Destabilization of the Human Epigenome: Consequences of Foreign DNA Insertions

References

• Sutter D , WestphalM , DoerflerW . Patterns of integration of viral DNA sequences in the genomes of adenovirus type 12-transformed hamster cells . Cell14 , 569 – 585 ( 1978 ).
   PubMed Web of Science ®Google Scholar
• Doerfler W , GahlmannR , StabelSet al. On the mechanism of recombination between adenoviral and cellular DNAs: the structure of junction sites . Curr. Top. Microbiol. Immunol.109 , 193 – 228 ( 1983 ).
   Web of Science ®Google Scholar
• Hochstein N , MuiznieksI , MangelL , BrondkeH , DoerflerW . The epigenetic status of an adenovirus transgenome upon long-term cultivation in hamster cells . J. Virol.81 , 5349 – 5361 ( 2007 ).
   PubMed Web of Science ®Google Scholar
• Doerfler W . DNA methylation and gene activity . Ann. Rev. Biochem.52 , 93 – 124 ( 1983 ).
   PubMed Web of Science ®Google Scholar
• Heller H , KämmerC , WilgenbusP , DoerflerW . Chromosomal insertion of foreign (adenovirus type 12, plasmid, or bacteriophage lambda) DNA is associated with enhanced methylation of cellular DNA segments . Proc. Natl Acad. Sci. USA92 , 5515 – 5519 ( 1995 ).
   PubMed Web of Science ®Google Scholar
• Remus R , KämmerC , HellerH , SchmitzB , SchellG , DoerflerW . Insertion of foreign DNA into an established mammalian genome can alter the methylation of cellular DNA sequences . J. Virol.73 , 1010 – 1022 ( 1999 ).
   PubMed Web of Science ®Google Scholar
• Müller K , HellerH , DoerflerW . Foreign DNA integration. Genome-wide perturbations of methylation and transcription in the recipient genomes . J. Biol. Chem.276 , 14271 – 14278 ( 2001 ).
   PubMed Web of Science ®Google Scholar
• Doerfler W . A new concept in (adenoviral) oncogenesis: integration of foreign DNA and its consequences . BBA Rev. Cancer1288 , F79 – F99 ( 1996 ).
   PubMed Web of Science ®Google Scholar
• Doerfler W . Epigenetic consequences of foreign DNA integration: Global alterations of methylation and transcription patterns in recipient genomes . Rev. Med. Virol.21 , 336 – 346 ( 2011 ).
   PubMedGoogle Scholar
• Doerfler W . The impact of foreign DNA integration on tumor biology and evolution via epigenetic alterations . Epigenomics4 , 41 – 49 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Grafodatskaya D , ChoufaniS , FerreiraJCet al. EBV transformation and cell culturing destabilizes DNA methylation in human lymphoblastoid cell lines . Genomics95 , 73 – 83 ( 2010 ).
   PubMed Web of Science ®Google Scholar
• Birdwell CE , QueenKI , KilgorePCet al. Genome-wide DNA methylation as an epigenetic consequence of Epstein–Barr virus infection of immortalized keratinocytes . J. Virol.88 , 11442 – 11458 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Soto-Girón MJ , Garcia-VallejoF . Changes in the topology of gene expression networks by human immunodeficiency virus type 1 (HIV-1) integration in macrophages . Virus Res.163 , 91 – 97 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Doi A , ParkIH , WenBet al. Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts . Nat. Genet.41 , 1350 – 1353 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Naumann A , HochsteinN , WeberS , FanningE , DoerflerW . A distinct DNA methylation boundary in the 5′-upstream sequence of the FMR1 promoter binds nuclear proteins and is lost in fragile X syndrome . Am. J. Hum. Genet.85 , 606 – 616 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Naumann A , KrausC , HoogeveenA , RamirezCM , DoerflerW . Stable DNA methylation boundaries and expanded trinucleotide repeats: Role of DNA insertions . J. Mol. Biol.426 , 2554 – 2566 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Brattain MG , FineWD , KhaledFM , ThompsonJ , BrattainDE . Heterogeneity of malignant cells from a human colonic carcinoma . Cancer Res.41 , 1751 – 1756 ( 1981 ).
   PubMed Web of Science ®Google Scholar
• Sambrook J , RussellDW . Molecular Cloning, 3rd Edition . Cold Spring Harbor Laboratory Press , Cold Spring Harbor, New York, NY, USA ( 2001 ).
   Google Scholar
• Minami M , PoussinK , Bre’ChotC , PaterliniP . A novel PCR technique using Alu-specific primers to identify unknown flanking sequences from the human genome . Genomics29 , 403 – 408 ( 1995 ).
   PubMed Web of Science ®Google Scholar
• Irizarry RA , HobbsB , CollinFet al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data . Biostatistics4 , 249 – 264 ( 2003 ).
   PubMed Web of Science ®Google Scholar
• Touleimat N , TostJ . Complete pipeline for Infinium® Human Methylation 450K BeadChip data processing using subset quantile normalization for accurate DNA methylation estimation . Epigenomics4 , 325 – 341 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Chen YA , LemireM , Choufaniet al. Discovery of cross-reactive probes and polymorphic CpG’s in the Illumina Infinium Human Methylation450 microarray . Epigenetics8 , 203 – 209 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Benjamin Y , HochbergY . Controlling of false discovery rate: a practical and powerful approach to multiple testing . J. R. Stat. Soc.289 , 289 – 300 ( 1995 ).
   Google Scholar
• Verkerk AJMH , PierettiM , SutcliffeSSet al. Identification of a gene (FMR-1) containing a CGG repeat coincident with a breakpoint cluster region exhibiting length variation in fragile X syndrome . Cell65 , 905 – 914 ( 1991 ).
   PubMed Web of Science ®Google Scholar
• McMahon M , ContrerasA , RuggeroD . Small RNAs with big implications: new insights into H/ACA snoRNA function and their role in human disease . Wiley Interdiscip. Rev. RNA6 , 173 – 189 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Jähner D , JaenischR . Retrovirus-induced de novo methylation of flanking host sequences correlaes with gene inactivation . Nature315 , 594 – 597 ( 1985 ).
   PubMed Web of Science ®Google Scholar
• Lichtenberg U , ZockC , DoerflerW . Integration of foreign DNA into mammalian genome can be associated with hypo-methylation at site of insertion . Virus Res.11 , 335 – 342 ( 1988 ).
   PubMed Web of Science ®Google Scholar
• Akhtar W , de JongJ , PindyurinAVet al. Chromatin position effects assayed by thousands of reporters integrated in parallel . Cell154 , 914 – 927 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• The ENCODE Project Consortium . An integrated encyclopedia of DNA elements in the human genome . Nature489 , 57 – 74 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• FANTOM Consortium and the RIKEN PMI and CLST (DGT) . A promoter-level mammalian expression atlas . Nature507 , 462 – 470 ( 2014 ).
   PubMed Web of Science ®Google Scholar