Lee Lab

Jeannie Lee, M.D./Ph.D.

Department of Molecular Biology
Simches Research Center
Boston, MA 02114

Phone: (617) 726-5943
Fax: (617) 726-6893

  1. Sun S, Payer B, Namekawa S, An JY, Press W, Catalan-Dibene J, Sunwoo H, Lee JT. Xist imprinting is promoted by the hemizygous (unpaired) state in the male germ line. Proc. Natl. Acad. Sci. U.S.A. 2015 Nov 24; 112(47):14415-22.

  2. Sunwoo H, Wu JY, Lee JT. The Xist RNA-PRC2 complex at 20-nm resolution reveals a low Xist stoichiometry and suggests a hit-and-run mechanism in mouse cells. Proc. Natl. Acad. Sci. U.S.A. 2015 Aug 4; 112(31):E4216-25.

  3. Minajigi A, Froberg JE, Wei C, Sunwoo H, Kesner B, Colognori D, Lessing D, Payer B, Boukhali M, Haas W, Lee JT. Chromosomes. A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation. Science 2015 Jul 17; 349(6245)

  4. Maier VK, Feeney CM, Taylor JE, Creech AL, Qiao JW, Szanto A, Das PP, Chevrier N, Cifuentes-Rojas C, Orkin SH, Carr SA, Jaffe JD, Mertins P, Lee JT. Functional Proteomic Analysis of Repressive Histone Methyltransferase Complexes Reveals ZNF518B as a G9A Regulator. Mol. Cell Proteomics 2015 Jun; 14(6):1435-46.

  5. Pinter SF, Colognori D, Beliveau BJ, Sadreyev RI, Payer B, Yildirim E, Wu CT, Lee JT. Allelic Imbalance Is a Prevalent and Tissue-Specific Feature of the Mouse Transcriptome. Genetics 2015 Jun; 200(2):537-49.

  6. O'Connell KE, Mikkola AM, Stepanek AM, Vernet A, Hall CD, Sun CC, Yildirim E, Staropoli JF, Lee JT, Brown DE. Practical murine hematopathology: a comparative review and implications for research. Comp. Med. 2015 Apr; 65(2):96-113.

  7. Davidovich C, Wang X, Cifuentes-Rojas C, Goodrich KJ, Gooding AR, Lee JT, Cech TR. Toward a consensus on the binding specificity and promiscuity of PRC2 for RNA. Mol. Cell 2015 Feb 5; 57(3):552-8.

  8. Kung JT, Kesner B, An JY, Ahn JY, Cifuentes-Rojas C, Colognori D, Jeon Y, Szanto A, del Rosario BC, Pinter SF, Erwin JA, Lee JT. Locus-specific targeting to the X chromosome revealed by the RNA interactome of CTCF. Mol. Cell 2015 Jan 22; 57(2):361-75.

  9. Creech AL, Taylor JE, Maier VK, Wu X, Feeney CM, Udeshi ND, Peach SE, Boehm JS, Lee JT, Carr SA, Jaffe JD. Building the Connectivity Map of epigenetics: chromatin profiling by quantitative targeted mass spectrometry. Methods 2015 Jan 15; 72:57-64.

  10. Beliveau BJ, Boettiger AN, Jungmann R, McCole RB, Joyce EF, Kim-Kiselak C, Bantignies F, Fonseka CY, Erceg J, Hannan MA, Hoang HG, Colognori D, Lee JT, Shih WM, Yin P, Zhuang X, Wu CT. Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes. Nat Commun 2015; 6:7147.

  11. 2014
  12. Sarma K, Cifuentes-Rojas C, Ergun A, Del Rosario A, Jeon Y, White F, Sadreyev R, Lee JT. ATRX directs binding of PRC2 to Xist RNA and Polycomb targets. Cell 2014 Nov 6; 159(4):869-83.

  13. Cifuentes-Rojas C, Hernandez AJ, Sarma K, Lee JT. Regulatory interactions between RNA and polycomb repressive complex 2. Mol. Cell 2014 Jul 17; 55(2):171-85.

  14. Broering TJ, Alavattam KG, Sadreyev RI, Ichijima Y, Kato Y, Hasegawa K, Camerini-Otero RD, Lee JT, Andreassen PR, Namekawa SH. BRCA1 establishes DNA damage signaling and pericentric heterochromatin of the X chromosome in male meiosis. J. Cell Biol. 2014 Jun 9; 205(5):663-75.

  15. Dimitrova N, Zamudio JR, Jong RM, Soukup D, Resnick R, Sarma K, Ward AJ, Raj A, Lee JT, Sharp PA, Jacks T. LincRNA-p21 activates p21 in cis to promote Polycomb target gene expression and to enforce the G1/S checkpoint. Mol. Cell 2014 Jun 5; 54(5):777-90.

  16. Payer B, Lee JT. Coupling of X-chromosome reactivation with the pluripotent stem cell state. RNA Biol 2014; 11(7):798-807.

  17. 2013
  18. Simon MD, Pinter SF, Fang R, Sarma K, Rutenberg-Schoenberg M, Bowman SK, Kesner BA, Maier VK, Kingston RE, Lee JT. High-resolution Xist binding maps reveal two-step spreading during X-chromosome inactivation. Nature 2013 Dec 19; 504(7480):465-9.

  19. Froberg JE, Yang L, Lee JT. Guided by RNAs: X-inactivation as a model for lncRNA function. J. Mol. Biol. 2013 Jun 28.

  20. Sun S, Del Rosario BC, Szanto A, Ogawa Y, Jeon Y, Lee JT. Jpx RNA Activates Xist by Evicting CTCF. Cell 2013 Jun 20; 153(7):1537-51.

  21. Lessing D, Anguera MC, Lee JT. X Chromosome Inactivation and Epigenetic Responses to Cellular Reprogramming. Annu Rev Genomics Hum Genet 2013 May 6.

  22. Sadreyev RI, Yildirim E, Pinter SF, Lee JT. Bimodal quantitative relationships between histone modifications for X-linked and autosomal loci. Proc. Natl. Acad. Sci. U.S.A. 2013 Apr 23; 110(17):6949-54.

  23. Kung JT, Lee JT. RNA in the loop. Dev. Cell 2013 Mar 25; 24(6):565-7.

  24. Lee JT, Bartolomei MS. X-Inactivation, Imprinting, and Long Noncoding RNAs in Health and Disease. Cell 2013 Mar 14; 152(6):1308-23.

  25. Kung JT, Colognori D, Lee JT. Long noncoding RNAs: past, present, and future. Genetics 2013 Mar; 193(3):651-69.

  26. Yildirim E, Kirby JE, Brown DE, Mercier FE, Sadreyev RI, Scadden DT, Lee JT. Xist RNA is a potent suppressor of hematologic cancer in mice. Cell 2013 Feb 14; 152(4):727-42.

  27. 2012
  28. Lee JT. Epigenetic regulation by long noncoding RNAs. Science 2012 Dec 14; 338(6113):1435-9.

  29. Erwin JA, Del Rosario B, Payer B, Lee JT. An ex Vivo Model for Imprinting: Mutually Exclusive Binding of Cdx2 and Oct4 as a Switch for Imprinted and Random X-Inactivation. Genetics 2012 Nov; 192(3):857-68.

  30. Pinter SF, Sadreyev RI, Yildirim E, Jeon Y, Ohsumi TK, Borowsky M, Lee JT. Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations. Genome Res. 2012 Oct; 22(10):1864-76.

  31. Anguera MC, Sadreyev R, Zhang Z, Szanto A, Payer B, Sheridan SD, Kwok S, Haggarty SJ, Sur M, Alvarez J, Gimelbrant A, Mitalipova M, Kirby JE, Lee JT. Molecular signatures of human induced pluripotent stem cells highlight sex differences and cancer genes. Cell Stem Cell 2012 Jul 6; 11(1):75-90.

  32. Jeon Y, Sarma K, Lee JT. New and Xisting regulatory mechanisms of X chromosome inactivation. Curr. Opin. Genet. Dev. 2012 Apr; 22(2):62-71.

  33. Yildirim E, Sadreyev RI, Pinter SF, Lee JT. X-chromosome hyperactivation in mammals via nonlinear relationships between chromatin states and transcription. Nat. Struct. Mol. Biol. 2012 Jan; 19(1):56-61.

  34. 2011
  35. Lee JT. Gracefully ageing at 50, X-chromosome inactivation becomes a paradigm for RNA and chromatin control. Nat. Rev. Mol. Cell Biol. 2011 Dec; 12(12):815-26.

  36. Spencer RJ, del Rosario BC, Pinter SF, Lessing D, Sadreyev RI, Lee JT. A boundary element between Tsix and Xist binds the chromatin insulator Ctcf and contributes to initiation of X-chromosome ina Genetics 2011 Oct; 189(2):441-54.

  37. Payer B, Lee JT, Namekawa SH. X-inactivation and X-reactivation: epigenetic hallmarks of mammalian reproduction and pluripotent stem cells. Hum. Genet. 2011 Aug; 130(2):265-80.

  38. Jeon Y, Lee JT. YY1 tethers Xist RNA to the inactive X nucleation center. Cell 2011 Jul 8; 146(1):119-33.

  39. Namekawa SH, Lee JT. Detection of nascent RNA, single-copy DNA and protein localization by immunoFISH in mouse germ cells and preimplantation embr Nat Protoc 2011 Mar; 6(3):270-84.

  40. Sun S, Fukue Y, Nolen L, Sadreyev R, Lee JT. Characterization of Xpr (Xpct) reveals instability but no effects on X-chromosome pairing or Xist expression. Transcription ; 1(1):46-56.

  41. 2010
  42. Zhao J, Ohsumi TK, Kung JT, Ogawa Y, Grau DJ, Sarma K, Song JJ, Kingston RE, Borowsky M, Lee JT. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Mol. Cell 2010 Dec 22; 40(6):939-53.

  43. Sarma K, Levasseur P, Aristarkhov A, Lee JT. Locked nucleic acids (LNAs) reveal sequence requirements and kinetics of Xist RNA localization to the X chromosome. Proc. Natl. Acad. Sci. U.S.A. 2010 Dec 21; 107(51):22196-201.

  44. Tian D, Sun S, Lee JT. The long noncoding RNA, Jpx, is a molecular switch for X chromosome inactivation. Cell 2010 Oct 29; 143(3):390-403.

  45. Ahn JY, Lee JT. Retinoic acid accelerates downregulation of the Xist repressor, Oct4, and increases the likelihood of Xist activation when Ts BMC Dev. Biol. 2010; 10:90.

  46. Lee JT. The X as model for RNA's niche in epigenomic regulation. Cold Spring Harb Perspect Biol 2010 Sep; 2(9):a003749.

  47. Namekawa SH, Payer B, Huynh KD, Jaenisch R, Lee JT. Two-step imprinted X inactivation: repeat versus genic silencing in the mouse. Mol. Cell. Biol. 2010 Jul; 30(13):3187-205.

  48. Lengner CJ, Gimelbrant AA, Erwin JA, Cheng AW, Guenther MG, Welstead GG, Alagappan R, Frampton GM, Xu P, Muffat J, Santagata S, Powers D, Barrett CB, Young RA, Lee JT, Jaenisch R, Mitalipova M. Derivation of pre-X inactivation human embryonic stem cells under physiological oxygen concentrations. Cell 2010 May 28; 141(5):872-83.

  49. Paro R, Lee JT. Extending the frontiers of epigenetic regulation. Curr. Opin. Genet. Dev. 2010 Apr; 20(2):107-9.

  50. Erwin JA, Lee JT. Characterization of X-chromosome inactivation status in human pluripotent stem cells. Curr Protoc Stem Cell Biol 2010 Feb; Chapter 1:Unit 1B.6.

  51. 2009
  52. Zhou D, Conrad C, Xia F, Park JS, Payer B, Yin Y, Lauwers GY, Thasler W, Lee JT, Avruch J, Bardeesy N. Mst1 and Mst2 maintain hepatocyte quiescence and suppress hepatocellular carcinoma development through inactivation of the Ya Cancer Cell 2009 Nov 6; 16(5):425-38.

  53. Lee JT. Lessons from X-chromosome inactivation: long ncRNA as guides and tethers to the epigenome. Genes Dev. 2009 Aug 15; 23(16):1831-42.

  54. Donohoe ME, Silva SS, Pinter SF, Xu N, Lee JT. The pluripotency factor Oct4 interacts with Ctcf and also controls X-chromosome pairing and counting. Nature 2009 Jul 2; 460(7251):128-32.

  55. Zhang LF, Ogawa Y, Ahn JY, Namekawa SH, Silva SS, Lee JT. Telomeric RNAs mark sex chromosomes in stem cells. Genetics 2009 Jul; 182(3):685-98.

  56. Namekawa SH, Lee JT. XY and ZW: is meiotic sex chromosome inactivation the rule in evolution? PLoS Genet. 2009 May; 5(5):e1000493.

  57. 2008
  58. Anguera MC, Liu M, Avruch J, Lee JT. Characterization of two Mst1-deficient mouse models. Dev. Dyn. 2008 Nov; 237(11):3424-34.

  59. Zhao J, Sun BK, Erwin JA, Song JJ, Lee JT. Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science 2008 Oct 31; 322(5902):750-6.

  60. Lee JT. Jeannie T. Lee. Curr. Biol. 2008 Oct 28; 18(20):R940-1.

  61. Lindroth AM, Park YJ, McLean CM, Dokshin GA, Persson JM, Herman H, Pasini D, Miró X, Donohoe ME, Lee JT, Helin K, Soloway PD. Antagonism between DNA and H3K27 methylation at the imprinted Rasgrf1 locus. PLoS Genet. 2008; 4(8):e1000145.

  62. Tsai CL, Rowntree RK, Cohen DE, Lee JT. Higher order chromatin structure at the X-inactivation center via looping DNA. Dev. Biol. 2008 Jul 15; 319(2):416-25.

  63. Ogawa Y, Sun BK, Lee JT. Intersection of the RNA interference and X-inactivation pathways. Science 2008 Jun 6; 320(5881):1336-41.

  64. Erwin JA, Lee JT. New twists in X-chromosome inactivation. Curr. Opin. Cell Biol. 2008 Jun; 20(3):349-55.

  65. Silva SS, Rowntree RK, Mekhoubad S, Lee JT. X-chromosome inactivation and epigenetic fluidity in human embryonic stem cells. Proc. Natl. Acad. Sci. U.S.A. 2008 Mar 25; 105(12):4820-5.

  66. Payer B, Lee JT. X chromosome dosage compensation: how mammals keep the balance. Annu. Rev. Genet. 2008; 42:733-72.

  67. 2007
  68. Lin H, Gupta V, Vermilyea MD, Falciani F, Lee JT, O'Neill LP, Turner BM. Dosage compensation in the mouse balances up-regulation and silencing of X-linked genes. PLoS Biol. 2007 Dec; 5(12):e326.

  69. Xu N, Donohoe ME, Silva SS, Lee JT. Evidence that homologous X-chromosome pairing requires transcription and Ctcf protein. Nat. Genet. 2007 Nov; 39(11):1390-6.

  70. Namekawa SH, VandeBerg JL, McCarrey JR, Lee JT. Sex chromosome silencing in the marsupial male germ line. Proc. Natl. Acad. Sci. U.S.A. 2007 Jun 5; 104(23):9730-5.

  71. Zhang LF, Huynh KD, Lee JT. Perinucleolar targeting of the inactive X during S phase: evidence for a role in the maintenance of silencing. Cell 2007 May 18; 129(4):693-706.

  72. Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, Duke S, Garber M, Gentles AJ, Goodstadt L, Heger A, Jurka J, Kamal M, Mauceli E, Searle SM, Sharpe T, Baker ML, Batzer MA, Benos PV, Belov K, Clamp M, Cook A, Cuff J, Das R, Davidow L, Deakin JE, Fazzari MJ, Glass JL, Grabherr M, Greally JM, Gu W, Hore TA, Huttley GA, Kleber M, Jirtle RL, Koina E, Lee JT, Mahony S, Marra MA, Miller RD, Nicholls RD, Oda M, Papenfuss AT, Parra ZE, Pollock DD, Ray DA, Schein JE, Speed TP, Thompson K, VandeBerg JL, Wade CM, Walker JA, Waters PD, Webber C, Weidman JR, Xie X, Zody MC, Broad Institute Genome Sequencing Platform, Broad Institute Whole Genome Assembly Team, Graves JA, Ponting CP, Breen M, Samollow PB, Lander ES, Lindblad-Toh K. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature 2007 May 10; 447(7141):167-77.

  73. Kim S, Namekawa SH, Niswander LM, Ward JO, Lee JT, Bardwell VJ, Zarkower D. A mammal-specific Doublesex homolog associates with male sex chromatin and is required for male meiosis. PLoS Genet. 2007 Apr 20; 3(4):e62.

  74. Davidow LS, Breen M, Duke SE, Samollow PB, McCarrey JR, Lee JT. The search for a marsupial XIC reveals a break with vertebrate synteny. Chromosome Res. 2007; 15(2):137-46.

  75. Donohoe ME, Zhang LF, Xu N, Shi Y, Lee JT. Identification of a Ctcf cofactor, Yy1, for the X chromosome binary switch. Mol. Cell 2007 Jan 12; 25(1):43-56.

  76. Cohen DE, Davidow LS, Erwin JA, Xu N, Warshawsky D, Lee JT. The DXPas34 repeat regulates random and imprinted X inactivation. Dev. Cell 2007 Jan; 12(1):57-71.

  77. 2006
  78. Lewis A, Green K, Dawson C, Redrup L, Huynh KD, Lee JT, Hemberger M, Reik W. Epigenetic dynamics of the Kcnq1 imprinted domain in the early embryo. Development 2006 Nov; 133(21):4203-10.

  79. Rowntree RK, Lee JT. Mapping of DNA replication origins to noncoding genes of the X-inactivation center. Mol. Cell. Biol. 2006 May; 26(10):3707-17.

  80. Namekawa SH, Park PJ, Zhang LF, Shima JE, McCarrey JR, Griswold MD, Lee JT. Postmeiotic sex chromatin in the male germline of mice. Curr. Biol. 2006 Apr 4; 16(7):660-7.

  81. Sun BK, Deaton AM, Lee JT. A transient heterochromatic state in Xist preempts X inactivation choice without RNA stabilization. Mol. Cell 2006 Mar 3; 21(5):617-28.

  82. Boumil RM, Ogawa Y, Sun BK, Huynh KD, Lee JT. Differential methylation of Xite and CTCF sites in Tsix mirrors the pattern of X-inactivation choice in mice. Mol. Cell. Biol. 2006 Mar; 26(6):2109-17.

  83. Xu N, Tsai CL, Lee JT. Transient homologous chromosome pairing marks the onset of X inactivation. Science 2006 Feb 24; 311(5764):1149-52.

  84. 2005
  85. Lee JT. Regulation of X-chromosome counting by Tsix and Xite sequences. Science 2005 Jul 29; 309(5735):768-71.

  86. Huynh KD, Lee JT. X-chromosome inactivation: a hypothesis linking ontogeny and phylogeny. Nat. Rev. Genet. 2005 May; 6(5):410-8.

  87. Lee JT. Sex chromosome inactivation: the importance of pairing. Curr. Biol. 2005 Apr 12; 15(7):R249-52.

  88. Stavropoulos N, Rowntree RK, Lee JT. Identification of developmentally specific enhancers for Tsix in the regulation of X chromosome inactivation. Mol. Cell. Biol. 2005 Apr; 25(7):2757-69.

  89. 2004
  90. Shibata S, Lee JT. Tsix transcription- versus RNA-based mechanisms in Xist repression and epigenetic choice. Curr. Biol. 2004 Oct 5; 14(19):1747-54.

  91. 2003
  92. Huynh KD, Lee JT. Inheritance of a pre-inactivated paternal X chromosome in early mouse embryos. Nature 2003 Dec 18; 426(6968):857-62.

  93. Lee JT. X-chromosome inactivation: a multi-disciplinary approach. Semin. Cell Dev. Biol. 2003 Dec; 14(6):311-2.

  94. Lee JT. Functional intergenic transcription: a case study of the X-inactivation centre. Philos. Trans. R. Soc. Lond., B, Biol. Sci. 2003 Aug 29; 358(1436):1417-23; discussion .

  95. O'Neill LP, Randall TE, Lavender J, Spotswood HT, Lee JT, Turner BM. X-linked genes in female embryonic stem cells carry an epigenetic mark prior to the onset of X inactivation. Hum. Mol. Genet. 2003 Aug 1; 12(15):1783-90.

  96. Lee JT. Molecular biology: Complicity of gene and pseudogene. Nature 2003 May 1; 423(6935):26-8.

  97. Lee JT. Molecular links between X-inactivation and autosomal imprinting: X-inactivation as a driving force for the evolution of impri Curr. Biol. 2003 Mar 18; 13(6):R242-54.

  98. Ogawa Y, Lee JT. Xite, X-inactivation intergenic transcription elements that regulate the probability of choice. Mol. Cell 2003 Mar; 11(3):731-43.

  99. Shibata S, Lee JT. Characterization and quantitation of differential Tsix transcripts: implications for Tsix function. Hum. Mol. Genet. 2003 Jan 15; 12(2):125-36.

  100. 2002
  101. Lee JT. Homozygous Tsix mutant mice reveal a sex-ratio distortion and revert to random X-inactivation. Nat. Genet. 2002 Sep; 32(1):195-200.

  102. Cohen DE, Lee JT. X-chromosome inactivation and the search for chromosome-wide silencers. Curr. Opin. Genet. Dev. 2002 Apr; 12(2):219-24.

  103. Lee JT. Is X-chromosome inactivation a homology effect? Adv. Genet. 2002; 46:25-48.

  104. Chao W, Huynh KD, Spencer RJ, Davidow LS, Lee JT. CTCF, a candidate trans-acting factor for X-inactivation choice. Science 2002 Jan 11; 295(5553):345-7.

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