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Publications

Jones Laboratory

Selected Publications

For a full list of publications, please visit Google Scholar here.

2017

Helbo AS, Lay FD, Jones PA, Liang G, Grønbæk K. 2017. Nucleosome positioning and NDR structure at RNA polymerase III promoters. Sci Rep 7:41947.

Mundbjerg K, Chopra S, Alemozaffar M, Duymich C, Lakshminarasimhan R, Nichols PW, Aron M, Siegmund KD, Ukimura O, Aron M, Stern M, Gill P, Carpten JD, Ørntoft TF, Sørensen KD, Weisenberger DJ, Jones PA, Duddalwar V, Gill I, Liang G. 2017. Identifying aggressive prostate cancer foci using a DNA methylation classifier. Genome Biol 18(1):3.

Lakshminarasimhan R, Andreu-Vieyra C, Lawrenson K, Duymich CE, Gayther SA, Liang G, Jones PA. 2017. Down-regulation of ARID1A is sufficient to initiate neoplastic transformation along with epigenetic reprogramming in non-tumorigenic endometriotic cells. Cancer Lett 401:11–19.

2016

Charlet J, Duymich CE, Lay FD, Mundbjerg K, Dalsgaard Sørensen K, Liang G, Jones PA. 2016. Bivalent regions of cytosine methylation and H3K27 acetylation suggest an active role for DNA methylation at enhancers. Mol Cell 62(3):422–431.

Becket E, Chopra S, Duymich CE, Lin JJ, You JS, Pandiyan K, Nichols PW, Siegmund KD, Charlet J, Weisenberger DJ, Jones PA, Liang G. 2016. Identification of DNA methylation-independent epigenetic events underlying clear cell renal cell carcinoma. Cancer Res 76(7):1954–1964.

Duymich CE, Charlet J, Yang X, Jones PA, Liang G. 2016. DNMT3B isoforms without catalytic activity stimulate gene body methylation as accessory proteins in somatic cells. Nat Commun 7:11453.

Baylin SB, Jones PA. 2016. Epigenetic determinants of cancer. Cold Spring Harb Perspect Biol 8(9): pii:a019505.

Jones PA, Issa JP, Baylin S. 2016. Targeting the cancer epigenome for therapy. Nat Rev Genet 17(10):630 –641.

Liu M, Ohtani H, Zhou W, ørskov AD, Charlet J, Zhang YW, Shen H, Baylin SB, Liang G*, Grønbæk K*, Jones PA*. 2016. Vitamin C increases viral mimicry induced by 5-aza2’-deoxycytidineProc Natl Acad Sci U S A 113(37):10238–10244.
*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 transcriptsCell 162(5):961–973.

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 epigenomeGenome Res 25(4): 467–477. 

2014

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

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

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

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, Ahuja N. 2014. Immune regulation by low doses of the DNA methyltransferase inhibitor 5-azacitidine in common human epithelial cancersOncotarget. 5(3):587–598. 

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

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, Orlando L. 2014. Genome-wide nucleosome map and cytosine methylation levels of an ancient human genomeGenome Res 24(3):454–466. 

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 expressionNucleic Acids Res. 42(4):2245–2256. 

Statham AL, Taberlay PC, Kelly TK, Jones PA, Clark SJ. 2014. Genome-wide nucleosome occupancy and DNA methylation profiling of four human cell lines. Genom Data 3:94–96.

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, Baylin SB. 2013. Alterations of immune response of non-small cell lung cancer with azacytidineOncotarget 4(11):2067–2079. 

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, 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 modelUrology 82(1): 253.e9-253.e15. 

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

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

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

2012

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

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

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

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

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

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

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, Grønbaek K. 2012. Allelic methylation levels of the noncoding VTRNA2-1 located on chromosome 5q31.1 predict outcome in AMLBlood 119(1):206–216. 

2011

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

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

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