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Review

In Junk We Trust: Repetitive Dna, Epigenetics and Facioscapulohumeral Muscular Dystrophy

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Pages 271-287 | Published online: 14 Apr 2010

Bibliography

  • Taft RJ , PheasantM, MattickJS: The relationship between non-protein-coding DNA and eukaryotic complexity.Bioessays29 , 288–299 (2007).
  • Siepel A , BejeranoG, PedersenJSet al.: Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.Genome Res.15 , 1034–1050 (2005).
  • Carninci P , KasukawaT, KatayamaSet al.: The transcriptional landscape of the mammalian genome.Science309 , 1559–1563 (2005).
  • Kapranov P , ChengJ, DikeSet al.: RNA maps reveal new RNA classes and a possible function for pervasive transcription.Science316 , 1484–1488 (2007).
  • Wang ET , SandbergR, LuoSet al.: Alternative isoform regulation in human tissue transcriptomes.Nature456 , 470–476 (2008).
  • Pan Q , ShaiO, LeeLJ, FreyBJ, BlencoweBJ: Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing.Nat. Genet.40 , 1413–1415 (2008).
  • Prasanth KV , SpectorDL: Eukaryotic regulatory RNAs: an answer to the ‘genome complexity‘ conundrum.Genes Dev.21 , 11–42 (2007).
  • Kurokawa R , RosenfeldMG, GlassCK: Transcriptional regulation through noncoding RNAs and epigenetic modifications.RNA Biol.6 , 233–236 (2009).
  • Mattick JS , AmaralPP, DingerME, MercerTR, MehlerMF: RNA regulation of epigenetic processes.Bioessays31 , 51–59 (2009).
  • Faulkner GJ , CarninciP: Altruistic functions for selfish DNA.Cell Cycle8 , 2895–2900 (2009).
  • Taft RJ , PangKC, MercerTR, DingerM, MattickJS: Non-coding RNAs: regulators of disease.J. Pathol.220(2) , 126–139 (2009).
  • Pandya S , KingWM, TawilR: Facioscapulohumeral dystrophy.Phys. Ther.88 , 105–113 (2008).
  • Shahrizaila N , WillsAJ: Significance of Beevor‘s sign in facioscapulohumeral dystrophy and other neuromuscular diseases.J. Neurol. Neurosurg. Psychiatry76 , 869–870 (2005).
  • van der Maarel SM , FrantsRR, PadbergGW: Facioscapulohumeral muscular dystrophy.Biochim. Biophys. Acta1772 , 186–194 (2007).
  • Tupler R , GabelliniD: Molecular basis of facioscapulohumeral muscular dystrophy.Cell. Mol. Life Sci.61 , 557–566 (2004).
  • Tonini MM , Passos-BuenoMR, CerqueiraA, MatioliSR, PavanelloR, ZatzM: Asymptomatic carriers and gender differences in facioscapulohumeral muscular dystrophy (FSHD).Neuromuscul. Disord.14 , 33–38 (2004).
  • Winokur ST , BarrettK, MartinJHet al.: Facioscapulohumeral muscular dystrophy (FSHD) myoblasts demonstrate increased susceptibility to oxidative stress.Neuromuscul. Disord.13 , 322–333 (2003).
  • Barro M , CarnacG, FlavierS, MercierJ, VassetzkyY, Laoudj-ChenivesseD: Myoblasts from affected and non affected FSHD muscles exhibit morphological differentiation defects.J. Cell. Mol. Med. (2008) (Epub ahead of print).
  • Trevisan CP , PastorelloE, TomelleriGet al.: Facioscapulohumeral muscular dystrophy: hearing loss and other atypical features of patients with large 4q35 deletions.Eur. J. Neurol.15 , 1353–1358 (2008).
  • Tawil R , Van Der Maarel SM: Facioscapulohumeral muscular dystrophy. Muscle Nerve34 , 1–15 (2006).
  • Trevisan CP , PastorelloE, ArmaniMet al.: Facioscapulohumeral muscular dystrophy and occurrence of heart arrhythmia.Eur. Neurol.56 , 1–5 (2006).
  • Galetta F , FranzoniF, SpositoRet al.: Subclinical cardiac involvement in patients with facioscapulohumeral muscular dystrophy.Neuromuscul. Disord.15 , 403–408 (2005).
  • Wohlgemuth M , van der Kooi EL, van Kesteren RG, van der Maarel SM, Padberg GW: Ventilatory support in facioscapulohumeral muscular dystrophy. Neurology63 , 176–178 (2004).
  • Jensen MP , HoffmanAJ, StoelbBL, AbreschRT, CarterGT, McDonaldCM: Chronic pain in persons with myotonic dystrophy and facioscapulohumeral dystrophy.Arch. Phys. Med. Rehabil.89 , 320–328 (2008).
  • Padua L , AprileI, FruscianteRet al.: Quality of life and pain in patients with facioscapulohumeral muscular dystrophy.Muscle Nerve40 , 200–205 (2009).
  • de Greef JC , FrantsRR, van der Maarel SM: Epigenetic mechanisms of facioscapulohumeral muscular dystrophy. Mutat. Res.647 , 94–102 (2008).
  • Rossi M , RicciE, ColantoniLet al.: The facioscapulohumeral muscular dystrophy region on 4qter and the homologous locus on 10qter evolved independently under different evolutionary pressure.BMC Med. Genet.8 , 8 (2007).
  • Thomas NS , WisemanK, SpurlockG, MacDonaldM, UstekD, UpadhyayaM: A large patient study confirming that facioscapulohumeral muscular dystrophy (FSHD) disease expression is almost exclusively associated with an FSHD locus located on a 4qA-defined 4qter subtelomere.J. Med. Genet.44 , 215–218 (2007).
  • Lemmers RJ , WohlgemuthM, van der Gaag KJ et al.: Specific sequence variations within the 4q35 region are associated with facioscapulohumeral muscular dystrophy. Am. J. Hum. Genet.81 , 884–894 (2007).
  • Lemmers RJ , WohlgemuthM, FrantsRR, PadbergGW, MoravaE, van der Maarel SM: Contractions of D4Z4 on 4qB subtelomeres do not cause facioscapulohumeral muscular dystrophy. Am. J. Hum. Genet.75 , 1124–1130 (2004).
  • Arashiro P , EisenbergI, KhoATet al.: Transcriptional regulation differs in affected facioscapulohumeral muscular dystrophy patients compared with asymptomatic related carriers.Proc. Natl Acad. Sci. USA106 , 6220–6225 (2009).
  • Bastress KL , StajichJM, SpeerMC, GilbertJR: The genes encoding for D4Z4-binding proteins HMGB2, YY1, NCL and MYOD1 are excluded as candidate genes for FSHD1B.Neuromuscul. Disord.15 , 316–320 (2005).
  • Tsumagari K , QiL, JacksonKet al.: Epigenetics of a tandem DNA repeat: chromatin DNaseI sensitivity and opposite methylation changes in cancers.Nucleic Acids Res.36 , 2196–2207 (2008).
  • Jabbari K , BernardiG: Cytosine methylation and CpG, TpG (CpA) and TpA frequencies.Gene333 , 143–149 (2004).
  • Caiafa P , ZampieriM: DNA methylation and chromatin structure: the puzzling CpG islands.J. Cell. Biochem.94 , 257–265 (2005).
  • Simons C , PheasantM, MakuninIV, MattickJS: Transposon-free regions in mammalian genomes.Genome Res.16 , 164–172 (2006).
  • Clapp J , MitchellLM, BollandDJet al.: Evolutionary conservation of a coding function for D4Z4, the tandem DNA repeat mutated in facioscapulohumeral muscular dystrophy.Am. J. Hum. Genet.81 , 264–279 (2007).
  • de Greef JC , LemmersRJ, van Engelen BG et al.: Common epigenetic changes of D4Z4 in contraction-dependent and contraction-independent FSHD. Hum. Mutat.30 , 1449–1459 (2009).
  • van Overveld PG , EnthovenL, RicciEet al.: Variable hypomethylation of D4Z4 in facioscapulohumeral muscular dystrophy.Ann. Neurol.58 , 569–576 (2005).
  • de Greef JC , WohlgemuthM, ChanOAet al.: Hypomethylation is restricted to the D4Z4 repeat array in phenotypic FSHD.Neurology69 , 1018–1026 (2007).
  • Kim JD , HinzAK, BergmannAet al.: Identification of clustered YY1 binding sites in imprinting control regions.Genome Res.16 , 901–911 (2006).
  • Ottaviani A , Rival-GervierS, BoussouarAet al.: The D4Z4 macrosatellite repeat acts as a CTCF and A-type lamins-dependent insulator in facio-scapulo-humeral dystrophy.PLoS Genet.5 , E1000394 (2009).
  • Ottaviani A , Schluth-BolardC, Rival-GervierSet al.: Identification of a perinuclear positioning element in human subtelomeres that requires A-type lamins and CTCF.EMBO J.28 , 2428–2436 (2009).
  • Sasai N , DefossezPA: Many paths to one goal? The proteins that recognize methylated DNA in eukaryotes.Int. J. Dev. Biol.53 , 323–334 (2009).
  • Taverna SD , LiH, RuthenburgAJ, AllisCD, PatelDJ: How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers.Nat. Struct. Mol. Biol.14 , 1025–1040 (2007).
  • Latham JA , DentSY: Cross-regulation of histone modifications.Nat. Struct. Mol. Biol.14 , 1017–1024 (2007).
  • Sims RJ 3rd, Reinberg D: Is there a code embedded in proteins that is based on post-translational modifications? Nat. Rev. Mol. Cell Biol.9 , 815–820 (2008).
  • Bodega B , RamirezGD, GrasserFet al.: Remodeling of the chromatin structure of the facioscapulohumeral muscular dystrophy (FSHD) locus and upregulation of FSHD-related gene 1 (FRG1) expression during human myogenic differentiation.BMC Biol.7 , 41 (2009).
  • Zeng W , de Greef JC, Chen YY et al.: Specific loss of histone H3 lysine 9 trimethylation and HP1γ/cohesin binding at D4Z4 repeats is associated with facioscapulohumeral dystrophy (FSHD). PLoS Genet.5 , E1000559 (2009).
  • Kwon SH , WorkmanJL: The heterochromatin protein 1 (HP1) family: put away a bias toward HP1.Mol. Cells26 , 217–227 (2008).
  • Fanti L , PimpinelliS: HP1: a functionally multifaceted protein.Curr. Opin. Genet. Dev.18 , 169–174 (2008).
  • Dorsett D : Roles of the sister chromatid cohesion apparatus in gene expression, development, and human syndromes.Chromosoma116 , 1–13 (2007).
  • Parelho V , HadjurS, SpivakovMet al.: Cohesins functionally associate with CTCF on mammalian chromosome arms.Cell132 , 422–433 (2008).
  • Hadjur S , WilliamsLM, RyanNKet al.: Cohesins form chromosomal cis-interactions at the developmentally regulated IFNG locus.Nature460 , 410–413 (2009).
  • Gabellini D , GreenMR, TuplerR: When enough is enough: genetic diseases associated with transcriptional derepression.Curr. Opin. Genet. Dev.14 , 301–307 (2004).
  • Ko CY , HsuHC, ShenMR, ChangWC, WangJM: Epigenetic silencing of CCAAT/enhancer-binding protein d activity by YY1/polycomb group/DNA methyltransferase complex.J. Biol. Chem.283 , 30919–30932 (2008).
  • Wu S , HuYC, LiuH, ShiY: Loss of YY1 impacts the heterochromatic state and meiotic double-strand breaks during mouse spermatogenesis.Mol. Cell. Biol.29 , 6245–6256 (2009).
  • Kosak ST , GroudineM: Gene order and dynamic domains.Science306 , 644–647 (2004).
  • Kosak ST , GroudineM: Form follows function: the genomic organization of cellular differentiation.Genes Dev.18 , 1371–1384 (2004).
  • Fedorova E , ZinkD: Nuclear architecture and gene regulation.Biochim. Biophys. Acta1783 , 2174–2184 (2008).
  • Rajapakse I , PerlmanMD, ScalzoD, KooperbergC, GroudineM, KosakST: The emergence of lineage-specific chromosomal topologies from coordinate gene regulation.Proc. Natl Acad. Sci. USA106 , 6679–6684 (2009).
  • Tam R , SmithKP, LawrenceJB: The 4q subtelomere harboring the FSHD locus is specifically anchored with peripheral heterochromatin unlike most human telomeres.J. Cell Biol.167 , 269–279 (2004).
  • Masny PS , BengtssonU, ChungSAet al.: Localization of 4q35.2 to the nuclear periphery: is FSHD a nuclear envelope disease?Hum. Mol. Genet.13 , 1857–1871 (2004).
  • Worman HJ , FongLG, MuchirA, YoungSG: Laminopathies and the long strange trip from basic cell biology to therapy.J. Clin. Invest.119 , 1825–1836 (2009).
  • Gaszner M , FelsenfeldG: Insulators: exploiting transcriptional and epigenetic mechanisms.Nat. Rev. Genet.7 , 703–713 (2006).
  • Filippova GN : Genetics and epigenetics of the multifunctional protein CTCF.Curr. Top. Dev. Biol.80 , 337–360 (2008).
  • Pombo A , BrancoMR: Functional organisation of the genome during interphase.Curr. Opin. Genet. Dev.17 , 451–455 (2007).
  • Goetze S , Mateos-LangerakJ, van Driel R: Three-dimensional genome organization in interphase and its relation to genome function. Semin. Cell Dev. Biol.18 , 707–714 (2007).
  • Lieberman-Aiden E , van Berkum NL, Williams L et al.: Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science326 , 289–293 (2009).
  • Petrov A , AllinneJ, PirozhkovaI, LaoudjD, LipinskiM, VassetzkyYS: A nuclear matrix attachment site in the 4q35 locus has an enhancer-blocking activity in vivo: implications for the facio-scapulo-humeral dystrophy.Genome Res.18 , 39–45 (2008).
  • Pirozhkova I , PetrovA, DmitrievP, LaoudjD, LipinskiM, VassetzkyY: A functional role for 4qA/B in the structural rearrangement of the 4q35 region and in the regulation of FRG1 and ANT1 in facioscapulohumeral dystrophy.PLoS ONE3 , E3389 (2008).
  • Petrov A , PirozhkovaI, CarnacG, LaoudjD, LipinskiM, VassetzkyYS: Chromatin loop domain organization within the 4q35 locus in facioscapulohumeral dystrophy patients versus normal human myoblasts.Proc. Natl Acad. Sci. USA103 , 6982–6987 (2006).
  • Xu X , TsumagariK, SowdenJet al.: DNaseI hypersensitivity at gene-poor, FSH dystrophy-linked 4q35.2.Nucleic Acids Res.37(22) , 7381–7393 (2009).
  • Hanel ML , WuebblesRD, JonesPL: Muscular dystrophy candidate gene FRG1 is critical for muscle development.Dev. Dyn.238 , 1502–1512 (2009).
  • van Koningsbruggen S , DirksRW, MommaasAMet al.: FRG1P is localised in the nucleolus, Cajal bodies, and speckles.J. Med. Genet.41 , E46 (2004).
  • Bessonov S , AnokhinaM, WillCL, UrlaubH, LuhrmannR: Isolation of an active step I spliceosome and composition of its RNP core.Nature452 , 846–850 (2008).
  • van Koningsbruggen S , StraasheijmKR, SterrenburgEet al.: FRG1P-mediated aggregation of proteins involved in pre-mRNA processing.Chromosoma116 , 53–64 (2007).
  • Chari A , PakniaE, FischerU: The role of RNP biogenesis in spinal muscular atrophy.Curr. Opin. Cell Biol.21 , 387–393 (2009).
  • Abu-Baker A , RouleauGA: Oculopharyngeal muscular dystrophy: recent advances in the understanding of the molecular pathogenic mechanisms and treatment strategies.Biochim. Biophys. Acta1772 , 173–185 (2007).
  • Gabellini D , D‘AntonaG, MoggioMet al.: Facioscapulohumeral muscular dystrophy in mice overexpressing FRG1.Nature439 , 973–977 (2006).
  • Davidovic L , SacconiS, BecharaEGet al.: Alteration of expression of muscle specific isoforms of the fragile X related protein 1 (FXR1P) in facioscapulohumeral muscular dystrophy patients.J. Med. Genet.45 , 679–685 (2008).
  • Wuebbles RD , HanelML, JonesPL: FSHD region gene 1 (FRG1) is crucial for angiogenesis linking FRG1 to facioscapulohumeral muscular dystrophy-associated vasculopathy.Dis. Model. Mech.2 , 267–274 (2009).
  • Lemmers RJ , OsbornM, HaafTet al.: D4F104S1 deletion in facioscapulohumeral muscular dystrophy: phenotype, size, and detection.Neurology61 , 178–183 (2003).
  • Winokur ST , BarrettK, MartinJHet al.: Facioscapulohumeral muscular dystrophy (FSHD) myoblasts demonstrate increased susceptibility to oxidative stress.Neuromuscul. Disord.13 , 322–333 (2003).
  • Jiang G , YangF, van Overveld PG, Vedanarayanan V, van der Maarel S, Ehrlich M: Testing the position-effect variegation hypothesis for facioscapulohumeral muscular dystrophy by analysis of histone modification and gene expression in subtelomeric 4q. Hum. Mol. Genet.12 , 2909–2921 (2003).
  • Masny PS , ChanOY, de Greef JC et al.: Analysis of allele-specific RNA transcription in FSHD by RNA-DNA FISH in single myonuclei. Eur. J. Hum. Genet.18(4) , 448–456 (2010).
  • Klooster R , StraasheijmK, ShahBet al.: Comprehensive expression analysis of FSHD candidate genes at the mRNA and protein level.Eur. J. Hum. Genet.17 , 1615–1624 (2009).
  • Buckingham M , RelaixF: The role of Pax genes in the development of tissues and organs: Pax3 and Pax7 regulate muscle progenitor cell functions.Annu. Rev. Cell Dev. Biol.23 , 645–673 (2007).
  • Dixit M , AnsseauE, TassinAet al.: DUX4, a candidate gene of facioscapulohumeral muscular dystrophy, encodes a transcriptional activator of PITX1.Proc. Natl Acad. Sci. USA104 , 18157–18162 (2007).
  • Kowaljow V , MarcowyczA, AnsseauEet al.: The DUX4 gene at the FSHD1A locus encodes a pro-apoptotic protein.Neuromuscul. Disord.17 , 611–623 (2007).
  • Bosnakovski D , LambS, SimsekTet al.: DUX4c, an FSHD candidate gene, interferes with myogenic regulators and abolishes myoblast differentiation.Exp. Neurol. (2008) (Epub ahead of print).
  • Ansseau E , Laoudj-ChenivesseD, MarcowyczAet al.: DUX4c is up-regulated in FSHD. It induces the MYF5 protein and human myoblast proliferation.PLoS ONE4 , E7482 (2009).
  • Lemmers RJ , van der Maarel SM, van Deutekom JC et al.: Inter- and intrachromosomal sub-telomeric rearrangements on 4q35: implications for facioscapulohumeral muscular dystrophy (FSHD) aetiology and diagnosis. Hum. Mol. Genet.7 , 1207–1214 (1998).
  • Deak KL , LemmersRJ, StajichJMet al.: Genotype-phenotype study in an FSHD family with a proximal deletion encompassing p13E-11 and D4Z4.Neurology68 , 578–582 (2007).
  • Bosnakovski D , XuZ, GangEJet al.: An isogenetic myoblast expression screen identifies DUX4-mediated FSHD-associated molecular pathologies.EMBO J.27 , 2766–2779 (2008).
  • Bosnakovski D , DaughtersRS, XuZ, SlackJM, KybaM: Biphasic myopathic phenotype of mouse DUX, an ORF within conserved FSHD-related repeats.PLoS ONE4 , E7003 (2009).
  • Rowat AC , LammerdingJ, HerrmannH, AebiU: Towards an integrated understanding of the structure and mechanics of the cell nucleus.Bioessays30 , 226–236 (2008).
  • Phillips JE , CorcesVG: CTCF: master weaver of the genome.Cell137 , 1194–1211 (2009).
  • Wendt KS , PetersJM: How cohesin and CTCF cooperate in regulating gene expression.Chromosome Res.17 , 201–214 (2009).
  • Cao R , ZhangY: The functions of E(Z)/EZH2-mediated methylation of lysine 27 in histone H3.Curr. Opin. Genet. Dev.14 , 155–164 (2004).

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