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Your Environment. Your Health.

Selected Publications

Eukaryotic Transcriptional Regulation Group

2016 - present

  1. Grimm SA, Shimbo T, Takaku M, Thomas JW, Auerbach S, Bennett BD, Bucher JR, Burkholder AB, Day F, Du Y, Duncan CG, French JE, Foley JF, Li JY, Merrick BA, Tice RR, Wang TY, Xu XJ, Bushel PR, Fargo DC, Mullikin JC, Wade PA. DNA methylation in mice is influenced by genetics as well as sex and life experience. Nature Comm (2019) 10:article number 305. [Abstract Grimm SA, Shimbo T, Takaku M, Thomas JW, Auerbach S, Bennett BD, Bucher JR, Burkholder AB, Day F, Du Y, Duncan CG, French JE, Foley JF, Li JY, Merrick BA, Tice RR, Wang TY, Xu XJ, Bushel PR, Fargo DC, Mullikin JC, Wade PA. DNA methylation in mice is influenced by genetics as well as sex and life experience. Nature Comm (2019) 10:article number 305.] 
  2. Blok LS, Rousseau J, Twist J, Ehresmann S, Takaku M, Venselaar H, Rodan LH, Nowak CB, Douglas J, Swoboda KJ, Steeves MA, Sahai I, Stumpel CTRM, Stegmann APA, Wheeler P, Willing M, Fiala E, Kochhar A, Gibson WT, Cohen ASA, Agbahovbe R, Innes AM, Au, PYB, Rankin J, Anderson IJ, Skinner SA, Louie RJ, Warren HE, Afenjar A, Keren B, Nava C, Buratti J, Isapof A, Rodriguez D, Lewandowski R, Propst J, van Essen T, Choi M, Lee S, Chae JH, Price S, Schnur RE, Douglas G, Wentzensen IM, Zweier C, Reis A, Bialer MG, Moore C, Koopmans M, Brilstra EH, Monroe GR, van Gassen KLI, van Binsbergen E, Newbury-Ecob R, Bownass L, Bader I, Mayr JA, Wortmann SB, Jakielski KJ, Strand EA, Kloth K, Bierhals T, Roberts JD, Petrovich RM, Machida S, Kurumizaka H, Lelieveld S, Pfundt R, Jansen S, Deriziotis P, Faive L, Thevenon J, Assoum M, Shriberg L, Kleefstra T, Brunner HG, Wade PA, Fisher SE, Campeau, PM. CHD3 helicase domain mutations cause a neurodevelopmental syndrome with macrocephaly and impaired speech and language. Nature Comm 2018 9:article number 4619. [Abstract Blok LS, Rousseau J, Twist J, Ehresmann S, Takaku M, Venselaar H, Rodan LH, Nowak CB, Douglas J, Swoboda KJ, Steeves MA, Sahai I, Stumpel CTRM, Stegmann APA, Wheeler P, Willing M, Fiala E, Kochhar A, Gibson WT, Cohen ASA, Agbahovbe R, Innes AM, Au, PYB, Rankin J, Anderson IJ, Skinner SA, Louie RJ, Warren HE, Afenjar A, Keren B, Nava C, Buratti J, Isapof A, Rodriguez D, Lewandowski R, Propst J, van Essen T, Choi M, Lee S, Chae JH, Price S, Schnur RE, Douglas G, Wentzensen IM, Zweier C, Reis A, Bialer MG, Moore C, Koopmans M, Brilstra EH, Monroe GR, van Gassen KLI, van Binsbergen E, Newbury-Ecob R, Bownass L, Bader I, Mayr JA, Wortmann SB, Jakielski KJ, Strand EA, Kloth K, Bierhals T, Roberts JD, Petrovich RM, Machida S, Kurumizaka H, Lelieveld S, Pfundt R, Jansen S, Deriziotis P, Faive L, Thevenon J, Assoum M, Shriberg L, Kleefstra T, Brunner HG, Wade PA, Fisher SE, Campeau, PM. CHD3 helicase domain mutations cause a neurodevelopmental syndrome with macrocephaly and impaired speech and language. Nature Comm 2018 9:article number 4619.] 
  3. Duncan CG, Grimm SA, Morgan DL, Bushel PR, Bennett BD, NISC Comparative Sequencing Program, Roberts JD, Tyson FL, Merrick BA, Wade PA. Dosage compensation and DNA methylation landscape of the X chromosome in mouse liver. Sci Reports 2018 8:10138. [Abstract Duncan CG, Grimm SA, Morgan DL, Bushel PR, Bennett BD, NISC Comparative Sequencing Program, Roberts JD, Tyson FL, Merrick BA, Wade PA. Dosage compensation and DNA methylation landscape of the X chromosome in mouse liver. Sci Reports 2018 8:10138.] 
  4. Wilczewski CM, Hepperla AJ, Shimbo T, Wasson L, Robbe ZL, Davis IJ, Wade PA, Conlon FL. CHD4 and the NuRD complex directly control cardiac sarcomere formation. Proc Natl Acad Sci USA 2018 115 (26): 6727-6732. [Abstract Wilczewski CM, Hepperla AJ, Shimbo T, Wasson L, Robbe ZL, Davis IJ, Wade PA, Conlon FL. CHD4 and the NuRD complex directly control cardiac sarcomere formation. Proc Natl Acad Sci USA 2018 115 (26): 6727-6732.] 
  5. Thomas SY, Whitehead GS, Takaku M, Ward JM, Xu X, Nakano K, Lyons-Cohen MR, Nakano H, Gowdy KM, Wade PA, Cook DN. MyD88-dependent dentritic and epithelial cell crosstalk orchestrates immune responses to allergens. Mucosal Immunol 2018 11(3): 796-810. [Abstract Thomas SY, Whitehead GS, Takaku M, Ward JM, Xu X, Nakano K, Lyons-Cohen MR, Nakano H, Gowdy KM, Wade PA, Cook DN. MyD88-dependent dentritic and epithelial cell crosstalk orchestrates immune responses to allergens. Mucosal Immunol 2018 11(3): 796-810.] 
  6. Li Y, Hamilton KJ, Wang T, Coons LA, Jefferson WN, Li R, Wang Y, Grimm SA, Ramsey JT, Liu L, Gerrish KE, Williams CJ, Wade PA, Korach KS. DNA methylation and transcriptome aberrations mediated by ERalpha in mouse seminal vesicles following developmental DES exposure. Proc Natl Acad Sci USA 2018 115 (18): E4189-E4198. [Abstract Li Y, Hamilton KJ, Wang T, Coons LA, Jefferson WN, Li R, Wang Y, Grimm SA, Ramsey JT, Liu L, Gerrish KE, Williams CJ, Wade PA, Korach KS. DNA methylation and transcriptome aberrations mediated by ERalpha in mouse seminal vesicles following developmental DES exposure. Proc Natl Acad Sci USA 2018 115 (18): E4189-E4198.] 
  7. Takaku M, Grimm SA, Roberts JD, Chrysovergis K, Bennett BD, Myers P, Perera L, Tucker CJ, Perou CM, Wade PA. GATA3 zinc finger 2 mutations reprogram the breast cancer transcriptional network. Nature Comm 2018 9:1059 – 1072. [Abstract Takaku M, Grimm SA, Roberts JD, Chrysovergis K, Bennett BD, Myers P, Perera L, Tucker CJ, Perou CM, Wade PA. GATA3 zinc finger 2 mutations reprogram the breast cancer transcriptional network. Nature Comm 2018 9:1059 – 1072.] 
  8. Duncan CG, Kondilis-Mangum HD, Grimm SA, Bushel PR, Chrysovergis K, Roberts JD, Tyson FL, Merrick BA, Wade PA. Base-resolution analysis of DNA methylation patterns downstream of DNMT3a in mouse naïve B cells. G3-Genes Genomes Genetics 2018 8(3): 805-813. [Abstract Duncan CG, Kondilis-Mangum HD, Grimm SA, Bushel PR, Chrysovergis K, Roberts JD, Tyson FL, Merrick BA, Wade PA. Base-resolution analysis of DNA methylation patterns downstream of DNMT3a in mouse naïve B cells. G3-Genes Genomes Genetics 2018 8(3): 805-813.] 
  9. Qin Y, Wade PA. Crosstalk between the microbiome and epigenome: messages from bugs. J Biochem 2018 163(2): 105-112. [Abstract Qin Y, Wade PA. Crosstalk between the microbiome and epigenome: messages from bugs. J Biochem 2018 163(2): 105-112.] 
  10. Qin Y, Roberts JD, Grimm SA, Lih FB, Deterding LJ, Li R, Chrysovergis K, Wade PA. An obesity-associated gut microbiome reprograms the intestinal epigenome and leads to altered colonic gene expression. Genome Biology 2018 19: article 7. [Abstract Qin Y, Roberts JD, Grimm SA, Lih FB, Deterding LJ, Li R, Chrysovergis K, Wade PA. An obesity-associated gut microbiome reprograms the intestinal epigenome and leads to altered colonic gene expression. Genome Biology 2018 19: article 7.] 
  11. Li R, Grimm SA, Mav D, Gu H, Djukovic D, Shah R, Merrick BA, Raftery D, Wade PA. Transcriptome and DNA methylome analysis in a mouse model of diet-induced obesity predicts increased risk of colorectal cancer. Cell Reports 2018 22(3): 624-637. [Abstract Li R, Grimm SA, Mav D, Gu H, Djukovic D, Shah R, Merrick BA, Raftery D, Wade PA. Transcriptome and DNA methylome analysis in a mouse model of diet-induced obesity predicts increased risk of colorectal cancer. Cell Reports 2018 22(3): 624-637.] 
  12. Li PS, Wang L, Bennett BD, Wang JJ, Li JL, Qin YF, Takaku M, Wade PA, Wong JM, Hu G. Rif1 promotes a repressive chromatin state to safeguard against endogenous retrovirus activation. Nucleic Acids Research 2017 45 (22): 12723 – 12738. [Abstract Li PS, Wang L, Bennett BD, Wang JJ, Li JL, Qin YF, Takaku M, Wade PA, Wong JM, Hu G. Rif1 promotes a repressive chromatin state to safeguard against endogenous retrovirus activation. Nucleic Acids Research 2017 45 (22): 12723 – 12738.] 
  13. Zhang S, Takaku M, Zou LY, Gu AD, Chou WC, Shang G, Wu B, Kong Q, Thomas SY, Serody JS, Chen X, Xu SJ, Wade PA, Cook DN, Ting JPY, Wan YSY. Reversing SKI-SMAD4-mediated suppression is essential for T(H)17 cell differentiation. Nature 2017 551 (7678): 105. [Abstract Zhang S, Takaku M, Zou LY, Gu AD, Chou WC, Shang G, Wu B, Kong Q, Thomas SY, Serody JS, Chen X, Xu SJ, Wade PA, Cook DN, Ting JPY, Wan YSY. Reversing SKI-SMAD4-mediated suppression is essential for T(H)17 cell differentiation. Nature 2017 551 (7678): 105.] 
  14. Tencer AH, Cox KL, Di L, Bridgers JB, Lyu J, Wang XD, Sims JK, Weaver TM, Allen HF, Shang Y, Gatchalian J, Darcy MA, Gibson MD, Ikebe J, Li W, Wade PA, Hayes JJ, Strahl BD, Kono H, Poirier MG, Musselman CA, Kutateladze TG. Covalent modifications of histone H3K9 promote binding of CHD3. Cell Reports 2017 21 (2): 455-466. [Abstract Tencer AH, Cox KL, Di L, Bridgers JB, Lyu J, Wang XD, Sims JK, Weaver TM, Allen HF, Shang Y, Gatchalian J, Darcy MA, Gibson MD, Ikebe J, Li W, Wade PA, Hayes JJ, Strahl BD, Kono H, Poirier MG, Musselman CA, Kutateladze TG. Covalent modifications of histone H3K9 promote binding of CHD3. Cell Reports 2017 21 (2): 455-466.] 
  15. Lu R, Wang P, Parton T, Zhou Y, Chrysovergis K, Rockowitz S, Chen WY, Abdel-Wahab O, Wade PA, Zheng DY, Wang GG. Epigenetic perturbations by Arg882-mutated DNMT3A potentiate aberrant stem cell gene-expression program and acute leukemia development. Cancer Cell 2016 30 (1): 92-107. [Abstract Lu R, Wang P, Parton T, Zhou Y, Chrysovergis K, Rockowitz S, Chen WY, Abdel-Wahab O, Wade PA, Zheng DY, Wang GG. Epigenetic perturbations by Arg882-mutated DNMT3A potentiate aberrant stem cell gene-expression program and acute leukemia development. Cancer Cell 2016 30 (1): 92-107.] 
  16. Markunas CA, Wilcox AJ, Xu ZL, Joubert BR, Harlid S, Panduri V, Haberg SE, Nystad W, London SJ, Sandler DP, Lie RT, Wade PA, Taylor JA. Maternal age at delivery is associated with epigenetic signature in both newborns and adults. PLOS One 2016 11 (7): e0156361. [Abstract Markunas CA, Wilcox AJ, Xu ZL, Joubert BR, Harlid S, Panduri V, Haberg SE, Nystad W, London SJ, Sandler DP, Lie RT, Wade PA, Taylor JA. Maternal age at delivery is associated with epigenetic signature in both newborns and adults. PLOS One 2016 11 (7): e0156361.] 
  17. Shimbo T, Takaku M, Wade PA. High-quality ChIP-seq analysis of MBD3 in human breast cancer cells. Genomics Data 2016 7: 173-174. [Abstract Shimbo T, Takaku M, Wade PA. High-quality ChIP-seq analysis of MBD3 in human breast cancer cells. Genomics Data 2016 7: 173-174.] 
  18. Takaku M, Grimm SA, Shimbo T, Perera L, Menafra R, Stunnenberg HG, Archer TK, Machida S, Kurumizaka H, Wade PA. GATA3-dependent cellular reprogramming requires activation-domain dependent recruitment of a chromatin remodeler. Genome Biology 2016 17:article number 36. [Abstract Takaku M, Grimm SA, Shimbo T, Perera L, Menafra R, Stunnenberg HG, Archer TK, Machida S, Kurumizaka H, Wade PA. GATA3-dependent cellular reprogramming requires activation-domain dependent recruitment of a chromatin remodeler. Genome Biology 2016 17:article number 36.]
  19. Li RF, Wade PA. Epigenetics, obesity, and colon cancer. Epigenetics, Energy Balance and Cancer (book series: Energy Balance and Cancer) 2016: 211-233. [Abstract Li RF, Wade PA. Epigenetics, obesity, and colon cancer. Epigenetics, Energy Balance and Cancer (book series: Energy Balance and Cancer) 2016: 211-233.] 
  20. Shimbo T, Wade PA. Proteins that read DNA methylation. DNA Methyltransferases – Role and Function (book series: Advances in Experimental Medicine and Biology) 2016 945: 303-320. [Abstract Shimbo T, Wade PA. Proteins that read DNA methylation. DNA Methyltransferases – Role and Function (book series: Advances in Experimental Medicine and Biology) 2016 945: 303-320.] 
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