Sommer RJ , HijaziZM , RhodesJFJr . Pathophysiology of congenital heart disease in the adult: part I: shunt lesions . Circulation117 ( 8 ), 1090 – 1099 ( 2008 ).
   PubMed Web of Science ®Google Scholar
• Cordell HJ , BenthamJ , TopfAet al. Genome-wide association study of multiple congenital heart disease phenotypes identifies a susceptibility locus for atrial septal defect at chromosome 4p16 . Nat. Genet.45 ( 7 ), 822 – 824 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Rasmussen S , IrgensLM . The effects of smoking and hypertensive disorders on fetal growth . BMC Pregnancy Childbirth6 , 16 ( 2006 ).
   PubMedGoogle Scholar
• Gittenberger-De Groot AC , CalkoenEE , PoelmannRE , BartelingsMM , JongbloedMR . Morphogenesis and molecular considerations on congenital cardiac septal defects . Ann. Med.46 ( 8 ), 640 – 652 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Zhong GW , JiangP , QiaoWR , ZhangYW , WeiWF , LuL . Protein phosphatase 2A (PP2A) regulatory subunits ParA and PabA orchestrate septation and conidiation and are essential for PP2A activity in Aspergillus nidulans . Eukaryot. Cell13 ( 12 ), 1494 – 1506 ( 2014 ).
   PubMedGoogle Scholar
• Obermann-Borst SA , VujkovicM , De VriesJHet al. A maternal dietary pattern characterised by fish and seafood in association with the risk of congenital heart defects in the offspring . BJOG118 ( 10 ), 1205 – 1215 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Smedts HP , De VriesJH , RakhshandehrooMet al. High maternal vitamin E intake by diet or supplements is associated with congenital heart defects in the offspring . BJOG116 ( 3 ), 416 – 423 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Smedts HP , RakhshandehrooM , Verkleij-HagoortACet al. Maternal intake of fat, riboflavin and nicotinamide and the risk of having offspring with congenital heart defects . Eur. J. Nutr.47 ( 7 ), 357 – 365 ( 2008 ).
   PubMed Web of Science ®Google Scholar
• Rachfall N , JohnsonAE , MehtaS , ChenJS , GouldKL . CDK1 promotes cytokinesis in fission yeast through activation of the septation initiation network . Mol. Biol. Cell25 ( 15 ), 2250 – 2259 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Steegers-Theunissen RP , TwigtJ , PestingerV , SinclairKD . The periconceptional period, reproduction and long-term health of offspring: the importance of one-carbon metabolism . Hum. Reprod. Update19 ( 6 ), 640 – 655 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Chowdhury S , ClevesMA , MacleodSL , JamesSJ , ZhaoW , HobbsCA . Maternal DNA hypomethylation and congenital heart defects . Birth Defects Res. A Clin. Mol. Teratol.91 ( 2 ), 69 – 76 ( 2011 ).
   PubMedGoogle Scholar
• Obermann-Borst SA , Van DrielLM , HelbingWAet al. Congenital heart defects and biomarkers of methylation in children: a case-control study . Eur. J. Clin. Invest.41 ( 2 ), 143 – 150 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Bibikova M , BarnesB , TsanCet al. High density DNA methylation array with single CpG site resolution . Genomics98 ( 4 ), 288 – 295 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Verkleij-Hagoort AC , VerlindeM , UrsemNTet al. Maternal hyperhomocysteinaemia is a risk factor for congenital heart disease . BJOG113 ( 12 ), 1412 – 1418 ( 2006 ).
   PubMed Web of Science ®Google Scholar
• Pidsley R , CcYW , VoltaM , LunnonK , MillJ , SchalkwykLC . A data-driven approach to preprocessing Illumina 450K methylation array data . BMC Genomics14 , 293 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Du P , ZhangX , HuangCCet al. Comparison of beta-value and M-value methods for quantifying methylation levels by microarray analysis . BMC Bioinformatics11 , 587 ( 2010 ).
   PubMed Web of Science ®Google Scholar
• Joubert BR , HabergSE , NilsenRMet al. 450K epigenome-wide scan identifies differential DNA methylation in newborns related to maternal smoking during pregnancy . Environ. Health Perspect.120 ( 10 ), 1425 – 1431 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Reinius LE , AcevedoN , JoerinkMet al. Differential DNA methylation in purified human blood cells: implications for cell lineage and studies on disease susceptibility . PLoS ONE7 ( 7 ), e41361 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Houseman EA , AccomandoWP , KoestlerDCet al. DNA methylation arrays as surrogate measures of cell mixture distribution . BMC Bioinformatics13 , 86 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Alexa A , RahnenfuhrerJ , LengauerT . Improved scoring of functional groups from gene expression data by decorrelating GO graph structure . Bioinformatics22 ( 13 ), 1600 – 1607 ( 2006 ).
   PubMed Web of Science ®Google Scholar
• Ingenuity . www.ingenuity.com .
   Google Scholar
• Chi J , CohenP . The multifaceted roles of PRDM16: adipose biology and beyond . Trends Endocrinol. Metab.27 ( 1 ), 11 – 23 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Seale P , KajimuraS , YangWet al. Transcriptional control of brown fat determination by PRDM16 . Cell Metabol.6 ( 1 ), 38 – 54 ( 2007 ).
   PubMed Web of Science ®Google Scholar
• Nagano G , OhnoH , OkiKet al. Activation of classical brown adipocytes in the adult human perirenal depot is highly correlated with PRDM16-EHMT1 complex expression . PLoS ONE10 ( 3 ), e0122584 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Harms MJ , LimHW , HoYet al. PRDM16 binds MED1 and controls chromatin architecture to determine a brown fat transcriptional program . Genes Dev.29 ( 3 ), 298 – 307 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Arndt AK , SchaferS , DrenckhahnJDet al. Fine mapping of the 1p36 deletion syndrome identifies mutation of PRDM16 as a cause of cardiomyopathy . Am. J. Hum. Genet.93 ( 1 ), 67 – 77 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Bjork BC , Turbe-DoanA , PrysakM , HerronBJ , BeierDR . PRDM16 is required for normal palatogenesis in mice . Hum. Mol. Genet.19 ( 5 ), 774 – 789 ( 2010 ).
   PubMed Web of Science ®Google Scholar
• Hong KW , LimJE , KimJWet al. Identification of three novel genetic variations associated with electrocardiographic traits (QRS duration and PR interval) in East Asians . Hum. Mol. Genet.23 ( 24 ), 6659 – 6667 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Pinheiro I , MargueronR , ShukeirNet al. PRDM3 and PRDM16 are H3K9me1 methyltransferases required for mammalian heterochromatin integrity . Cell150 ( 5 ), 948 – 960 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Aguilo F , AvagyanS , LabarAet al. PRDM16 is a physiologic regulator of hematopoietic stem cells . Blood117 ( 19 ), 5057 – 5066 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Arthur HM , BamforthSD . TGFbeta signaling and congenital heart disease: insights from mouse studies . Birth Defects Res. A Clin. Mol. Teratol.91 ( 6 ), 423 – 434 ( 2011 ).
   PubMedGoogle Scholar
• Bartram U , MolinDG , WisseLJet al. Double-outlet right ventricle and overriding tricuspid valve reflect disturbances of looping, myocardialization, endocardial cushion differentiation, and apoptosis in TGF-beta(2)-knockout mice . Circulation103 ( 22 ), 2745 – 2752 ( 2001 ).
   PubMed Web of Science ®Google Scholar
• Warner DR , HornKH , MuddL , WebbCL , GreeneRM , PisanoMM . PRDM16/MEL1: a novel Smad binding protein expressed in murine embryonic orofacial tissue . Biochim. Biophys. Acta1773 ( 6 ), 814 – 820 ( 2007 ).
   PubMed Web of Science ®Google Scholar
• Chen Q , ChenH , ZhengDet al. Smad7 is required for the development and function of the heart . J. Biol. Chem.284 ( 1 ), 292 – 300 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Glass C , WuertzerC , CuiXet al. Global identification of EVI1 target genes in acute myeloid leukemia . PLoS ONE8 ( 6 ), e67134 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Modlich U , SchambachA , BrugmanMHet al. Leukemia induction after a single retroviral vector insertion in EVI1 or PRDM16 . Leukemia22 ( 8 ), 1519 – 1528 ( 2008 ).
   PubMed Web of Science ®Google Scholar
• Perkins AS , MercerJA , JenkinsNA , CopelandNG . Patterns of EVI-1 expression in embryonic and adult tissues suggest that EVI-1 plays an important regulatory role in mouse development . Development111 ( 2 ), 479 – 487 ( 1991 ).
   PubMed Web of Science ®Google Scholar
• Doyle AJ , DoyleJJ , BesslingSLet al. Mutations in the TGF-beta repressor SKI cause Shprintzen-Goldberg syndrome with aortic aneurysm . Nat. Genet.44 ( 11 ), 1249 – 1254 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Turner J , CrossleyM . Cloning and characterization of mCtBP2, a co-repressor that associates with basic Kruppel-like factor and other mammalian transcriptional regulators . EMBO J.17 ( 17 ), 5129 – 5140 ( 1998 ).
   PubMed Web of Science ®Google Scholar
• Hinck L . The versatile roles of “axon guidance” cues in tissue morphogenesis . Dev. Cell7 ( 6 ), 783 – 793 ( 2004 ).
   PubMed Web of Science ®Google Scholar
• Sanchez-Castro M , PichonO , BriandAet al. Disruption of the SEMA3D gene in a patient with congenital heart defects . Hum. Mutat.36 ( 1 ), 30 – 33 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Butler JE , KadonagaJT . The RNA polymerase II core promoter: a key component in the regulation of gene expression . Genes Dev.16 ( 20 ), 2583 – 2592 ( 2002 ).
   PubMed Web of Science ®Google Scholar
• Lagha M , BothmaJP , EspositoEet al. Paused Pol II coordinates tissue morphogenesis in the Drosophila embryo . Cell153 ( 5 ), 976 – 987 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Zhu C , YuZB , ChenXHet al. Screening for differential methylation status in fetal myocardial tissue samples with ventricular septal defects by promoter methylation microarrays . Mol. Med. Report4 ( 1 ), 137 – 143 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Serra-Juhe C , CuscoI , HomsA , FloresR , ToranN , Perez-JuradoLA . DNA methylation abnormalities in congenital heart disease . Epigenetics10 ( 2 ), 167 – 177 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Michels KB , BinderAM , DedeurwaerderSet al. Recommendations for the design and analysis of epigenome-wide association studies . Nat. Methods10 ( 10 ), 949 – 955 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Ma B , WilkerEH , Willis-OwenSAet al. Predicting DNA methylation level across human tissues . Nucleic Acids Res.42 ( 6 ), 3515 – 3528 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Talens RP , BoomsmaDI , TobiEWet al. Variation, patterns, and temporal stability of DNA methylation: considerations for epigenetic epidemiology . FASEB J.24 ( 9 ), 3135 – 3144 ( 2010 ).
   PubMed Web of Science ®Google Scholar
• Liu Y , AryeeMJ , PadyukovLet al. Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in rheumatoid arthritis . Nat. Biotechnol.31 ( 2 ), 142 – 147 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Souren NY , LutsikP , GasparoniGet al. Adult monozygotic twins discordant for intra-uterine growth have indistinguishable genome-wide DNA methylation profiles . Genome Biol.14 ( 5 ), R44 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Steegers-Theunissen RP , Obermann-BorstSA , KremerDet al. Periconceptional maternal folic acid use of 400 μg per day is related to increased methylation of the IGF2 gene in the very young child . PLoS ONE4 ( 11 ), e7845 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Grunert M , DornC , CuiHet al. Comparative DNA methylation and gene expression analysis identifies novel genes for structural congenital heart diseases . Cardiovasc. Res.112 ( 1 ), 464 – 477 ( 2016 ).
   PubMed Web of Science ®Google Scholar