Identification and Characterization of Cis-Regulatory Elements ‘Insulator and Repressor’ in PPARD Gene

References

• Pertea M , SalzbergSL . Between a chicken and a grape: estimating the number of human genes . Genome Biol.11 ( 5 ), 206 ( 2010 ).
   PubMed Web of Science ®Google Scholar
• Dunham I , KundajeA , AldredSFet al. An integrated encyclopedia of DNA elements in the human genome . Nature489 ( 7414 ), 57 – 74 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Gerstein MB , KundajeA , HariharanMet al. Architecture of the human regulatory network derived from ENCODE data . Nature489 ( 7414 ), 91 – 100 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Maston GA , EvansSK , GreenMR . Transcriptional regulatory elements in the human genome . Annu. Rev. Genomics Hum. Genet.7 , 29 – 59 ( 2006 ).
   PubMed Web of Science ®Google Scholar
• Ogbourne S , AntalisTM . Transcriptional control and the role of silencers in transcriptional regulation in eukaryotes . Biochem. J.331 , 1 – 14 ( 1998 ).
   PubMed Web of Science ®Google Scholar
• Gaszner M , FelsenfeldG . Insulators: exploiting transcriptional and epigenetic mechanisms . Nat. Rev. Genet.7 ( 9 ), 703 – 713 ( 2006 ).
   PubMed Web of Science ®Google Scholar
• Udvardy A , MaineE , SchedlP . The 87A7 chromomere. Identification of novel chromatin structures flanking the heat shock locus that may define the boundaries of higher order domains . J. Mol. Biol.185 ( 2 ), 341 – 358 ( 1985 ).
   PubMed Web of Science ®Google Scholar
• Kellum R , SchedlP . A position-effect assay for boundaries of higher order chromosomal domains . Cell64 ( 5 ), 941 – 950 ( 1991 ).
   PubMed Web of Science ®Google Scholar
• Holdridge C , DorsettD . Repression of Hsp70 heat shock gene transcription by the suppressor of hairy-wing protein of Drosophila melanogaster . Mol. Cell Biol.11 ( 4 ), 1894 – 1900 ( 1991 ).
   PubMed Web of Science ®Google Scholar
• Geyer PK , CorcesVG . DNA position-specific repression of transcription by a Drosophila zinc finger protein . Genes Dev.6 ( 10 ), 1865 – 1873 ( 1992 ).
   PubMed Web of Science ®Google Scholar
• Dorsett D . Distance-independent inactivation of an enhancer by the suppressor of hairy-wing DNA-binding protein of Drosophila . Genetics134 ( 4 ), 1135 – 1144 ( 1993 ).
   PubMed Web of Science ®Google Scholar
• Bell AC , WestAG , FelsenfeldG . The protein CTCF is required for the enhancer blocking activity of vertebrate insulators . Cell98 ( 3 ), 387 – 396 ( 1999 ).
   PubMed Web of Science ®Google Scholar
• Ali T , RenkawitzR , BartkuhnM . Insulators and domains of gene expression . Curr. Opin. Genet. Dev.37 , 17 – 26 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Ohlsson R , RenkawitzR , LobanenkovV . CTCF is a uniquely versatile transcription regulator linked to epigenetics and disease . Trends Genet.17 ( 9 ), 520 – 527 ( 2001 ).
   PubMed Web of Science ®Google Scholar
• Perissi V , JepsenK , GlassCK , RosenfeldMG . Deconstructing repression: evolving models of co-repressor action . Nat. Rev. Genet.11 ( 2 ), 109 – 123 ( 2010 ).
   PubMed Web of Science ®Google Scholar
• Grant SF , ThorleifssonG , ReynisdottirIet al. Variant of transcription factor 7-like 2 (TCF7L2) gene confers risk of Type 2 diabetes . Nat. Genet.38 ( 3 ), 320 – 323 ( 2006 ).
   PubMed Web of Science ®Google Scholar
• Frayling TM , TimpsonNJ , WeedonMNet al. A common variant in the FTO gene is associated with body mass index and predisposes to childhood and adult obesity . Science316 ( 5826 ), 889 – 894 ( 2007 ).
   PubMed Web of Science ®Google Scholar
• Alharbi KK , KhanIA , MunshiA , AlharbiFK , Al-SheikhY , AlnbaheenMS . Association of the genetic variants of insulin receptor substrate 1 (IRS-1) with Type 2 diabetes mellitus in a Saudi population . Endocrine47 ( 2 ), 472 – 477 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Morris AP , VoightBF , TeslovichTMet al. Large-scale association analysis provides insights into the genetic architecture and pathophysiology of Type 2 diabetes . Nat. Genet.44 ( 9 ), 981 – 990 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Han J , WeiM , WangQet al. Association of genetic variants of SIRT1 with Type 2 diabetes mellitus . Gene Expr.16 ( 4 ), 177 – 185 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Dong C , ZhouH , ShenCet al. Role of peroxisome proliferator-activated receptors gene polymorphisms in Type 2 diabetes and metabolic syndrome . World J. Diabetes6 ( 4 ), 654 – 661 ( 2015 ).
   PubMedGoogle Scholar
• Bishop-Bailey D . Peroxisome proliferator-activated receptors in the cardiovascular system . Brit. J. Pharmacol.129 ( 5 ), 823 – 833 ( 2000 ).
   PubMed Web of Science ®Google Scholar
• Brown PJ , Smith-OliverTA , CharifsonPSet al. Identification of peroxisome proliferator-activated receptor ligands from a biased chemical library . Chem. Biol.4 ( 12 ), 909 – 918 ( 1997 ).
   PubMedGoogle Scholar
• Kent WJ , SugnetCW , FureyTSet al. The human genome browser at UCSC . Genome Res.12 ( 6 ), 996 – 1006 ( 2002 ).
   PubMed Web of Science ®Google Scholar
• Margulies EH , CooperGM , AsimenosGet al. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome . Genome Res.17 ( 6 ), 760 – 774 ( 2007 ).
   PubMed Web of Science ®Google Scholar
• Rosenbloom KR , SloanCA , MalladiVSet al. ENCODE Data in the UCSC Genome Browser: year 5 update . Nucleic Acids Res.41 ( D1 ), D56 – D63 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Birney E , StamatoyannopoulosJA , DuttaAet al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project . Nature447 ( 7146 ), 799 – 816 ( 2007 ).
   PubMed Web of Science ®Google Scholar
• Petrykowska HM , VockleyCM , ElnitskiL . Detection and characterization of silencers and enhancer-blockers in the greater CFTR locus . Genome Res.18 ( 8 ), 1238 – 1246 ( 2008 ).
   PubMed Web of Science ®Google Scholar
• Shen Y , YueF , McClearyDFet al. A map of the cis-regulatory sequences in the mouse genome . Nature488 ( 7409 ), 116 – 120 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Bao L , ZhouM , CuiY . CTCFBSDB: a CTCF-binding site database for characterization of vertebrate genomic insulators . Nucleic Acids Res.36 ( Database issue ), 2 ( 2008 ).
   Google Scholar
• Liu S , HatanoB , ZhaoMet al. Role of peroxisome proliferator-activated receptor {delta}/{beta} in hepatic metabolic regulation . J. Biol. Chem.286 ( 2 ), 1237 – 1247 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Luquet S , GaudelC , HolstDet al. Roles of PPAR delta in lipid absorption and metabolism: a new target for the treatment of Type 2 diabetes . Biochim. Biophys. Acta1740 ( 2 ), 313 – 317 ( 2005 ).
   PubMed Web of Science ®Google Scholar
• Wang YX , LeeCH , TiepSet al. Peroxisome-proliferator-activated receptor delta activates fat metabolism to prevent obesity . Cell113 ( 2 ), 159 – 170 ( 2003 ).
   PubMed Web of Science ®Google Scholar
• Lee CH , OlsonP , HevenerAet al. PPARdelta regulates glucose metabolism and insulin sensitivity . Proc. Natl Acad. Sci. USA103 ( 9 ), 3444 – 3449 ( 2006 ).
   PubMed Web of Science ®Google Scholar
• Tanaka T , YamamotoJ , IwasakiSet al. Activation of peroxisome proliferator-activated receptor delta induces fatty acid beta-oxidation in skeletal muscle and attenuates metabolic syndrome . Proc. Natl Acad. Sci. USA100 ( 26 ), 15924 – 15929 ( 2003 ).
   PubMed Web of Science ®Google Scholar
• Saitoh N , BellAC , Recillas-TargaFet al. Structural and functional conservation at the boundaries of the chicken beta-globin domain . Embo J.19 ( 10 ), 2315 – 2322 ( 2000 ).
   PubMed Web of Science ®Google Scholar
• Recillas-Targa F , PikaartMJ , Burgess-BeusseBet al. Position-effect protection and enhancer blocking by the chicken beta-globin insulator are separable activities . Proc. Natl Acad. Sci. USA99 ( 10 ), 6883 – 6888 ( 2002 ).
   PubMed Web of Science ®Google Scholar
• Privalsky ML . The role of corepressors in transcriptional regulation by nuclear hormone receptors . Annu. Rev. Physiol.66 , 315 – 360 ( 2004 ).
   PubMed Web of Science ®Google Scholar
• Li L , HeS , SunJM , DavieJR . Gene regulation by Sp1 and Sp3 . Biochem. Cell Biol.82 ( 4 ), 460 – 471 ( 2004 ).
   PubMed Web of Science ®Google Scholar
• Harris MB , MosteckiJ , RothmanPB . Repression of an interleukin-4-responsive promoter requires cooperative BCL-6 function . J. Biol. Chem.280 ( 13 ), 13114 – 13121 ( 2005 ).
   PubMed Web of Science ®Google Scholar
• Gudynaite-Savitch L , JohnsonDA , MikiBL . Strategies to mitigate transgene-promoter interactions . Plant Biotechnol. J.7 ( 5 ), 472 – 485 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Kim SR , KimY , AnG . Identification of methyl jasmonate and salicylic acid response elements from the nopaline synthase (nos) promoter . Plant Physiol.103 ( 1 ), 97 – 103 ( 1993 ).
   PubMed Web of Science ®Google Scholar
• Ni M , CuiD , EinsteinJ , NarasimhuluS , VergaraCE , GelvinSB . Strength and tissue-specificity of chimeric promoters derived from the octopine and mannopine synthase genes . Plant J.7 ( 4 ), 661 – 676 ( 1995 ).
   Web of Science ®Google Scholar
• Cui KR , ZangCZ , RohTYet al. Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation . Cell Stem Cell.4 ( 1 ), 80 – 93 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Orford K , KharchenkoP , LaiWet al. Differential H3K4 methylation identifies developmentally poised hematopoietic genes . Dev. Cell.14 ( 5 ), 798 – 809 ( 2008 ).
   PubMed Web of Science ®Google Scholar
• Lu L , WuY , QiQBet al. Associations of Type 2 diabetes with common variants in PPARD and the modifying effect of vitamin D among middle-aged and elderly Chinese . PLoS ONE7 ( 4 ), e34985 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Bell AC , FelsenfeldG . Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene . Nature405 ( 6785 ), 482 – 485 ( 2000 ).
   PubMed Web of Science ®Google Scholar
• Hark AT , SchoenherrCJ , KatzDJ , IngramRS , LevorseJM , TilghmanSM . CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/Igf2 locus . Nature405 ( 6785 ), 486 – 489 ( 2000 ).
   PubMed Web of Science ®Google Scholar
• Lunyak VV , PrefontaineGG , NunezEet al. Developmentally regulated activation of a SINE B2 repeat as a domain boundary in organogenesis . Science317 ( 5835 ), 248 – 251 ( 2007 ).
   PubMed Web of Science ®Google Scholar