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Publications

Jones Laboratory

Selected Publications

For a full list of Dr. Jones’s publications, please visit PubMed here.

In Press

Liu M, Ohtani H, Zhou W, ørskov AD, Charlet J, Zhang YW, Shen H, Baylin SB, Liang G*, Grønbæk K*, Jones PA*. In press. Vitamin C increases viral mimicry induced by 5-aza2’-deoxycytidine. Proc Natl Acad Sci U S A. Article
*Co-senior authors

2015

Roulois D, Yau HL, Singhania R, Wang Y, Danesh, A, Shen SY, Han H, Liang G, Jones PA, Pugh T, O’Brein C, De Carvalho DD. 2015. DNA-demethylating agents target colorectal cancer cells by inducing viral mimicry by endogenous transcripts. Cell 162(5):961–973 PubMed

Lay FD, Liu Y, Kelly TK, Witt H, Farnham PJ,Jones PA, Berman BP. 2015. The role of DNA methylation in directing the functional organization of the cancer epigenome. Genome Res 25(4): 467–477. PubMed

2014

Yang X, Han H, De Carvalho DD, Lay FD, Jones PA, and Liang G. 2014. Gene body methylation can alter gene expression and is a therapeutic target in cancer. Cancer Cell 26(4):577-590.  PubMed

Taberlay PC, Statham AL, Kelly TK, Clark SJ, and Jones PA. 2014. Reconfiguration of nucleosome depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer. Genome Res 24(9):1421-1432. PubMed

Su SF, de Castro Abreu AL, Chihara Y, Tsai Y, Andreu-Vieyra C, Daneshmand S, Skinner EC, Jones PA, Siegmund KD, and Liang G. 2014. A panel of three markers hyper- and hypomethylated in urine sediments accurately predicts bladder cancer recurrence. Clin Cancer Res. 20(7):1978-1989. PubMed      Article

Li H, Chiappinelli KB, Guzzetta AA, Easwaran H, Yen RW, Vatapalli R, Topper MJ, Luo J, Connolly RM, Azad NS, Stearns V, Pardoll DM, Davidson N, Jones PA, Slamon DJ, Baylin SB, Zahnow CA, and Ahuja N. 2014. Immune regulation by low doses of the DNA methyltransferase inhibitor 5-azacitidine in common human epithelial cancers. Oncotarget. 5(3):587-598. PubMed      Article

Lay FD, Triche TJ, Tsai YC, Su SF, Martin SE, Daneshmand S, Skinner EC, Liang G, Chihara Y, and Jones PA. 2014. Reprogramming of the intestinal epigenome by surgical tissue transposition. Genome Res. 24(4):545-553. PubMed      Article

Pedersen JS, Valen E, Velazquez AM, Parker BJ, Rasmussen M, Lindgreen S, Lilje B, Tobin DJ, Kelly TK, Vang S, Andersson R, Jones PA, Hoover CA, Tikhonov A, Prokhortchouk E, Rubin EM, Sandelin A, Gilbert MT, Krogh A, Willerslev E, and Orlando L. 2014. Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome. Genome Res. 24(3):454-466. PubMed      Article

Jeong KW, Andreu-Vieyra C, You JS, Jones PA, and Stallcup MR. 2014. Establishment of active chromatin structure at enhancer elements by mixed-lineage leukemia 1 to initiate estrogen-dependent gene expression. Nucleic Acids Res. 42(4):2245-2256. PubMed      Article

2013

Wrangle J, Wang W, Koch A, Easwaran H, Mohammad HP, Vendetti F, Vancriekinge W, Demeyer T, Du Z, Parsana P, Rodgers K, Yen RW, Zahnow CA, Taube JM, Brahmer JR, Tykodi SS, Easton K, Carvajal RD, Jones PA, Laird PW, Weisenberger DJ, Tsai S, Juergens RA, Topalian SL, Rudin CM, Brock MV, Pardoll D, and Baylin SB. 2013. Alterations of immune response of non-small cell lung cancer with azacytidine. Oncotarget. 4(11):2067-2079. PubMed      Article

Choi IS, Yu K, Kim J, De Guzman E, Weisenberger DJ, Oghamian S, Kim HJ, Lee KH, Carroll C, Trinh BN, Kim M, Houshdaran S, Laird PW, Jones PA, Warburton D, Liang G and Koh CJ. 2013. Alterations in deoxyribonucleic acid (DNA) methylation patterns of Calca, Timp3, Mmp2, and Igf2r are associated with chronic cystitis in a cyclophosphamide-induced mouse model. Urology. 82(1): 253.e9-253.e15. PubMed      Article

Chihara Y, Kanai Y, Fujimoto H, Sugano K, Kawashima K, Liang G, Jones PA, Fujimoto K, Kuniyasu H, and Hirao Y. 2013. Diagnostic markers of urothelial cancer based on DNA methylation analysis. BMC Cancer. 13: 275. PubMed      Article

You JS, De Carvalho DD, Dai C, Liu M, Pandiyan K, Zhou XJ, Liang G, and Jones PA. 2013. SNF5 is an essential executor of epigenetic regulation during differentiation. PLoS Genet. 9:e1003459. PubMed      Article

Pandiyan K, You JS, Yang X, Dai C, Zhou XJ, Baylin SB, Jones PA, and Liang G. 2013. Functional DNA demethylation is accompanied by chromatin accessibility. Nucleic Acids Res. 41(7):3973-3985. PubMed      Article

2012

Kelly TK, Liu Y, Lay FD, Liang G, Berman BP, and Jones PA. 2012. Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules. Genome Res. 22(12): 2497-2506. PubMed      Article

Jones PA. 2012. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat. Rev. Genet. 13: 484-492. PubMed      Article

You JS and Jones PA. 2012. Cancer genetics and epigenetics: two sides of the same coin? Cancer Cell. 22(1): 9-20. PubMed      Article

De Carvalho DD, Sharma S, You JS, Su SF, Taberlay PC, Kelly TK, Yang X, Liang G, and Jones PA. 2012. DNA methylation screening identifies driver epigenetic events of cancer cell survival. Cancer Cell. 21(5): 655-667. PubMed      Article

Yang X, Noushmehr H, Han H, Andreu-Vieyra C, Liang G, and Jones PA. 2012. Gene reactivation by 5-aza-2’-deoxycytidine-induced demethylation requires SRCAP-mediated H2A.Z insertion to establish nucleosome depleted regions. PLoS Genet. 8:e1002604. PubMed      Article

Sharma S, Gerke DS, Han HF, Jeong S, Stallcup MR, Jones PA, and Liang G. 2012. Lysine methyltransferase G9a is not required for DNMT3A/3B anchoring to methylated nucleosomes and maintenance of DNA methylation in somatic cells. Epigenetics Chromatin. 5(1):3. PubMed      Article

Treppendahl MB, Qiu X, Søgaard A, Yang X, Nandrup-Bus C, Hother C, Andersen MK, Kjeldsen L, Möllgaard L, Hellström-Lindberg E, Jendholm J, Porse BT, Jones PA, Liang G, and Grønbaek K. 2012. Allelic methylation levels of the noncoding VTRNA2-1 located on chromosome 5q31.1 predict outcome in AML. Blood. 119(1): 206-216. PubMed      Article

2011

Andreu-Vieyra C, Lai J, Berman BP, Frenkel B, Jia L, Jones PA, and Coetzee GA. 2011. Dynamic nucleosome-depleted regions at androgen receptor enhancers in the absence of ligand in prostate cancer cells. Mol. Cell. Biol. 31(23):4648-4662. PubMed      Article

Han H, Cortez CC, Yang X, Nichols PW, Jones PA, and Liang G. 2011. DNA methylation directly silences genes with non-CpG island promoters and establishes a nucleosome occupied promoter. Hum. Mol. Genet. 20(22):4299-4310. PubMed      Article

Taberlay PC, Kelly TK, Liu CC, You JS, De Carvalho DD, Miranda TB, Zhou XJ, Liang G, and Jones PA. 2011. Polycomb-repressed genes have permissive enhancers that initiate reprogramming. Cell. 147(6):1283-1294 PubMed      Article