5,783
Views
0
CrossRef citations to date
0
Altmetric
Special Report

Disruption of the 3D Cancer Genome Blueprint

&
Pages 47-55 | Received 01 Sep 2016, Accepted 24 Oct 2016, Published online: 12 Dec 2016

References

  • Dekker J , MirnyL . The 3D Genome as moderator of chromosomal communication . Cell164 ( 6 ), 1110 – 1121 ( 2016 ).
  • Dekker J , RippeK , DekkerM , KlecknerN . Capturing chromosome conformation . Science295 ( 5558 ), 1306 – 1311 ( 2002 ).
  • Zhao Z , TavoosidanaG , SjolinderMet al. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions . Nat. Genet.38 ( 11 ), 1341 – 1347 ( 2006 ).
  • Simonis M , KlousP , SplinterEet al. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C) . Nat. Genet.38 ( 11 ), 1348 – 1354 ( 2006 ).
  • Dostie J , RichmondTA , ArnaoutRAet al. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements . Genome Res.16 ( 10 ), 1299 – 1309 ( 2006 ).
  • Gheldof N , SmithEM , TabuchiTMet al. Cell-type-specific long-range looping interactions identify distant regulatory elements of the CFTR gene . Nucleic Acids Res.38 ( 13 ), 4325 – 4336 ( 2010 ).
  • Sanyal A , LajoieBR , JainG , DekkerJ . The long-range interaction landscape of gene promoters . Nature489 ( 7414 ), 109 – 113 ( 2012 ).
  • Lieberman-Aiden E , Van BerkumNL , WilliamsLet al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome . Science326 ( 5950 ), 289 – 293 ( 2009 ).
  • Fullwood MJ , LiuMH , PanYFet al. An oestrogen-receptor-alpha-bound human chromatin interactome . Nature462 ( 7269 ), 58 – 64 ( 2009 ).
  • Dixon JR , SelvarajS , YueFet al. Topological domains in mammalian genomes identified by analysis of chromatin interactions . Nature485 ( 7398 ), 376 – 380 ( 2012 ).
  • Nora EP , LajoieBR , SchulzEGet al. Spatial partitioning of the regulatory landscape of the X-inactivation centre . Nature485 ( 7398 ), 381 – 385 ( 2012 ).
  • Zhang Y , MccordRP , HoYJet al. Spatial organization of the mouse genome and its role in recurrent chromosomal translocations . Cell148 ( 5 ), 908 – 921 ( 2012 ).
  • Dixon JR , JungI , SelvarajSet al. Chromatin architecture reorganization during stem cell differentiation . Nature518 ( 7539 ), 331 – 336 ( 2015 ).
  • Smith EM , LajoieBR , JainG , DekkerJ . Invariant TAD boundaries constrain cell-type-specific looping interactions between promoters and distal elements around the CFTR locus . Am. J. Hum. Genet.98 ( 1 ), 185 – 201 ( 2016 ).
  • Phillips-Cremins JE , SauriaME , SanyalAet al. Architectural protein subclasses shape 3D organization of genomes during lineage commitment . Cell153 ( 6 ), 1281 – 1295 ( 2013 ).
  • Beagan JA , GilgenastTG , KimJet al. Local genome topology can exhibit an incompletely rewired 3D-folding state during somatic cell reprogramming . Cell Stem Cell18 ( 5 ), 611 – 624 ( 2016 ).
  • Krijger PH , Di StefanoB , De WitEet al. Cell-of-origin-specific 3D genome structure acquired during somatic cell reprogramming . Cell Stem Cell18 ( 5 ), 597 – 610 ( 2016 ).
  • Ong CT , CorcesVG . CTCF: an architectural protein bridging genome topology and function . Nat. Rev. Genet.15 ( 4 ), 234 – 246 ( 2014 ).
  • Nichols MH , CorcesVG . A CTCF code for 3D genome architecture . Cell162 ( 4 ), 703 – 705 ( 2015 ).
  • Li Y , HuangW , NiuL , UmbachDM , CovoS , LiL . Characterization of constitutive CTCF/cohesin loci: a possible role in establishing topological domains in mammalian genomes . BMC Genomics14 , 553 ( 2013 ).
  • Rao SS , HuntleyMH , DurandNCet al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping . Cell159 ( 7 ), 1665 – 1680 ( 2014 ).
  • Splinter E , HeathH , KoorenJet al. CTCF mediates long-range chromatin looping and local histone modification in the beta-globin locus . Genes. Dev.20 ( 17 ), 2349 – 2354 ( 2006 ).
  • Dowen JM , FanZP , HniszDet al. Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes . Cell159 ( 2 ), 374 – 387 ( 2014 ).
  • Narendra V , RochaPP , AnDet al. CTCF establishes discrete functional chromatin domains at the Hox clusters during differentiation . Science347 ( 6225 ), 1017 – 1021 ( 2015 ).
  • Guo Y , XuQ , CanzioDet al. CRISPR inversion of CTCF sites alters genome topology and enhancer/promoter function . Cell162 ( 4 ), 900 – 910 ( 2015 ).
  • De Wit E , VosES , HolwerdaSJet al. CTCF binding polarity determines chromatin looping . Mol. Cell60 ( 4 ), 676 – 684 ( 2015 ).
  • Sanborn AL , RaoSS , HuangSCet al. Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes . Proc. Natl Acad. Sci. USA112 ( 47 ), E6456 – 6465 ( 2015 ).
  • Tsujimura T , KleinFA , LangenfeldK , GlaserJ , HuberW , SpitzF . A discrete transition zone organizes the topological and regulatory autonomy of the adjacent tfap2c and bmp7 genes . PLoS Genet.11 ( 1 ), e1004897 ( 2015 ).
  • Giorgio E , RobyrD , SpielmannMet al. A large genomic deletion leads to enhancer adoption by the lamin B1 gene: a second path to autosomal dominant adult-onset demyelinating leukodystrophy (ADLD) . Hum. Mol. Gen.24 ( 11 ), 3143 – 3154 ( 2015 ).
  • Symmons O , UsluVV , TsujimuraTet al. Functional and topological characteristics of mammalian regulatory domains . Genome Res.24 ( 3 ), 390 – 400 ( 2014 ).
  • Lupianez DG , KraftK , HeinrichVet al. Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions . Cell161 ( 5 ), 1012 – 1025 ( 2015 ).
  • Franke M , IbrahimDM , AndreyGet al. Formation of new chromatin domains determines pathogenicity of genomic duplications . Nature538 ( 7624 ), 265 – 269 ( 2016 ).
  • Katainen R , DaveK , PitkanenEet al. CTCF/cohesin-binding sites are frequently mutated in cancer . Nat. Genet.47 ( 7 ), 818 – 821 ( 2015 ).
  • Lawrence MS , StojanovP , MermelCHet al. Discovery and saturation analysis of cancer genes across 21 tumour types . Nature505 ( 7484 ), 495 – 501 ( 2014 ).
  • Kaiser VB , TaylorMS , SempleCA . Mutational Biases Drive Elevated Rates of Substitution at Regulatory Sites across Cancer Types . PLoS Genet.12 ( 8 ), e1006207 ( 2016 ).
  • Hnisz D , WeintraubAS , DayDSet al. Activation of proto-oncogenes by disruption of chromosome neighborhoods . Science351 ( 6280 ), 1454 – 1458 ( 2016 ).
  • Phillips JE , CorcesVG . CTCF: master weaver of the genome . Cell137 ( 7 ), 1194 – 1211 ( 2009 ).
  • Wang H , MauranoMT , QuHet al. Widespread plasticity in CTCF occupancy linked to DNA methylation . Genome Res.22 ( 9 ), 1680 – 1688 ( 2012 ).
  • Filippova GN , FagerlieS , KlenovaEMet al. An exceptionally conserved transcriptional repressor, CTCF, employs different combinations of zinc fingers to bind diverged promoter sequences of avian and mammalian c-myc oncogenes . Mol. Cell. Biol.16 ( 6 ), 2802 – 2813 ( 1996 ).
  • Maurano MT , WangH , JohnSet al. Role of DNA methylation in modulating transcription factor occupancy . Cell Rep.12 ( 7 ), 1184 – 1195 ( 2015 ).
  • Flavahan WA , DrierY , LiauBBet al. Insulator dysfunction and oncogene activation in IDH mutant gliomas . Nature529 ( 7584 ), 110 – 114 ( 2016 ).
  • Pomerantz MM , AhmadiyehN , JiaLet al. The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer . Nat. Genet.41 ( 8 ), 882 – 884 ( 2009 ).
  • Sotelo J , EspositoD , DuhagonMAet al. Long-range enhancers on 8q24 regulate c-Myc . Proc. Natl Acad. Sci. USA107 ( 7 ), 3001 – 3005 ( 2010 ).
  • Wright JB , BrownSJ , ColeMD . Upregulation of c-MYC in cis through a large chromatin loop linked to a cancer risk-associated single-nucleotide polymorphism in colorectal cancer cells . Mol. Cell Biol.30 ( 6 ), 1411 – 1420 ( 2010 ).
  • Ahmadiyeh N , PomerantzMM , GrisanzioCet al. 8q24 prostate, breast, and colon cancer risk loci show tissue-specific long-range interaction with MYC . Proc. Natl Acad. Sci. USA107 ( 21 ), 9742 – 9746 ( 2010 ).
  • Rickman DS , SoongTD , MossBet al. Oncogene-mediated alterations in chromatin conformation . Proc. Natl Acad. Sci. USA109 ( 23 ), 9083 – 9088 ( 2012 ).
  • Rousseau M , FerraiuoloMA , CrutchleyJLet al. Classifying leukemia types with chromatin conformation data . Genome Biol.15 ( 4 ), R60 ( 2014 ).
  • Dryden NH , BroomeLR , DudbridgeFet al. Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-C . Genome Res.24 ( 11 ), 1854 – 1868 ( 2014 ).
  • Du M , TillmansL , GaoJet al. Chromatin interactions and candidate genes at ten prostate cancer risk loci . Sci. Rep.6 , 23202 ( 2016 ).
  • Jager R , MiglioriniG , HenrionMet al. Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci . Nat. Commun.6 , 6178 ( 2015 ).
  • Groschel S , SandersMA , HoogenboezemRet al. A single oncogenic enhancer rearrangement causes concomitant EVI1 and GATA2 deregulation in leukemia . Cell157 ( 2 ), 369 – 381 ( 2014 ).
  • Walker BA , WardellCP , BrioliAet al. Translocations at 8q24 juxtapose MYC with genes that harbor superenhancers resulting in overexpression and poor prognosis in myeloma patients . Blood Cancer J.4 , e191 ( 2014 ).
  • Taberlay PC , Achinger-KaweckaJ , LunATet al. Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations . Genome Res.26 ( 6 ), 719 – 731 ( 2016 ).
  • Frigola J , SongJ , StirzakerC , HinshelwoodRA , PeinadoMA , ClarkSJ . Epigenetic remodeling in colorectal cancer results in coordinate gene suppression across an entire chromosome band . Nat. Genet.38 ( 5 ), 540 – 549 ( 2006 ).
  • Stransky N , VallotC , ReyalFet al. Regional copy number-independent deregulation of transcription in cancer . Nat. Genet.38 ( 12 ), 1386 – 1396 ( 2006 ).
  • Hitchins MP , LinVA , BuckleAet al. Epigenetic inactivation of a cluster of genes flanking MLH1 in microsatellite-unstable colorectal cancer . Cancer Res.67 ( 19 ), 9107 – 9116 ( 2007 ).
  • Novak P , JensenT , OshiroMM , WattsGS , KimCJ , FutscherBW . Agglomerative epigenetic aberrations are a common event in human breast cancer . Cancer Res.68 ( 20 ), 8616 – 8625 ( 2008 ).
  • Seng TJ , CurreyN , CooperWAet al. DLEC1 and MLH1 promoter methylation are associated with poor prognosis in non-small cell lung carcinoma . Br. J. Cancer99 ( 2 ), 375 – 382 ( 2008 ).
  • Dallosso AR , HancockAL , SzemesMet al. Frequent long-range epigenetic silencing of protocadherin gene clusters on chromosome 5q31 in Wilms’ tumor . PLoS Genet.5 ( 11 ), e1000745 ( 2009 ).
  • Rafique S , ThomasJS , SproulD , BickmoreWA . Estrogen-induced chromatin decondensation and nuclear re-organization linked to regional epigenetic regulation in breast cancer . Genome Biol.16 , 145 ( 2015 ).
  • Bert SA , RobinsonMD , StrbenacDet al. Regional activation of the cancer genome by long-range epigenetic remodeling . Cancer Cell23 ( 1 ), 9 – 22 ( 2013 ).
  • Coolen MW , StirzakerC , SongJZet al. Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity . Nat. Cell Biol.12 ( 3 ), 235 – 246 ( 2010 ).
  • Barutcu AR , LajoieBR , MccordRPet al. Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells . Genome Biol.16 , 214 ( 2015 ).
  • Rondo: Visual Analytics of Chromosome Structure . www.rondo.ws .