3,141
Views
0
CrossRef citations to date
0
Altmetric
Research Article

Epigenetics of the Myotonic Dystrophy-Associated DMPK gene neighborhood

, &
Pages 13-31 | Received 02 Sep 2015, Accepted 19 Oct 2015, Published online: 12 Jan 2016

References

  • Reddy S , SmithDB , RichMMet al. Mice lacking the myotonic dystrophy protein kinase develop a late onset progressive myopathy . Nat. Genet.13 ( 3 ), 325 – 335 ( 1996 ).
  • Schulz PE , McIntoshAD , KastenMR , WieringaB , EpsteinHF . A role for myotonic dystrophy protein kinase in synaptic plasticity . J. Neurophysiol.89 ( 3 ), 1177 – 1186 ( 2003 ).
  • Harmon EB , HarmonML , LarsenTD , PaulsonAF , PerrymanMB . Myotonic dystrophy protein kinase is expressed in embryonic myocytes and is required for myotube formation . Dev. Dyn.237 ( 9 ), 2353 – 2366 ( 2008 ).
  • Llagostera E , CatalucciD , MartiLet al. Role of myotonic dystrophy protein kinase (DMPK) in glucose homeostasis and muscle insulin action . PLoS ONE2 ( 11 ), e1134 ( 2007 ).
  • Pantic B , TrevisanE , CittaAet al. Myotonic dystrophy protein kinase (DMPK) prevents ROS-induced cell death by assembling a hexokinase II-Src complex on the mitochondrial surface . Cell Death Dis.4 ( e858 ( 2013 ).
  • Benders AA , GroenenPJ , OerlemansFT , VeerkampJH , WieringaB . Myotonic dystrophy protein kinase is involved in the modulation of the Ca2+ homeostasis in skeletal muscle cells . J. Clin. Invest.100 ( 6 ), 1440 – 1447 ( 1997 ).
  • Mounsey JP , MistryDJ , AiCW , ReddyS , MoormanJR . Skeletal muscle sodium channel gating in mice deficient in myotonic dystrophy protein kinase . Hum. Mol. Genet.9 ( 15 ), 2313 – 2320 ( 2000 ).
  • Bush EW , TaftCS , MeixellGE , PerrymanMB . Overexpression of myotonic dystrophy kinase in BC3H1 cells induces the skeletal muscle phenotype . J. Biol. Chem.271 ( 1 ), 548 – 552 ( 1996 ).
  • Llagostera E , AlvarezLopez MJ , ScimiaCet al. Altered beta-adrenergic response in mice lacking myotonic dystrophy protein kinase . Muscle Nerve45 ( 1 ), 128 – 130 ( 2012 ).
  • Berul CI , MaguireCT , AronovitzMJet al. DMPK dosage alterations result in atrioventricular conduction abnormalities in a mouse myotonic dystrophy model . J. Clin. Invest.103 ( 4 ), R1 – R7 ( 1999 ).
  • Pham YC , ManN , LamLT , MorrisGE . Localization of myotonic dystrophy protein kinase in human and rabbit tissues using a new panel of monoclonal antibodies . Hum. Mol. Genet.7 ( 12 ), 1957 – 1965 ( 1998 ).
  • Jansen G , MahadevanM , AmemiyaCet al. Characterization of the myotonic dystrophy region predicts multiple protein isoform-encoding mRNAs . Nat. Genet.1 ( 4 ), 261 – 266 ( 1992 ).
  • Sarkar PS , HanJ , ReddyS . In situ hybridization analysis of Dmpk mRNA in adult mouse tissues . Neuromuscul. Disord.14 ( 8–9 ), 497 – 506 ( 2004 ).
  • Oude Ophuis RJ , MuldersSA , Van HerpenRE , VanDe Vorstenbosch R , WieringaB , WansinkDG . DMPK protein isoforms are differentially expressed in myogenic and neural cell lineages . Muscle Nerve40 ( 4 ), 545 – 555 ( 2009 ).
  • Thornton CA . Myotonic dystrophy . Neurol. Clin.32 ( 3 ), 705 – 719 ( 2014 ).
  • Chau A , KalsotraA . Developmental insights into the pathology of and therapeutic strategies for DM1: back to the basics . Dev. Dyn.244 ( 3 ), 377 – 390 ( 2015 ).
  • Gomes-Pereira M , CooperTA , GourdonG . Myotonic dystrophy mouse models: towards rational therapy development . Trends Mol. Med.17 ( 9 ), 506 – 517 ( 2011 ).
  • Storbeck CJ , SabourinLA , WaringJD , KornelukRG . Definition of regulatory sequence elements in the promoter region and the first intron of the myotonic dystrophy protein kinase gene . J. Biol. Chem.273 ( 15 ), 9139 – 9147 ( 1998 ).
  • Filippova GN , ThienesCP , PennBHet al. CTCF-binding sites flank CTG/CAG repeats and form a methylation-sensitive insulator at the DM1 locus . Nat. Genet.28 ( 4 ), 335 – 343 ( 2001 ).
  • Harmon EB , HarmonML , LarsenTD , YangJ , GlasfordJW , PerrymanMB . Myotonic dystrophy protein kinase is critical for nuclear envelope integrity . J. Biol. Chem.286 ( 46 ), 40296 – 40306 ( 2011 ).
  • Moncaut N , RigbyPW , CarvajalJJ . Dial M(RF) for myogenesis . FEBS J.280 ( 17 ), 3980 – 3990 ( 2013 ).
  • Jansen G , GroenenP J , BachnerDet al. Abnormal myotonic dystrophy protein kinase levels produce only mild myopathy in mice . Nat. Genet.13 ( 3 ), 316 – 324 ( 1996 ).
  • Franke C , HattH , IaizzoPA , Lehmann-HornF . Characteristics of Na+ channels and Cl- conductance in resealed muscle fibre segments from patients with myotonic dystrophy . J. Physiol.425 , 391 – 405 ( 1990 ).
  • Varley KE , GertzJ , BowlingKMet al. Dynamic DNA methylation across diverse human cell lines and tissues . Genome Res.23 ( 3 ), 555 – 567 ( 2013 ).
  • Tsumagari K , BaribaultC , TerragniJet al. Early de novo DNA methylation and prolonged demethylation in the muscle lineage . Epigenetics8 ( 3 ), 317 – 332 ( 2013 ).
  • UCSC Genome Bioinformatics . http://genome.ucsc.edu/ .
  • Rosenbloom KR , ArmstrongJ , BarberGPet al. The UCSC Genome Browser database: 2015 update . Nucleic Acids Res.43 ( database issue ), D670 – D681 ( 2015 ).
  • Myers RM , StamatoyannopoulosJ , SnyderMet al. A user’s guide to the encyclopedia of DNA elements (ENCODE) . PLoS Biol.9 ( 4 ), e1001046 ( 2011 ).
  • Song L , ZhangZ , GrasfederLLet al. Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity . Genome Res.21 ( 10 ), 1757 – 1767 ( 2011 ).
  • Ernst J , KheradpourP , MikkelsenTSet al. Mapping and analysis of chromatin state dynamics in nine human cell types . Nature473 ( 7345 ), 43 – 49 ( 2011 ).
  • Trapnell C , WilliamsBA , PerteaGet al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation . Nat. Biotechnol.28 ( 5 ), 511 – 515 ( 2010 ).
  • Jiang L , SchlesingerF , DavisCAet al. Synthetic spike-in standards for RNA-seq experiments . Genome Res.21 ( 9 ), 1543 – 1551 ( 2011 ).
  • Valen E , PascarellaG , ChalkAet al. Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE . Genome Res.19 ( 2 ), 255 – 265 ( 2009 ).
  • Li G , FullwoodMJ , XuHet al. ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing . Genome Biol.11 ( 2 ), R22 ( 2010 ).
  • Trapnell C , RobertsA , GoffLet al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks . Nat. Protoc.7 ( 3 ), 562 – 578 ( 2012 ).
  • Epigenome Browser . http://epigenomebrowser.org .
  • Zhou X , WangT . Using the Wash U Epigenome Browser to examine genome-wide sequencing data . Curr. Protoc. Bioinformatics. doi:10.1002/0471250953.bi1010s40 ( 2012 ) ( Epub ahead of print ).
  • Lacey M R , BaribaultC , EhrlichM . Modeling, simulation and analysis of methylation profiles from reduced representation bisulfite sequencing experiments . Stat. Appl. Genet. Mol. Biol.12 ( 6 ), 723 – 742 ( 2013 ).
  • Song Q , DecatoB , HongEEet al. A reference methylome database and analysis pipeline to facilitate integrative and comparative epigenomics . PLoS ONE8 ( 12 ), e81148 ( 2013 ).
  • Meissner A , MikkelsenTS , GuHet al. Genome-scale DNA methylation maps of pluripotent and differentiated cells . Nature454 ( 7205 ), 766 – 770 ( 2008 ).
  • Carvajal JJ , RigbyPW . Regulation of gene expression in vertebrate skeletal muscle . Exp. Cell Res.316 ( 18 ), 3014 – 3018 ( 2010 ).
  • Chandra S , TerragniJ , ZhangGet al. Tissue-specific epigenetics in gene neighborhoods: myogenic transcription factor genes . Hum. Mol. Genet. doi:10.1093/hmg/ddv198 ( 2015 ) ( Epub ahead of print ).
  • GeneCards: The Human Gene Database . www.genecards.org/ .
  • Pohl AA , SugnetCW , ClarkTA , SmithK , FujitaPA , ClineMS . Affy exon tissues: exon levels in normal tissues in human, mouse and rat . Bioinformatics25 ( 18 ), 2442 – 2443 ( 2009 ).
  • Kikin O , D’antonioL , BaggaPS . QGRS Mapper: a web-based server for predicting G-quadruplexes in nucleotide sequences . Nucleic Acids Res.34 ( Web Server issue ), W676 – W682 ( 2006 ).
  • Tsumagari K , QiL , JacksonKet al. Epigenetics of a tandem DNA repeat: chromatin DNaseI sensitivity and opposite methylation changes in cancers . Nucleic Acids Res.36 ( 7 ), 2196 – 2207 ( 2008 ).
  • Cao Y , YaoZ , SarkarDet al. Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming . Dev. Cell18 ( 4 ), 662 – 674 ( 2010 ).
  • Marshall AD , BaileyCG , RaskoJE . CTCF and BORIS in genome regulation and cancer . Curr. Opin. Genet. Dev.24 , 8 – 15 ( 2014 ).
  • Wang J , ZhuangJ , IyerSet al. Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium . Nucleic Acids Res.41 ( Database issue ), D171 – D176 ( 2013 ).
  • Ziebarth JD , BhattacharyaA , CuiY . CTCFBSDB 2.0: a database for CTCF-binding sites and genome organization . Nucleic Acids Res.41 ( Database issue ), D188 – D194 ( 2013 ).
  • Klover P , ChenW , ZhuBM , HennighausenL . Skeletal muscle growth and fiber composition in mice are regulated through the transcription factors STAT5a/b: linking growth hormone to the androgen receptor . FASEB J.23 ( 9 ), 3140 – 3148 ( 2009 ).
  • Parakati R , DimarioJX . Dynamic transcriptional regulatory complexes, including E2F4, p107, p130, and Sp1, control fibroblast growth factor receptor 1 gene expression during myogenesis . J. Biol. Chem.280 ( 22 ), 21284 – 21294 ( 2005 ).
  • Tsuji-Takayama K , SuzukiM , YamamotoMet al. The production of IL-10 by human regulatory T cells is enhanced by IL-2 through a STAT5-responsive intronic enhancer in the IL-10 locus . J. Immunol.181 ( 6 ), 3897 – 3905 ( 2008 ).
  • Le Francois B , SooJ , MillarAMet al. Chronic mild stress and antidepressant treatment alter 5-HT1A receptor expression by modifying DNA methylation of a conserved Sp4 site . Neurobiol. Dis. doi:10.1016/j.nbd.2015.07.002 ( 2015 ) ( Epub ahead of print ).
  • Thierry-Mieg D , Thierry-MiegJ . AceView: a comprehensive cDNA-supported gene and transcripts annotation . Genome Biol.7 ( Suppl 1, S12 ), 11 – 14 ( 2006 ).
  • Terragni J , ZhangG , SunZet al. Notch signaling genes: myogenic DNA hypomethylation and 5-hydroxymethylcytosine . Epigenetics9 ( 6 ), 842 – 850 ( 2014 ).
  • Steger D J , LefterovaM I , YingLet al. DOT1L/KMT4 recruitment and H3K79 methylation are ubiquitously coupled with gene transcription in mammalian cells . Mol. Cell. Biol.28 ( 8 ), 2825 – 2839 ( 2008 ).
  • Cho DH , ThienesCP , MahoneySE , AnalauE , FilippovaGN , TapscottSJ . Antisense transcription and heterochromatin at the DM1 CTG repeats are constrained by CTCF . Mol. Cell20 ( 3 ), 483 – 489 ( 2005 ).
  • Jansen G , BachnerD , CoerwinkelM , WormskampN , HameisterH , WieringaB . Structural organization and developmental expression pattern of the mouse WD-repeat gene DMR-N9 immediately upstream of the myotonic dystrophy locus . Hum. Mol. Genet.4 ( 5 ), 843 – 852 ( 1995 ).
  • Som PM , RothschildMA , SilversAR , NortonKI . A painless retroauricular mass in a patient with myotonic dystrophy: computed tomographic documentation of the bone changes that occur in the skull base . Skull Base Surg.7 ( 4 ), 223 – 225 ( 1997 ).
  • Campanati A , GiannoniM , BurattiLet al. Skin features in myotonic dystrophy type 1: an observational study . Neuromuscul. Disord.25 ( 5 ), 409 – 413 ( 2015 ).
  • Bailey SD , ZhangX , DesaiKet al. ZNF143 provides sequence specificity to secure chromatin interactions at gene promoters . Nat. Commun.2 , 6186 ( 2015 ).
  • Groenen PJ , WansinkDG , CoerwinkelM , VanDen Broek W , JansenG , WieringaB . Constitutive and regulated modes of splicing produce six major myotonic dystrophy protein kinase (DMPK) isoforms with distinct properties . Hum. Mol. Genet.9 ( 4 ), 605 – 616 ( 2000 ).
  • Eriksson M , AnsvedT , EdstromLet al. Independent regulation of the myotonic dystrophy 1 locus genes postnatally and during adult skeletal muscle regeneration . J. Biol. Chem.275 ( 26 ), 19964 – 19969 ( 2000 ).
  • Pekowska A , BenoukrafT , Zacarias-CabezaJet al. H3K4 tri-methylation provides an epigenetic signature of active enhancers . EMBO J.30 ( 20 ), 4198 – 4210 ( 2011 ).
  • Lopez Castel A , NakamoriM , TomeSet al. Expanded CTG repeat demarcates a boundary for abnormal CpG methylation in myotonic dystrophy patient tissues . Hum. Mol. Genet.20 ( 1 ), 1 – 15 ( 2011 ).
  • Dubois-Chevalier J , OgerF , DehondtHet al. A dynamic CTCF chromatin binding landscape promotes DNA hydroxymethylation and transcriptional induction of adipocyte differentiation . Nucleic Acids Res.42 ( 17 ), 10943 – 10959 ( 2014 ).
  • Eriksson M , AnsvedT , AnvretM , CareyN . A mammalian radial spokehead-like gene, RSHL1, at the myotonic dystrophy-1 locus . Biochem. Biophys. Res. Commun.281 ( 4 ), 835 – 841 ( 2001 ).
  • Zhang XY , LoflinPT , GehrkeCW , AndrewsP A , EhrlichM . Hypermethylation of human DNA sequences in embryonal carcinoma cells and somatic tissues but not in sperm . Nucleic Acids Res.15 ( 22 ), 9429 – 9449 ( 1987 ).
  • Maizels N , GrayLT . The G4 genome . PLoS Genet.9 ( 4 ), e1003468 ( 2013 ).
  • Huppert J L , BugautA , KumariS , BalasubramanianS . G-quadruplexes: the beginning and end of UTRs . Nucleic Acids Res.36 ( 19 ), 6260 – 6268 ( 2008 ).
  • Simone R , FrattaP , NeidleS , ParkinsonGN , IsaacsAM . G-quadruplexes: emerging roles in neurodegenerative diseases and the non-coding transcriptome . FEBS Lett.589 ( 14 ), 1653 – 1668 ( 2015 ).
  • De S , MichorF . DNA secondary structures and epigenetic determinants of cancer genome evolution . Nat. Struct. Mol. Biol.18 ( 8 ), 950 – 955 ( 2011 ).
  • Mankodi A , LogigianE , CallahanLet al. Myotonic dystrophy in transgenic mice expressing an expanded CUG repeat . Science289 ( 5485 ), 1769 – 1773 ( 2000 ).
  • Dansithong W , WolfCM , SarkarPet al. Cytoplasmic CUG RNA foci are insufficient to elicit key DM1 features . PLoS ONE3 ( 12 ), e3968 ( 2008 ).
  • Brouwer JR , HuguetA , NicoleA , MunnichA , GourdonG . Transcriptionally repressive chromatin remodelling and CpG methylation in the presence of expanded CTG-repeats at the DM1 Locus . J. Nucleic Acids2013 , 567435 ( 2013 ).
  • Seznec H , Lia-BaldiniAS , DurosCet al. Transgenic mice carrying large human genomic sequences with expanded CTG repeat mimic closely the DM CTG repeat intergenerational and somatic instability . Hum. Mol. Genet.9 ( 8 ), 1185 – 1194 ( 2000 ).
  • Brock G J , AndersonNH , MoncktonDG . Cis-acting modifiers of expanded CAG/CTG triplet repeat expandability: associations with flanking GC content and proximity to CpG islands . Hum. Mol. Genet.8 ( 6 ), 1061 – 1067 ( 1999 ).
  • Lam LT , PhamYC , NguyenTM , MorrisGE . Characterization of a monoclonal antibody panel shows that the myotonic dystrophy protein kinase, DMPK, is expressed almost exclusively in muscle and heart . Hum. Mol. Genet.9 ( 14 ), 2167 – 2173 ( 2000 ).