Peter A Jones

Summary

Affiliation: University of Southern California
Country: USA

Publications

  1. pmc Nucleosomes containing methylated DNA stabilize DNA methyltransferases 3A/3B and ensure faithful epigenetic inheritance
    Shikhar Sharma
    Department of Urology, Biochemistry, and Molecular Biology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
    PLoS Genet 7:e1001286. 2011
  2. pmc SNF5 is an essential executor of epigenetic regulation during differentiation
    Jueng Soo You
    Departments of Urology and Biochemistry and Molecular Biology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angles, California, United States of America
    PLoS Genet 9:e1003459. 2013
  3. pmc Gene reactivation by 5-aza-2'-deoxycytidine-induced demethylation requires SRCAP-mediated H2A.Z insertion to establish nucleosome depleted regions
    Xiaojing Yang
    Department of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
    PLoS Genet 8:e1002604. 2012
  4. doi request reprint Functions of DNA methylation: islands, start sites, gene bodies and beyond
    Peter A Jones
    USC Norris Comprehensive Cancer Center, Keck School of Medicine of University of Southern California, Los Angeles, California 90089 99176, USA
    Nat Rev Genet 13:484-92. 2012
  5. pmc Lysine methyltransferase G9a is not required for DNMT3A/3B anchoring to methylated nucleosomes and maintenance of DNA methylation in somatic cells
    Shikhar Sharma
    Department of Biochemistry and Molecular Biology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 9181, USA
    Epigenetics Chromatin 5:3. 2012
  6. pmc H2A.Z maintenance during mitosis reveals nucleosome shifting on mitotically silenced genes
    Theresa K Kelly
    Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
    Mol Cell 39:901-11. 2010
  7. pmc DZNep is a global histone methylation inhibitor that reactivates developmental genes not silenced by DNA methylation
    Tina Branscombe Miranda
    Department of Urology, USC Norris Comprehensive Cancer Center, University of Southern California, 1441 Eastlake Avenue, Los Angeles, CA 90033, USA
    Mol Cancer Ther 8:1579-88. 2009
  8. pmc Selective anchoring of DNA methyltransferases 3A and 3B to nucleosomes containing methylated DNA
    ShinWu Jeong
    Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center Keck School of Medicine, University of Southern California, NOR 8302L, 9181, Los Angeles, CA 90089 9181, USA
    Mol Cell Biol 29:5366-76. 2009
  9. ncbi request reprint Role of the DNA methyltransferase variant DNMT3b3 in DNA methylation
    Daniel J Weisenberger
    Urologic Cancer Research Laboratory, Department of Biochemistry and Molecular Biology, University of Southern California Norris Comprehensive Cancer Center, Keck School of Medicine, 1441 Eastlake Avenue, Los Angeles, CA 90089 9181, USA
    Mol Cancer Res 2:62-72. 2004
  10. ncbi request reprint Preferential response of cancer cells to zebularine
    Jonathan C Cheng
    USC Norris Comprehensive Cancer Center, Departments of Urology, Biochemistry, and Molecular Biology, Keck School of Medicine, University of Southern California, 1441 Eastlake Avenue, Los Angeles, CA 90089, USA
    Cancer Cell 6:151-8. 2004

Collaborators

Detail Information

Publications74

  1. pmc Nucleosomes containing methylated DNA stabilize DNA methyltransferases 3A/3B and ensure faithful epigenetic inheritance
    Shikhar Sharma
    Department of Urology, Biochemistry, and Molecular Biology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
    PLoS Genet 7:e1001286. 2011
    ....
  2. pmc SNF5 is an essential executor of epigenetic regulation during differentiation
    Jueng Soo You
    Departments of Urology and Biochemistry and Molecular Biology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angles, California, United States of America
    PLoS Genet 9:e1003459. 2013
    ..Together, we demonstrate that SNF5 executes the switch between pluripotency and differentiation...
  3. pmc Gene reactivation by 5-aza-2'-deoxycytidine-induced demethylation requires SRCAP-mediated H2A.Z insertion to establish nucleosome depleted regions
    Xiaojing Yang
    Department of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
    PLoS Genet 8:e1002604. 2012
    ..Furthermore, we elucidate that chromatin remodeling translates the demethylation ability of DNMT inhibitors to their downstream efficacies, suggesting future therapeutic implications for chromatin remodelers...
  4. doi request reprint Functions of DNA methylation: islands, start sites, gene bodies and beyond
    Peter A Jones
    USC Norris Comprehensive Cancer Center, Keck School of Medicine of University of Southern California, Los Angeles, California 90089 99176, USA
    Nat Rev Genet 13:484-92. 2012
    ..Improving our understanding of the functions of DNA methylation is necessary for interpreting changes in this mark that are observed in diseases such as cancer...
  5. pmc Lysine methyltransferase G9a is not required for DNMT3A/3B anchoring to methylated nucleosomes and maintenance of DNA methylation in somatic cells
    Shikhar Sharma
    Department of Biochemistry and Molecular Biology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 9181, USA
    Epigenetics Chromatin 5:3. 2012
    ..abstract:..
  6. pmc H2A.Z maintenance during mitosis reveals nucleosome shifting on mitotically silenced genes
    Theresa K Kelly
    Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
    Mol Cell 39:901-11. 2010
    ..These key changes provide a potential mechanism for rapid silencing and reactivation of genes during the cell cycle...
  7. pmc DZNep is a global histone methylation inhibitor that reactivates developmental genes not silenced by DNA methylation
    Tina Branscombe Miranda
    Department of Urology, USC Norris Comprehensive Cancer Center, University of Southern California, 1441 Eastlake Avenue, Los Angeles, CA 90033, USA
    Mol Cancer Ther 8:1579-88. 2009
    ..This suggests that there is a homeostatic mechanism that returns the histone modifications to their "ground state" after DZNep treatment. Our data show the strong need for further development of histone methylation inhibitors...
  8. pmc Selective anchoring of DNA methyltransferases 3A and 3B to nucleosomes containing methylated DNA
    ShinWu Jeong
    Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center Keck School of Medicine, University of Southern California, NOR 8302L, 9181, Los Angeles, CA 90089 9181, USA
    Mol Cell Biol 29:5366-76. 2009
    ..These data suggest that inheritance of DNA methylation requires cues from the chromatin component in addition to hemimethylation...
  9. ncbi request reprint Role of the DNA methyltransferase variant DNMT3b3 in DNA methylation
    Daniel J Weisenberger
    Urologic Cancer Research Laboratory, Department of Biochemistry and Molecular Biology, University of Southern California Norris Comprehensive Cancer Center, Keck School of Medicine, 1441 Eastlake Avenue, Los Angeles, CA 90089 9181, USA
    Mol Cancer Res 2:62-72. 2004
    ..Methylation analyses of immunodeficiency, chromosomal instabilities, and facial abnormalities cells revealed that an Alu repeat sequence was highly methylated, suggesting that Alu sequences are not DNMT3b targets...
  10. ncbi request reprint Preferential response of cancer cells to zebularine
    Jonathan C Cheng
    USC Norris Comprehensive Cancer Center, Departments of Urology, Biochemistry, and Molecular Biology, Keck School of Medicine, University of Southern California, 1441 Eastlake Avenue, Los Angeles, CA 90089, USA
    Cancer Cell 6:151-8. 2004
    ..Our results demonstrate that zebularine can be selective toward cancer cells and may hold clinical promise as an anticancer therapy...
  11. pmc DNA methylation screening identifies driver epigenetic events of cancer cell survival
    Daniel D De Carvalho
    Department of Urology, Biochemistry and Molecular Biology, University of Southern California Norris Comprehensive Cancer Center Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 9181, USA
    Cancer Cell 21:655-67. 2012
    ..We further showed experimentally that these genes must be silenced by DNA methylation for cancer cell survival, suggesting these are key epigenetic events associated with tumorigenesis...
  12. ncbi request reprint Role of nucleosomal occupancy in the epigenetic silencing of the MLH1 CpG island
    Joy C Lin
    Department of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
    Cancer Cell 12:432-44. 2007
    ..Activation of the promoter by demethylation with 5-aza-2'-deoxycytidine involves nucleosome eviction. Epigenetic silencing of tumor suppressor genes may involve heritable changes in nucleosome occupancy enabled by cytosine methylation...
  13. pmc Dynamic nucleosome-depleted regions at androgen receptor enhancers in the absence of ligand in prostate cancer cells
    Claudia Andreu-Vieyra
    Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
    Mol Cell Biol 31:4648-62. 2011
    ..This allows the recruitment of histone modifiers, chromatin remodelers, and ultimately gene activation. The "receptive" state described here could help explain AR signaling activation under very low ligand concentrations...
  14. pmc Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules
    Theresa K Kelly
    Department of Urology, Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
    Genome Res 22:2497-506. 2012
    ....
  15. pmc Frequent switching of Polycomb repressive marks and DNA hypermethylation in the PC3 prostate cancer cell line
    Einav Nili Gal-Yam
    Department of Urology, Biochemistry and Molecular Biology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 9181, USA
    Proc Natl Acad Sci U S A 105:12979-84. 2008
    ....
  16. pmc Distinct localization of histone H3 acetylation and H3-K4 methylation to the transcription start sites in the human genome
    Gangning Liang
    Department of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1441 Eastlake Avenue, MS 8302L, Los Angeles, CA 90089 9181
    Proc Natl Acad Sci U S A 101:7357-62. 2004
    ..Common models depicting widespread histone acetylation and K4 methylation throughout the transcribed unit do not therefore apply to the majority of human genes...
  17. doi request reprint Long-term epigenetic therapy with oral zebularine has minimal side effects and prevents intestinal tumors in mice
    Christine B Yoo
    Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, California 90033 9181, USA
    Cancer Prev Res (Phila) 1:233-40. 2008
    ..Importantly, prolonged treatment of mice with epigenetic drugs resulted in only minor developmental and histologic changes...
  18. ncbi request reprint Comparison of biological effects of non-nucleoside DNA methylation inhibitors versus 5-aza-2'-deoxycytidine
    Jody C Chuang
    USC Norris Comprehensive Cancer Center, Department of Urology, Biochemistry, and Molecular Biology, University of Southern California, 1441 Eastlake Avenue, Los Angeles, CA 90089, USA
    Mol Cancer Ther 4:1515-20. 2005
    ..We found that 5-Aza-CdR is far more effective in DNA methylation inhibition as well as in reactivating genes, compared with non-nucleoside inhibitors...
  19. ncbi request reprint Inhibition of histone deacetylation does not block resilencing of p16 after 5-aza-2'-deoxycytidine treatment
    Gerda Egger
    Department of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1441 Eastlake Avenue, Los Angeles, CA 90089, USA
    Cancer Res 67:346-53. 2007
    ..Altogether, our data provide new insights into the mechanism of epigenetic drugs and have important implications for epigenetic therapy...
  20. doi request reprint The putative tumor suppressor microRNA-101 modulates the cancer epigenome by repressing the polycomb group protein EZH2
    Jeffrey M Friedman
    Department of Urology, Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
    Cancer Res 69:2623-9. 2009
    ..We conclude that miR-101 may be a potent tumor suppressor by altering global chromatin structure through repression of EZH2...
  21. pmc Polycomb-repressed genes have permissive enhancers that initiate reprogramming
    Phillippa C Taberlay
    Department of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
    Cell 147:1283-94. 2011
    ..Genome-wide, a high percentage of Polycomb targets are associated with putative enhancers in permissive states, suggesting that they may provide a widespread avenue for the initiation of cell-fate reprogramming...
  22. pmc DNA methylation directly silences genes with non-CpG island promoters and establishes a nucleosome occupied promoter
    Han Han
    Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90033, USA
    Hum Mol Genet 20:4299-310. 2011
    ....
  23. ncbi request reprint Detection of methylated apoptosis-associated genes in urine sediments of bladder cancer patients
    Martin G Friedrich
    Departments of Urology, Clinical Pathology, and Preventive Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90089 9176, USA
    Clin Cancer Res 10:7457-65. 2004
    ....
  24. ncbi request reprint Histone H3-lysine 9 methylation is associated with aberrant gene silencing in cancer cells and is rapidly reversed by 5-aza-2'-deoxycytidine
    Carvell T Nguyen
    Department of Biochemistry and Molecular Biology, University of Southern California Norris Comprehensive Cancer Center and Hospital, University of Southern California, Keck School of Medicine, Los Angeles, California 90089, USA
    Cancer Res 62:6456-61. 2002
    ..In addition, 5-Aza-CdR increased acetylation and H3-K4 methylation at the unmethylated p14 promoter, suggesting it can induce chromatin remodeling independently of its effects on cytosine methylation...
  25. pmc Identification of DNMT1 (DNA methyltransferase 1) hypomorphs in somatic knockouts suggests an essential role for DNMT1 in cell survival
    Gerda Egger
    Norris Comprehensive Cancer Center, Departments of Urology and Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, 1441 Eastlake Avenue, Los Angeles, CA 90089, USA
    Proc Natl Acad Sci U S A 103:14080-5. 2006
    ..Our data suggest that DNMT1 might be essential for maintenance of DNA methylation, proliferation, and survival of cancer cells...
  26. pmc Unique DNA methylation patterns distinguish noninvasive and invasive urothelial cancers and establish an epigenetic field defect in premalignant tissue
    Erika M Wolff
    Department of Urology, USC Epigenome Center, and Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, University of Southern California, Keck School of Medicine, Los Angeles, CA 90089, USA
    Cancer Res 70:8169-78. 2010
    ..In addition, an epithelium-wide epigenetic defect in bladders with cancer might contribute to a loss of epithelial integrity and create a permissible environment for tumors to arise...
  27. ncbi request reprint Specific activation of microRNA-127 with downregulation of the proto-oncogene BCL6 by chromatin-modifying drugs in human cancer cells
    Yoshimasa Saito
    Department of Urology, Biochemistry, and Molecular Biology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90089, USA
    Cancer Cell 9:435-43. 2006
    ..These results suggest that DNA demethylation and histone deacetylase inhibition can activate expression of miRNAs that may act as tumor suppressors...
  28. pmc S110, a 5-Aza-2'-deoxycytidine-containing dinucleotide, is an effective DNA methylation inhibitor in vivo and can reduce tumor growth
    Jody C Chuang
    Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
    Mol Cancer Ther 9:1443-50. 2010
    ..We also show that S110 is effective by both i.p. and s.c. deliveries. S110 therefore is a promising new agent that acts similarly to 5-Aza-CdR and has better stability and less toxicity...
  29. pmc Hypomethylation of a LINE-1 promoter activates an alternate transcript of the MET oncogene in bladders with cancer
    Erika M Wolff
    Department of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
    PLoS Genet 6:e1000917. 2010
    ..These data show that, in addition to contributing to chromosomal instability, hypomethylation of LINE-1s can alter the functional transcriptome and plays a role not only in human disease but also in disease predisposition...
  30. pmc Footprinting of mammalian promoters: use of a CpG DNA methyltransferase revealing nucleosome positions at a single molecule level
    Mehrnaz Fatemi
    Department of Urology, Biochemistry and Molecular Biology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California Los Angeles, CA 90089 9181, USA
    Nucleic Acids Res 33:e176. 2005
    ..Our high resolution approach gives a 'digitized' visualization of each promoter providing information regarding nucleosome occupancy and may be utilized to define transcription factor binding and chromatin remodeling...
  31. pmc Functional DNA demethylation is accompanied by chromatin accessibility
    Kurinji Pandiyan
    Department of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033 USA
    Nucleic Acids Res 41:3973-85. 2013
    ....
  32. ncbi request reprint Delivery of 5-aza-2'-deoxycytidine to cells using oligodeoxynucleotides
    Christine B Yoo
    Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
    Cancer Res 67:6400-8. 2007
    ..This approach may pave the way for more stable and potent inhibitors of DNA methylation as well as provide means for improving existing therapeutics...
  33. ncbi request reprint Prognostic relevance of methylation markers in patients with non-muscle invasive bladder carcinoma
    Martin G Friedrich
    Department of Urology, University of Southern California, 1441 Eastlake Avenue, Los Angeles, CA 90089 9176, USA
    Eur J Cancer 41:2769-78. 2005
    ..We identified one gene (TIMP-3) where methylation was associated with a more favourable outcome. Our data strongly support the usefulness of gene methylation as a prognostic marker in patients with non-muscle invasive bladder cancer...
  34. pmc OCT4 establishes and maintains nucleosome-depleted regions that provide additional layers of epigenetic regulation of its target genes
    Jueng Soo You
    Department of Urology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
    Proc Natl Acad Sci U S A 108:14497-502. 2011
    ..These data show the central role of the NDRs, established by OCT4, in ensuring the autoregulatory loop of pluripotency and, furthermore, that de novo methylation follows the loss of NDRs and stabilizes the suppressed state...
  35. pmc Targeting DNA methylation for epigenetic therapy
    Xiaojing Yang
    Department of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
    Trends Pharmacol Sci 31:536-46. 2010
    ..This review delineates the latest cancer epigenetic models, the recent discovery of hypomethylation agents as well as their application in the clinic...
  36. pmc Locus-wide chromatin remodeling and enhanced androgen receptor-mediated transcription in recurrent prostate tumor cells
    Li Jia
    Department of Urology, Norris Cancer Center, USC Keck School of Medicine, Los Angeles, California, USA
    Mol Cell Biol 26:7331-41. 2006
    ..These features contribute to the androgen-independent phenotype of these cells...
  37. ncbi request reprint Identification and characterization of alternatively spliced variants of DNA methyltransferase 3a in mammalian cells
    Daniel J Weisenberger
    Urologic Cancer Research Laboratory, Department of Biochemistry and Molecular Biology, University of Southern California Norris Comprehensive Cancer Center, Keck School of Medicine, 1441 Eastlake Avenue, Room 8302L, Los Angeles, CA 90089 9181, USA
    Gene 298:91-9. 2002
    ..The preferential expression of the beta transcript in ES cells suggests that this transcript, in addition to Dnmt3a2, may also be important for de novo methylation during development...
  38. pmc Constitutive nucleosome depletion and ordered factor assembly at the GRP78 promoter revealed by single molecule footprinting
    Einav Nili Gal-Yam
    Department of Urology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
    PLoS Genet 2:e160. 2006
    ..Studying the positioning of nucleosomes and transcription factors at the single promoter level provides a powerful tool to gain novel insights into the transcriptional process in eukaryotes...
  39. pmc Continuous zebularine treatment effectively sustains demethylation in human bladder cancer cells
    Jonathan C Cheng
    Department of Urology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089 9181, USA
    Mol Cell Biol 24:1270-8. 2004
    ..Last, sequential treatment with 5-aza-2'-deoxycytidine followed by zebularine hindered the remethylation of the p16 5' region and gene resilencing, suggesting the possible combination use of both drugs as a potential anticancer regimen...
  40. pmc Activation of p16 gene silenced by DNA methylation in cancer cells by phosphoramidate derivatives of 2'-deoxyzebularine
    Christine B Yoo
    Department of Biochemistry, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
    J Med Chem 51:7593-601. 2008
    ..Intriguingly, the activity of the ProTides was cell line-dependent, and activation of p16 was manifest only in Cf-Pac-1 pancreatic ductal adenocarcinoma cells...
  41. ncbi request reprint Cell division is required for de novo methylation of CpG islands in bladder cancer cells
    Mihaela Velicescu
    Urologic Cancer Research Laboratory, Department of Biochemistry and Molecular Biology, University of Southern California Norris Comprehensive Cancer Center, 1441 Eastlake Avenue, Los Angeles, CA 90089 9181, USA
    Cancer Res 62:2378-84. 2002
    ..Our results suggest that cell division is required for de novo methylation of CpG islands and that DNMT3a may play a role in methylating CpG poor regions or repetitive DNA elements outside of the S phase of the cell cycle...
  42. pmc Establishment of active chromatin structure at enhancer elements by mixed-lineage leukemia 1 to initiate estrogen-dependent gene expression
    Kwang Won Jeong
    Gachon Institute of Pharmaceutical Sciences, College of Pharmacy, Gachon University, Incheon 406 840, Republic of Korea, Departments of Urology and Biochemistry and Molecular Biology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 9176, USA, Department of Biochemistry, School of Medicine, Konkuk University, Seoul 143 701, Republic of Korea and Department of Biochemistry and Molecular Biology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 9176, USA
    Nucleic Acids Res 42:2245-56. 2014
    ....
  43. pmc DNA methylation analysis by digital bisulfite genomic sequencing and digital MethyLight
    Daniel J Weisenberger
    Department of Surgery, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
    Nucleic Acids Res 36:4689-98. 2008
    ..Using digital MethyLight, we identified single-molecule, cancer-specific DNA hypermethylation events in the CpG islands of RUNX3, CLDN5 and FOXE1 present in plasma samples from breast cancer patients...
  44. ncbi request reprint DNA methylation: the nuts and bolts of repression
    Tina Branscombe Miranda
    Department of Urology, Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
    J Cell Physiol 213:384-90. 2007
    ..In this review, we will discuss the mechanisms which lead to the long-term silencing of genes and will survey the progression that has been made in determining the targeted mechanisms for de novo DNA methylation...
  45. ncbi request reprint Identification of DNA methylation differences during tumorigenesis by methylation-sensitive arbitrarily primed polymerase chain reaction
    Gangning Liang
    Department of Biochemistry and Molecular Biology, Urologic Cancer Research Laboratory, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
    Methods 27:150-5. 2002
    ..We have demonstrated that this technique is a rapid and efficient method that can be used to screen for altered methylation patterns in genomic DNA and to isolate specific sequences associated with these changes...
  46. pmc The epigenomics of cancer
    Peter A Jones
    Department of Urology, Biochemistry, and Molecular Biology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
    Cell 128:683-92. 2007
    ....
  47. pmc Reprogramming of the human intestinal epigenome by surgical tissue transposition
    Fides D Lay
    Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
    Genome Res 24:545-53. 2014
    ....
  48. ncbi request reprint Epigenetics in carcinogenesis and cancer prevention
    Peter A Jones
    Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90089 9181, USA
    Ann N Y Acad Sci 983:213-9. 2003
    ....
  49. ncbi request reprint Cancer epigenetics: modifications, screening, and therapy
    Einav Nili Gal-Yam
    Department of Urology, Biochemistry and Molecular Biology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles 90089, USA
    Annu Rev Med 59:267-80. 2008
    ..We review these modifications in normal and cancer cells and the evolving approaches used to study them. Additionally, we outline advances in their potential use for cancer diagnostics and targeted epigenetic therapy...
  50. ncbi request reprint Epigenetics and microRNAs
    Jody C Chuang
    Department of Biochemistry and Molecular Biology, USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles 90089, USA
    Pediatr Res 61:24R-29R. 2007
    ..We examine the effects of miRNAs on epigenetic machinery, and the control of miRNA expression by epigenetic mechanisms. Epigenetics is defined as heritable changes in gene expression that do not involve a change in DNA sequence...
  51. ncbi request reprint Discovery of epigenetically masked tumor suppressor genes in endometrial cancer
    Noriyuki Takai
    Division of Hematology Oncology, Cedars Sinai Medical Center University of California at Los Angeles School of Medicine, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
    Mol Cancer Res 3:261-9. 2005
    ..Our data suggest that C/ebpalpha and Tig1 function as tumor suppressor proteins in endometrial cancers and that their reexpression may be a therapeutic target...
  52. pmc RUNX3 methylation reveals that bladder tumors are older in patients with a history of smoking
    Erika M Wolff
    Department of Urology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90089, USA
    Cancer Res 68:6208-14. 2008
    ..Because RUNX3 methylation is acquired early on in tumorigenesis, then its detection in biopsy or urine specimens could provide a marker to screen cigarette smokers long before any symptoms of bladder cancer are present...
  53. pmc Chromatin, cancer and drug therapies
    Connie C Cortez
    Department of Urology, University of Southern California, Los Angeles, CA 90089 9181, USA
    Mutat Res 647:44-51. 2008
    ..Progress has been made in the treatment of hematological malignancies and some solid tumors. As the knowledge of how chromatin regulates gene expression is enhanced, improvements in the treatment of cancer can be made...
  54. pmc DNA methylation and cellular reprogramming
    Daniel D De Carvalho
    Department of Urology, University of Southern California Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
    Trends Cell Biol 20:609-17. 2010
    ..Elucidation of the epigenetic changes taking place during cellular reprogramming will enhance our understanding of stem cell biology and facilitate therapeutic applications...
  55. ncbi request reprint p53 gene and protein status: the role of p53 alterations in predicting outcome in patients with bladder cancer
    Ben George
    Department of Pathology, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA
    J Clin Oncol 25:5352-8. 2007
    ..This study evaluated the clinical relationship of the p53 gene and protein statuses...
  56. ncbi request reprint Analysis of gene induction in human fibroblasts and bladder cancer cells exposed to the methylation inhibitor 5-aza-2'-deoxycytidine
    Gangning Liang
    USC Norris Comprehensive Cancer Center, Department of Urology, Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, California 90089 9181, USA
    Cancer Res 62:961-6. 2002
    ..Interestingly, a high percentage of genes activated in both cell types belonged to the IFN signaling pathway, confirming data from other tumor cell types...
  57. ncbi request reprint DNA methylation and cancer
    Peter A Jones
    USC Norris Comprehensive Cancer Center, Department of Urology, Keck School of Medicine of the University of Southern California, 1441 Eastlake Avenue, MS 8302L, Los Angeles, California, CA 90089 9181
    Oncogene 21:5358-60. 2002
    ..Understanding these processes is fundamental to understanding what goes awry during the process of aging and carcinogenesis where DNA methylation patterns become substantially altered and contribute to the malignant phenotype...
  58. ncbi request reprint A panel of three markers hyper- and hypomethylated in urine sediments accurately predicts bladder cancer recurrence
    Sheng Fang Su
    Authors Affiliations Departments of Urology and Preventive Medicine Program in Genetic, Molecular, and Cellular Biology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles and Department of Urology, School of Medicine, University of Stanford, Stanford, California
    Clin Cancer Res 20:1978-89. 2014
    ..Some urine markers have been used to help detect bladder tumors; however, their use in longitudinal tumor recurrence surveillance has yet to be established...
  59. ncbi request reprint Origins of bidirectional promoters: computational analyses of intergenic distance in the human genome
    Daiya Takai
    Department of Biochemistry and Molecular Biology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, USA
    Mol Biol Evol 21:463-7. 2004
    ..This exclusion might be responsible for the existence of these divergent transcripts...
  60. ncbi request reprint Epigenetic therapy of cancer: past, present and future
    Christine B Yoo
    USC Norris Comprehensive Cancer Center, Department of Urology, Keck School of Medicine, University of Southern California, 1441 Eastlake Avenue, Los Angeles, California 90089, USA
    Nat Rev Drug Discov 5:37-50. 2006
    ....
  61. pmc Differentially methylated alleles in a distinct region of the human interleukin-1alpha promoter are associated with allele-specific expression of IL-1alpha in CD4+ T cells
    Johanna G I van Rietschoten
    Department of Urology, Biochemistry, and Molecular Biology, Norris Comprehensive Cancer Center, University of Southern California, 1441 Eastlake Ave, Rm 7341, Los Angeles, CA 90089 9181, USA
    Blood 108:2143-9. 2006
    ..Taken together, these results suggest that allele-specific expression of IL-1alpha in CD4+ cells is achieved, at least in part, by differential methylation of the promoter...
  62. ncbi request reprint DNA methylation and cancer
    Phillippa C Taberlay
    Department of Urology, Biochemistry and Molecular Biology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
    Prog Drug Res 67:1-23. 2011
    ..Here, we will discuss the importance of both established and novel molecular concepts that may underlie the role of DNA methylation in cancer...
  63. ncbi request reprint Epigenetic activation of tumor suppressor microRNAs in human cancer cells
    Yoshimasa Saito
    Department of Urology, Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
    Cell Cycle 5:2220-2. 2006
    ..Activation of tumor suppressor miRNAs by chromatin modifying drugs may cause downregulation of target oncogenes and could be a novel strategy for the prevention and treatment of human cancer...
  64. pmc Epigenetics in cancer
    Shikhar Sharma
    Department of Urology, Biochemistry and Molecular Biology, USC Norris Comprehensive Cancer Center Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 9181, USA
    Carcinogenesis 31:27-36. 2010
    ....
  65. pmc Cancer genetics and epigenetics: two sides of the same coin?
    Jueng Soo You
    Department of Urology, USC Norris Comprehensive Cancer Center Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
    Cancer Cell 22:9-20. 2012
    ..This crosstalk between the genome and the epigenome offers new possibilities for therapy...
  66. ncbi request reprint Quantitative methylation analysis using methylation-sensitive single-nucleotide primer extension (Ms-SNuPE)
    Mark L Gonzalgo
    Department of Biochemistry and Molecular Biology, Urologic Cancer Research Laboratory, USC Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, CA 90089 9181, USA
    Methods 27:128-33. 2002
    ..The Ms-SNuPE technique can be adapted for high-throughput methylation analysis and therefore represents a novel approach for rapid quantitation of cytosine methylation suitable for a wide range of biological investigations...
  67. pmc MicroRNAs: critical mediators of differentiation, development and disease
    Jeffrey M Friedman
    Department of Urology, Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
    Swiss Med Wkly 139:466-72. 2009
    ..Moreover, many disease states, including cancer, occur or are sustained by miRNA dysregulation. In this article, the latest reports of miRNA involvement and aberrant expression in human disease are reviewed, with an emphasis on cancer...
  68. ncbi request reprint DNA methylation and breast carcinogenesis
    Martin Widschwendter
    USC Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, 1441 Eastlake Avenue, MS 8302L, Los Angeles, California, CA 90089 9181, USA
    Oncogene 21:5462-82. 2002
    ....
  69. ncbi request reprint A blueprint for a Human Epigenome Project: the AACR Human Epigenome Workshop
    Peter A Jones
    University of Southern California Norris Comprehensive Cancer Center, Los Angeles, 90089, USA
    Cancer Res 65:11241-6. 2005
    ..A timely workshop of leading experts, convened by the American Association for Cancer Research (AACR), confirmed that the technology is at hand to begin defining human epigenomes at high resolution...
  70. ncbi request reprint An epigenetic approach for finding tumor suppressors
    Peter A Jones
    Department of Urology, USC Norris Comprehensive Cancer Center, Los Angeles, CA 90089 9181, USA
    Cell Cycle 2:25-6. 2003
  71. pmc Rethinking how DNA methylation patterns are maintained
    Peter A Jones
    Peter A Jones and Gangning Liang are at the Department of Urology, Biochemistry and Molecular Biology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089 9181, USA
    Nat Rev Genet 10:805-11. 2009
    ....
  72. doi request reprint Methylation-sensitive single-molecule analysis of chromatin structure
    Tina B Miranda
    Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
    Curr Protoc Mol Biol . 2010
    ..SssI), followed by bisulfite sequencing of individual progeny DNA molecules. Unlike nuclease-based approaches, this method allows each molecule to be viewed as an individual entity instead of an average population...
  73. ncbi request reprint Association of breast cancer DNA methylation profiles with hormone receptor status and response to tamoxifen
    Martin Widschwendter
    Department of Urology, University of Southern California, Keck School of Medicine, Norris Comprehensive Cancer Center, Los Angeles, California, 90089 9176, USA
    Cancer Res 64:3807-13. 2004
    ....
  74. doi request reprint Molecular targets and targeted therapies in bladder cancer management
    Ramy F Youssef
    Departments of Pathology, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, 1441 Eastlake Avenue, Los Angeles, CA, 90033, USA
    World J Urol 27:9-20. 2009
    ..The current status of targeted therapies for bladder cancer is also presented as well as the ongoing clinical trials...