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Selected Publications

Neuroepigenomics Group

  1. Pao PC, Patnaik D, Watson LA, Gao F, Pan L, Wang J, Adaikkan C, Penney J, Cam HP, Huang WC, Pantano L, Lee A, Nott A, Phan TX, Gjoneska E, Elmsaouri S, Haggerty SJ, Tsai LH. 2020. HDAC1 modulates OGG1-initiated oxidative DNA damage repair in the aging brain and Alzheimer’s disease. Nat Commun; doi: 10.1038/s41467-020-16361-y [Online 18 May 2020]. [Abstract Pao PC, Patnaik D, Watson LA, Gao F, Pan L, Wang J, Adaikkan C, Penney J, Cam HP, Huang WC, Pantano L, Lee A, Nott A, Phan TX, Gjoneska E, Elmsaouri S, Haggerty SJ, Tsai LH. 2020. HDAC1 modulates OGG1-initiated oxidative DNA damage repair in the aging brain and Alzheimer’s disease. Nat Commun; doi: 10.1038/s41467-020-16361-y [Online 18 May 2020].]
  2. Amal H, Gong G, Gjoneska E, Lewis SM, Wishnok JS, Tsai LH, Tannenbaum SR. 2019. S-nitrosylatoin of E3 ubiquitin ligase RNF213 alters non-canonical Wnt/Ca+2 signaling in the P301S mouse model of tauopathy. Transl Psychiatry 9(1):44. [Abstract Amal H, Gong G, Gjoneska E, Lewis SM, Wishnok JS, Tsai LH, Tannenbaum SR. 2019. S-nitrosylatoin of E3 ubiquitin ligase RNF213 alters non-canonical Wnt/Ca+2 signaling in the P301S mouse model of tauopathy. Transl Psychiatry 9(1):44.]
  3. Klein HU, McCabe C, Gjoneska E, Sullivan SE, Kaskow BJ, Tang A, Smith RV, Xu J, Pfenning AR, Bernstein BE, Meissner A, Schneider JA, Mostafavi S, Tsai LH, Young-Pearse TL, Bennett DA, De Jager PL. 2019. Epigenome-wide study uncovers large-scale changes in histone acetylation driven by tau pathology in aging and Alzheimer’s human brains. Nat Neurosci 22(1):37-46. [Abstract Klein HU, McCabe C, Gjoneska E, Sullivan SE, Kaskow BJ, Tang A, Smith RV, Xu J, Pfenning AR, Bernstein BE, Meissner A, Schneider JA, Mostafavi S, Tsai LH, Young-Pearse TL, Bennett DA, De Jager PL. 2019. Epigenome-wide study uncovers large-scale changes in histone acetylation driven by tau pathology in aging and Alzheimer’s human brains. Nat Neurosci 22(1):37-46.]
  4. Lin YT, Seo J, Gao F, Feldman HM, Wen HL, Penney J, Cam HP, Gjoneska E, Raja WK, Cheng J, Rueda R, Kritskiy O, Abdurrob F, Peng Z, Milo B, Yu CJ, Elmsaouri S, Dey D, Ko T, Yankner BA, Tsai LH. 2018. APOE4 causes widespread molecular and cellular alterations associated with Alzheimer’s disease phenotypes in human iPSC-derived brain cell types. Neuron; doi: 10.1016/j.neuron.2018.06.011 [Online 27 June 2018]. [Abstract Lin YT, Seo J, Gao F, Feldman HM, Wen HL, Penney J, Cam HP, Gjoneska E, Raja WK, Cheng J, Rueda R, Kritskiy O, Abdurrob F, Peng Z, Milo B, Yu CJ, Elmsaouri S, Dey D, Ko T, Yankner BA, Tsai LH. 2018. APOE4 causes widespread molecular and cellular alterations associated with Alzheimer’s disease phenotypes in human iPSC-derived brain cell types. Neuron; doi: 10.1016/j.neuron.2018.06.011 [Online 27 June 2018].]
  5. Yamakawa H, Cheng J, Penney J, Gao F, Rueda R, Wang J, Yamakawa S, Kritskiy O, Gjoneska E, Tsai LH. 2017. The transcription factor Sp3 cooperates with HDAC2 to regulate synaptic function and plasticity in neurons. Cell Rep 20(6):1319-1334. [Abstract Yamakawa H, Cheng J, Penney J, Gao F, Rueda R, Wang J, Yamakawa S, Kritskiy O, Gjoneska E, Tsai LH. 2017. The transcription factor Sp3 cooperates with HDAC2 to regulate synaptic function and plasticity in neurons. Cell Rep 20(6):1319-1334.]
  6. Nott A, Cheng J, Gao F, Lin YT, Gjoneska E, Ko T, Minhas P, Zamudio AV, Meng J, Zhang F, Jin P, Tsai LH. 2016. Histone deacetylase 3 associates with MeCP2 to regulate FOXO and social behavior. Nat Neurosci 19(11):1497-1505. [Abstract Nott A, Cheng J, Gao F, Lin YT, Gjoneska E, Ko T, Minhas P, Zamudio AV, Meng J, Zhang F, Jin P, Tsai LH. 2016. Histone deacetylase 3 associates with MeCP2 to regulate FOXO and social behavior. Nat Neurosci 19(11):1497-1505.]
  7. Madabhushi R, Gao F, Pfenning AR, Pan L, Yamakawa S, Seo J, Rueda R, Phan TX, Yamakawa H, Pao PC, Stott RT, Gjoneska E, Nott A, Cho S, Kellis M, Tsai LH. 2015. Activity-induced DNA breaks govern the expression of neuronal early-response genes. Cell 161(7):1592-1605. [Abstract Madabhushi R, Gao F, Pfenning AR, Pan L, Yamakawa S, Seo J, Rueda R, Phan TX, Yamakawa H, Pao PC, Stott RT, Gjoneska E, Nott A, Cho S, Kellis M, Tsai LH. 2015. Activity-induced DNA breaks govern the expression of neuronal early-response genes. Cell 161(7):1592-1605.]
  8. Gjoneska E*, Pfenning AR*, Mathys H, Quon G, Kundaje A, Tsai LH, Kellis M. 2015. Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer’s disease. Nature 518(7539):365-369. [Abstract Gjoneska E*, Pfenning AR*, Mathys H, Quon G, Kundaje A, Tsai LH, Kellis M. 2015. Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer’s disease. Nature 518(7539):365-369.]
  9. Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M. 2015. Integrative analysis of 111 reference human epigenomes. Nature 518(7539):317-330. [Abstract Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M. 2015. Integrative analysis of 111 reference human epigenomes. Nature 518(7539):317-330.]
  10. Song X*, Gjoneska E*, Ren Q*, Taverna SD, Allis CD, Gorovsky MA. 2007. Phosphorylation of the SQ H2A.X motif is required for proper meiosis and mitosis in Tetrahymena thermophila. Mol Cell Biol 27(7):2648-2660. [Abstract Song X*, Gjoneska E*, Ren Q*, Taverna SD, Allis CD, Gorovsky MA. 2007. Phosphorylation of the SQ H2A.X motif is required for proper meiosis and mitosis in Tetrahymena thermophila. Mol Cell Biol 27(7):2648-2660.]
  11. Mason DX, Goneska E, Greider CW. 2003. Stem-loop IV of tetrahymena telomerase RNA stimulates processivity in trans. Mol Cell Biol 23(16):5606-5613. [Abstract Mason DX, Goneska E, Greider CW. 2003. Stem-loop IV of tetrahymena telomerase RNA stimulates processivity in trans. Mol Cell Biol 23(16):5606-5613.]

(* denotes equal contribution)

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