PUBLICATIONS

† Equal contribution, * Co-corresponding authors

2024
  1. Wesely J, Rusielewicz T, Chen YR, Hartley B, McKenzie D, Yim MK, Maguire C, Bia R, Franklin S, Makwana R, Marchi E, Nikte M, Patil S, Sapar M, Moroziewicz D; NYSCF Global Stem Cell Array® Team; Bauer L, Lee JT, Monsma FJ Jr, Paull D, Lyon GJ. A repository of Ogden syndrome patient derived iPSC lines and isogenic pairs by X-chromosome screening and genome-editing. bioRxiv [Preprint]. 2024 Sep 28:2024.09.28.615067. doi: 10.1101/2024.09.28.615067.
  2. Lee Y, Lee JT. 2024. PRC2-RNA interactions: Viewpoint from YongWoo Lee and Jeannie T. Lee. Mol Cell. 84, 3586-3592. doi: 10.1016/j.molcel.2024.09.006. 
  3. Lee YW† , Blum R† ​, Rosenberg M, Lee JT. 2024. Re-analysis of CLAP data affirms PRC2 as an RNA binding protein. BioRxiv [Preprint]. 2024 Sept 20. doi.org/10.1101/2024.09.19.613009. Read
  4. Yao S, Jeon Y, Kesner B, Lee JT. 2024. Xist RNA binds select autosomal genes and depends on Repeat B to regulate their expression. eLIFE. https://doi.org/10.7554/eLife.101197.1
  5. Lee YW, Weissbein U, Blum R, Lee JT. 2024. G-quadruplex folding in Xist RNA antagonizes PRC2 activity for stepwise regulation of X chromosome inactivation. Mol Cell. 2024 May 16;84(10):1870-1885.e9. doi: 10.1016/j.molcel.2024.04.015. Read
  6. Singhal A, Roth C, Micheva-Viteva SN, Venu V, Lappala A, Lee JT, Starkenburg SR, Steadman CR, Sanbonmatsu KY. 2024. Human Coronavirus Infection Reorganizes Spatial Genomic Architecture in Permissive Lung Cells. Res Sq [Preprint]. 2024 Mar 13:rs.3.rs-3979539. doi: 10.21203/rs.3.rs-3979539/v1. Read
  7. Wei C, Kesner B, Yin H, Lee JT. 2024. Imprinted X chromosome inactivation at the gamete-to-embryo transition. Mol Cell. 2024 Feb 29:S1097-2765(24)00132-1. doi: 10.1016/j.molcel.2024.02.013. Epub ahead of print.  Read
  8. Zito A, Lee JT. Variable expression of MECP2, CDKL5, and FMR1 in the human brain: Implications for gene restorative therapies. 2024. Proc Natl Acad Sci U S A. 2024 Feb 27;121(9):e2312757121. doi: 10.1073/pnas.2312757121. Epub 2024 Feb 22. Read


2023
  1. Lee HG, Imaichi S, Kraeutler E, Aguilar R, Lee YW, Sheridan SD, Lee JT. 2023. Site-specific R-loops induce CGG repeat contraction and fragile X gene reactivation. Cell, in press. May 16:S0092-8674(23)00469-5. doi: 10.1016/j.cell.2023.04.035. 
  2. Nickbarg EB*, Spencer KB, Mortison JD, Lee JT*. 2023. Targeting RNA with small molecules: lessons learned from Xist RNA. RNA. 2023 Apr;29(4):463-472. doi: 10.1261/rna.079523.122.  Read
  3. Generoso SF *, Neguembor MV, Hershberg EA, Sadreyev RI, Krimoto K, Yabuta Y, Ricci R, Audergon P, Bauer M, Saitou M, Hochedlinger K, Beliveau BJ, Cosma MP, Lee JT*, Payer B *. 2023 Cohesin controls X chromosome structure remodeling and X-reactivation during mouse iPSC-reprogramming. Proc Natl Acad Sci U S A. 2023 Jan 24;120(4):e2213810120.  Read
  4. Mattick JS, Amaral PP, Carninci P, Carpenter S, Chang HY, Chen LL, Chen R, Dean C, Dinger ME, Fitzgerald KA, Gingeras TR, Guttman M, Hirose T, Huarte M, Johnson R, Kanduri C, Kapranov P, Lawrence JB, Lee JT, Mendell JT, Mercer TR, Moore KJ, Nakagawa S, Rinn JL, Spector DL, Ulitsky I, Wan Y, Wilusz JE, Wu M. 2023. Long non-coding RNAs: definitions, functions, challenges and recommendations. Nat Rev Mol Cell Biol. 2023 Jan 3. doi: 10.1038/s41580-022-00566-8. Read

2022
  1. Tsai RX, Fang KC, Yang PC, Hsieh YH, Chiang IT, Chen Y, Lee HG, Lee JT, Chu HC. 2022. TERRA regulates DNA G-quadruplex formation and ATRX recruitment to chromatin. Nucleic Acids Res. Nov 28;50(21):12217-12234. doi: 10.1093/nar/gkac1114. Read
  2. Aguilar R, Spencer KB, Kesner B, Rizvi NF, Badmalia MD, Mrozowich T, Mortison JD, Rivera C, Smith GF, Burchard J, Dandliker PJ, Patel TR, Nickbarg EB, and Lee JT. 2022. Targeting Xist with compounds that disrupt RNA structure and X inactivation. Nature. https://doi.org/10.1038/s41586-022-04537-z. Read
  3. Rivera C †, Lee HG †, Lappala A, Wang D, Noches V, Olivares-Costa M, Sjoberg-Herrera M, Lee JT *, and Andres ME *. 2022. Unveiling RCOR1 as a rheostat at transcriptionally permissive chromatin. Nat Commun 13, 1550. https://doi.org/10.1038/s41467-022-29261-0. Read.
  4. Grimm NB and Lee JT. 2022. Selective Xi reactivation and alternative methods to restore MECP2 function in Rett syndrome. Trends in Genetics. Read

2021
  1. Oh HJ, Aguilar R, Kesner B, Lee HG, Kriz AJ, Chu H.-P., and Lee JT. 2021. Jpx RNA regulates CTCF anchor site selection and formation of chromosome loops. Cell doi.org/10.1016/j.cell.2021.11.012. Read
  2. Rivera C, Verbel-Vergara D, Arancibia D, Lappala A, González M, Guzmán F, Merello G, Lee JT* , Andrés ME* . 2021. Revealing RCOR2 as a regulatory component of nuclear speckles. Epigenetics Chromatin. 14(1):51.  Read
  3. Lappala A, Wang CY, Kriz A, Michalk H, Tan K, Lee JT*, Sanbonmatsu KY*. 2021. Four-dimensional chromosome reconstruction elucidates the spatiotemporal reorganization of the mammalian X chromosome. Proc Natl Acad Sci U S A. 118(42):e2107092118. doi: 10.1073/pnas.2107092118.  Read
  4. Rosenberg M, Levy V, Maier VK, Kesner B, Blum R, and Lee JT. 2021. Denaturing cross-linking immunoprecipitation to identify footprints for RNA-binding proteins. STAR Protoc. 2021 Sep 16;2(4):100819. Free Read
  5. Szanto A, Aguilar R, Kesner B, Blum R, Wang D, Cifuentes-Rojas C, Del Rosario BC, Kis-Toth K, Lee JT. 2021. A disproportionate impact of G9a methyltransferase deficiency on the X chromosome. Genes Dev. 35:1035-1054.
  6. Rivero-Hinojosa S, Pugacheva EM, Kang S, Méndez-Catalá CF, Kovalchuk AL, Strunnikov AV, Loukinov D, Lee JT, Lobanenkov VV. 2021. The combined action of CTCF and its testis-specific paralog BORIS is essential for spermatogenesis. Nat Commun. 12:3846. doi: 10.1038/s41467-021-24140-6.
  7. Yin H, We C, and Lee JT.  2021. Revisiting the consequences of deleting the X-inactivation center. PNAS ePub 2021 Jun 15.
  8. Chu HP, Minajigi A, Chen Y, Morris R, Guh C-Y, Yu HH, Boukhali M, Haas W, and Lee JT. 2021. iDRiP for the systematic discovery of proteins bound directly to noncoding RNA. Nature Protocols doi: 10.1038/s41596-021-00555-9.
  9. Colognori D, Sunwoo H, Wang D, Wang CY, Lee JT.  2021. Xist Repeat A contributes to early recruitment of Polycomb complexes during X-chromosome inactivation. Dev Cell 56(9):1236-1237. Read
  10. Kriz AJ, Colognori D, Sunwoo H, Nabet B, Lee JT. 2021. Balancing cohesin eviction and retention prevents aberrant chromosomal interactions, Polycomb-mediated repression, and X-inactivation. Molecular Cell 10.1016/j.molcel.2021.02.031. Read
  11. Rosenberg M†, Blum R†, Kesner B, Aeby E, Garant J-M, Szanto A, and Lee JT. 2021. Motif-driven interactions between RNA and PRC2 are rheostats that regulate transcription elongation. Nature Struct Mol Biol. 10.1038/s41594-020-00535-9. Free Read

​2020
  1. Aeby E, Lee H-G †, Lee Y-W †, Kriz A, del Rosario BC, Oh HJ, Boukhali M, Haas W, and Lee JT. 2020. Decapping enzyme 1A breaks X-chromosome symmetry by controlling Tsix elongation and RNA turnover. Nature Cell Biology, doi.org/10.1038/s41556-020-0558-0. Read for free
  2. Colognori D †, Sunwoo H †, Wang D, Wang CY, Lee JT. 2020. Xist Repeats A and B Account for Two Distinct Phases of X Inactivation Establishment.  Dev Cell. doi: 10.1016/j.devcel.2020.05.021. Read
  3. Kadota S, Ou J, Shi Y, Lee JT, Sun J, Yildirim E. 2020. Nucleoporin 153 links nuclear pore complex to chromatin architecture by mediating CTCF and cohesin binding.  Nat Commun. 2020 May 25;11(1):2606. doi: 10.1038/s41467-020-16394-3. Read
  4. Schmider AB, Bauer NC, Sunwoo H, Godin MD, Ellis GE, Lee JT, Nigrovic PA, Soberman RJ. 2020. Two- and three-color STORM analysis reveals higher-order assembly of leukotriene synthetic complexes on the nuclear envelope of murine neutrophils. J Biol Chem. 295:5761-5770. Read.
  5. Yang L, Yildirm E, Kirby JE, Press W, and Lee JT. 2020. Widespread organ tolerance of Xist loss and X reactivation except under chronic stress in the gut.  PNAS 117: 4262-4272. ​Read.
  6. Hernandez AJ †, Zovoilis A †, Cifuentes-Rojas C †, Han L, Bujisic B, Lee JT. 2020. B2 and ALU retrotransposons are self-cleaving ribozymes whose activity is enhanced by EZH2. Proc Natl Acad Sci U S A. 2019 Dec 23. pii: 201917190. doi: 10.1073/pnas.1917190117.  Read.

2019

  1. Oh HJ and Lee JT. 2019. Long noncoding RNA functionality beyond sequence: The Jpx model. J Molec Biol.  10.1016/j.jmb.2019.11.011.
  2. Lewandowski JP, Lee JC, Hwang T, Sunwoo H, Goldstein JM, Groff AF, Chang NP, Mallard W, Williams A, Henao-Meija J, Flavell RA, Lee JT, Gerhardinger C, Wagers AJ, Rinn JL. (2019) The Firre locus produces a trans-acting RNA molecule that functions in hematopoiesis. Nat Commun. 2019 Nov 13;10(1):5137. doi: 10.1038/s41467-019-12970-4. Read
  3. Rizvi NF, Santa Maria JP Jr, Nahvi A, Klappenbach J, Klein DJ, Curran PJ, Richards MP, Chamberlin C, Saradjian P, Burchard J, Aguilar R, Lee JT, Dandliker PJ, Smith GF, Kutchukian P, Nickbarg EB. (2019) Targeting RNA with Small Molecules: Identification of Selective, RNA-Binding Small Molecules Occupying Drug-Like Chemical Space. ​SLAS Discov. 2019 Nov 8:2472555219885373. doi: 10.1177/2472555219885373. Read
  4. Jagtap S, Thanos JM, Fu T, Wang J, Lalonde J, Dial TO, Feiglin A, Chen J, Kohane I, Lee JT, Sheridan SD, Perlis RH.  (2019) Aberrant mitochondrial function in patient-derived neural cells from CDKL5 deficiency disorder and Rett Syndrome. Hum Mol Genet. 2019 Sep 13. pii: ddz208. doi: 10.1093/hmg/ddz208. ​Read
  5. Wang CY, Brand H, Shaw ND, Talkowski ME, and Lee JT.  (2019) Role of the Chromosome Architectural Factor SMCHD1 in X Chromosome Inactivation, Gene Regulation, and Disease in Humans. Genetics ePub doi: 10.1534/genetics.119.302600. Read
  6. Wang CY, Colognori D†, Sunwoo H†, Wang D, and Lee JT. (2019) PRC1 collaborates with SMCHD1 to fold the X-chromosome and spread Xist RNA between chromosome compartments. Nat Communications  10:2950. doi.org/10.1038/s41467-019-10755.  Read
  7. Colognori D †, Sunwoo H †, Kriz A, Wang C-Y, and Lee JT. (2019) Xist deletional analysis reveals an interdependency between Xist RNA and Polycomb complexes for spreading along the inactive X. Molecular Cell   10.1016/j.molcel.2019.01.015.    Read
  8. Lee HJ †, Gopalappa R †, Sunwoo H †, Choi SW, Ramakrishna S, Lee JT, Kim HH, Nam JW.  2019. En bloc and segmental deletions of human XIST reveal X chromosome inactivation-involving RNA elements. Nucleic Acids Res. doi: 10.1093/nar/gkz109.  Read it here.
  9. Del Rosario BC †, Kriz AJ †, Del Rosario AM, Anselmo A, Fry CJ, White FM, Sadreyev RI, Lee JT. (2019) Exploration of CTCF post-translation modifications uncovers Serine-224 phosphorylation by PLK1 at pericentric regions during the G2/M transition. Elife. 2019 Jan 24;8. pii: e42341. doi: 10.7554/eLife.42341.  PDF here.
  10. Jegu, T. †, Blum R. †, Cochraine, J.C., Yang, L., Wang, C.Y., Gilles, M.-E., Colognori, D., Szanto, A., Marr, S.K., Kingston, R.E., and Lee, J.T. (2019) Xist RNA antagonizes the SWI/SNF chromatin remodeler, BRG1, on the inactive X chromosome. Nature Structural & Molecular Biology 10.1038/s41594-018-0176-8. To read for free, click here.
​

2018

  1. Froberg JE, Pinter SF, Kriz AJ, Jegu T, and Lee JT. (2018) Megadomains and superloops form dynamically but are dispensable for X chromosome inactivation and gene escape. Nature Communications 9, 5004.  Download article here.
  2. Saltzman AL, Soo MW, Aram R, and Lee JT. (2018) Multiple histone methyl-lysine readers ensure robust development and germline immortality in Caenorhabditis elegans. Genetics ePub Sept 5.
  3. Carrette LG, Blum R, Ma W, Kelleher RJ, Lee JT. (2018) A Tsix-Mecp2 female mouse model for Rett Syndrome reveals that low-level MECP2 expression extends life and improves neuromotor function. Proc Natl Acad Sci. USA, 115,8185-8190.
  4. Matoba S, Wang H, Jiang L, Lu F, Iwabuchi KA, Wu X, Inoue K, Yang L, Press W, Lee JT, Ogura A, Shen L, Zhang Y. (2018) Loss of H3K27me3 Imprinting in Somatic Cell Nuclear Transfer Embryos Disrupts Post-Implantation Development. Cell Stem Cell 23,343-354.
  5. Wang CY, Jegu, T, Chu HP, Oh HJ, and Lee JT. (2018) SMCHD1 merges chromosome compartments and assists formation of Super-structures on the inactive X. Cell 174, 406-421.
  6. Carrette LG, Wang CY, Press W, Ma W, Kelleher RJ, Lee JT. (2018) Xi-reactivation: A mixed modality approach to MECP2 restoration for Rett Syndrome and other X-linked disorders. Proc Natl Acad Sci. 1715124115 ePub Dec 27, 2017.


2017

  1. Del Rosario BC, Del Rosario AM, Anselmo A, Wang PI, Sadreyev RI, Lee JT. 2017. Genetic intersection of Tsix and Hedgehog signaling during the initiation of X chromosome inactivation. Dev Cell 43, 359-371.
  2. Rosenberg M, Blum R, Kesner B, Maier VK, Szanto A, Lee JT. 2017. Denaturing CLIP, dCLIP, pipeline identifies discrete RNA footprints on chromatin-associated proteins and reveals that CBX7 targets 3’ UTRs to regulate mRNA expression. Cell Syst. 5, 368-385.
  3. Sunwoo H, Colognori D, Froberg JE, Jeon Y, and Lee JT. 2017 Repeat E anchors Xist RNA to the inactive X chromosomal compartment through CDKN1A-interacting protein (CIZ1). PNAS 114, 10,654-10,659.
  4. Savol AJ, Wang PI, Jeon Y, Colognori D, Yildirim E, Pinter SF, Payer B, Lee JT, and Sadreyev R. 2017. Genome-wide identification of autosomal genes with allelic imbalance of chromatin state. Plos One e0182568.
  5. Jégu T, Aeby E, Lee JT. 2017. The X chromosome in space. Nat Rev Genet 18, 377-389.
  6. Chu HP, Froberg JE, Kesner B, Oh HJ, Ji F, Sadreyev R, Pinter SF, and Lee JT. 2017. PAR-TERRA directs homologous sex chromosome pairing. Nat Struct Mol Biol. 24,620-631.
  7. Chu HP, Cifuentes-Rojas C, Kesner B, Aeby E, Lee HG, Wei C, Oh HJ, Boukhali M, Haas W, and Lee JT. 2017. TERRA RNA antagonizes ATRX and protects telomeres. Cell 170:86-101
  8. Wang CY †, Froberg JE †, Blum R, Jeon Y, Lee JT. 2017. Comment: Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing. Science aal4976. ePub June 15, 2017.
  9. Kundu S, Ji F, Sunwoo H, Jain G, Lee JT, Sadreyev RI, Dekker J, Kingston RE. 2017. Polycomb repressive complex 1 generates discrete compacted domains that change during differentiation. Mol Cell 65:432-446.
  10. Sripathy S, Leko V, Adrianse RL, Loe T, Foss EJ, Dalrymple E, Lao U, Gatbonton-Schwager T, Carter KT, Payer B, Paddison PJ, Grady WM, Lee JT *, Bartolomei MS, Bedalov A *. 2017. Screen for rreractivation of MeCP2 on the inactive X chromosome identified the BMO/TGF-beta superfamily as a regulator of XIST expression. PNAS 114, 1619-1624.


2016

  1. Zovoilis, A., Cifuentes-Rojas, C., Chu, H.P., Nernandez, A.J., and Lee, J.T. 2016. Destabilization of B2 RNA by EZH2 activates the stress response. Cell 167, 1788-1802.
  2. Lessing, D. †, Dial, T. †, Wei, C., Carrette, L., Kesner, B., Payer, B., Szanto, A., Jadhav, A., Maloney, D., simeonov, A., Bedalov, A. Bartolomei, Theriault, J. Hasaka, T. Lee, J.T. 2016. A high-throughput small molecule screen identifies synergism between DNA methylation and Aurora kinase pathways for X-chromosome reactivation. Proc Natl Acad Sci 113, 14366-14371.
  3. Yang, L., Kirby, J.E., Sunwoo H., and Lee, J.T. 2016. Survival to term and partial dosage compensation in female mice lacking Xist RNA. Genes and Development 30, 1747-1760.


2015

  1. Sunwoo, H., Wu, J.Y., and Lee, J.T. 2015. The Xist RNA-PRC2 complex at 20-nm resolution reveals a low Xist stoichiometry and suggest a hit-and-run mechanism in mouse cells. PNAS 112:E4216-4225.
  2. Sun, S, Payer B, Namekawa S, An JY, Press W, Catalan-Dibene J, Sunwoo H, Lee JT. (2015). Xist imprinting is promoted by the hemizygous (unpaired) state in the male germline. PNAS 112: 14415-22.
  3. Minajigi, A. †, Froberg, J.E. †, Wei, C., Sunwoo, H., Kesner, B., Colognori, D., Lessing, D., Payer, B. Boukhali, M., Haas, W., and Lee, J.T. 2015. A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation. Science 349 (6245): aab2276.
  4. Pinter, S.F., Colognori, D., Beliveau, B.J., Sadreyev, R.I., Payer, B., Yildirim, E., Wu, C.T., Lee, J.T. 2015. Allelic imbalance is a prevalent and tissue-specific feature of the mouse transcriptome. Genetics 200, 537-549.
  5. Beliveau, B.J., Boettinger, A.N., Avendano, M.S., Jungmann, R., McCole, R.B., Joyce, E.F., Kim-Kiselak, C., Bantignies, F., Fonseka, C.Y., Erceg, J., Hannan, M.A., Hoang, H.G., Colognori, D., Lee, J.T., Shih, W.M., Yin, P., Zhuang, X., and Wu, C.T. 2015. Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using oligopaint FISH probes. Nat Commun 6, 7147.
  6. Maier, V.K., Feeney, C.M., Taylor, J.E., Creech, A.L., Qiao, J.W., Szanto, A., Das, P.P., Chevrier, N., Cifuentes-Rojas, C., Orkin, S.H., Carr, S.A., Jaffe, J.D., Mertins, P.*, and Lee, J.T.* 2015. Functional proteomic analysis of repressive histone methyltransferase complexes reveals ZNF518B as a G9A regulator. Mol Cell Proteomics 14, 1435-1446.
  7. Davidovich, C., Wang, C., Cifuentes-Rojas, C. Goodrich, K.J., Gooding, A.R., Lee, J.T.*, and Cech, T.R.* 2015. Toward a consensus on the binding specificity and promiscuity of PRC2 for RNA. Mol Cell 57, 552-558.
  8. Kung, J.T. †, Kesner, B. †, An, J.Y. †, Ahn, J.Y., Cifentes-Rojas, C., Colognori, D. Jeon, Y. Szanto, A., Del Rosario, B.C., Pinter, S.F., Erwin, J.A., and Lee, J.T. 2015. Locus-specific targeting to the X chromosome revealed by the RNA interactome of CTCF. Mol Cell 57, 361-375.
  9. Creech, A.L., Taylor, J.E., Maier, V.K., Wu, X., Feeney, C.M., Udeshi, N.D., Peach, S.E., Boehm, J.S., Lee, J.T., Carr, S.A., and Jaffe, J.D. 2015. Building the connectivity map of epigenetics: Chromatin profiling by quantitative targeted mass spectrometry. Methods 72, 57-64.


2014

  1. Sarma, K., Cifuentes-Rojas, C., Ergun, A., del Rosario, A., Jeon, Y., White, F. Sadreyev, R., and Lee, J.T. 2014. ATRX promotes binding of PRC2 to Xist RNA and Polycomb targets. Cell 159, 869-883.
  2. Broering, T. J., Alavattam, K.G., Sadreyev, R. I., Ichimima, Y., Kato, Y., Hasegawa, K., Camerini-Otero, R.D., Lee, J.T., Andreassen, P.R., and Namekawa, S.H. 2014. BRCA1 establishes DNA damage signaling and pericentric heterochromatin of X chromosome in meiotic sex chromosome inactivation. J Cell Biol. 205, 663-675.
  3. Dimitrova, N., Zamudio, J., Jong, R.M., Soukup, D., Resnick, R., Sarma, K., Ward, A.J., Raj, A., Lee, J.T., Sharp, P., and Jacks, T. 2014. The p53-regulated long non-coding RNA, linRNA-p21, promotes the expression of Polycomb target genes and enforces the G1/S checkpoint by activating p21 in cis. Mol Cell. 54, 777-790.
  4. Cifuentes-Rojas, C., Hernandez, A.J., Sarma, K., and Lee, J.T. 2014. Regulatory interactions between RNA and Polycomb repressive complex 2. Mol Cell. 55: 171-185.
  5. Payer, B., and Lee, J.T. 2014. Coupling of X-chromosome reactivation with the pluripotent stem cell state. RNA Biol. 11, 798-807.
  6. Yang., L., Froberg, J., and Lee, J.T. 2014. Long noncoding RNAs: Fresh perspectives into the RNA world. Trends Biochem Sci. 39, 35-43.


2013

  1. Payer, B. Rosenberg, M. Yamaji, M., Yabuta, Y., Koyanagi-Aoi, M., Hayashi, K., Yamanaka, S., Saitou, M, and Lee, J.T. 2013. Tsix RNA and the germline factor, PRDM14, link X reactivation and stem cell reprogramming. Mol Cell. 52, 805-818.
  2. Simon, M.D. †*, Pinter, S.F. †, Fang, R. †, Sarma, K., Rutenberg-Schoenberg, M., Bowman, S.K., Kesner, B.A., Maier, V.K., Kingston, R.E.*, and Lee, J.T.* (2013) High-resolution Xist bindings maps reveal 2-step spreading during X-inactivation. Nature 504, 465-469.
  3. Sun S, Del Rosario BC, Szanto A, Ogawa Y, Jeon Y, and Lee JT. (2013). Jpx RNA activates Xist by evicting CTCF. Cell 153, 1537-1551.
  4. Sadreyev, R.I., Yildirim, E., Pinter, S.F., and Lee, J.T. (2013) Bimodal quantitative relationships between histone modifications for X-linked and autosomal loci. PNAS 110:6949-6954.
  5. Yildirim, E., Kirby, J.E., Brown, D.E., Mercier, F.E. Sadreyev, R.I., Scadden, D.T., and Lee, J.T. (2013) Xist RNA is a potent suppressor of hematologic cancer in mice. Cell 152, 727-742.
  6. Froberg, J.E., Yang, L., Lee, J.T. 2013. Guided by RNAs: X-inactivation as a model for lncRNA function. J. Mol. Biol. 425, 3698-3706.
  7. Lessing, D., Anguera, M.C., and Lee, J.T. 2013. X chromosome inactivation and epigenetic responses to cellular reprogramming. Annu Rev Genomics Hum Genet. 14, 85-110.
  8. Lee, J.T. and Bartolomei, M.S. (2013) X-inactivation, imprinting, and long noncoding RNAs in health and disease. Cell 152: 1308-1323.
  9. Kung, J.T., Colognori, D., and Lee, J.T. 2013. RNA in the loop. Dev Cell 24, 565-567.


2012

  1. Pinter SF, Sadreyev RI, Yildirim E, Jeon Y, Ohsumi TK, Borowsky M, Lee, J.T. (2012) Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations. Genome Research 22:1864-1876.
  2. Ougland, R., Lando, D., Jonson, I., Dahl, J.A., Moen, M.N., Nordstrand, L.M., Rognes, T., Lee, J.T., Klungland A, Kouzarides T, Larsen E. (2012) ALKBH1 is a Histone H2A Dioxygenase Involved in Neural Differentiation. Stem Cells 30, 2672-2682.
  3. Erwin, J.A., DelRosario, B., Payer, B., Lee, J.T. (2012) An Ex Vivo Model for Imprinting: Mutually Exclusive Binding of Cdx2 and Oct4 as a Switch for Imprinted and Random X-inactivation. Genetics 192, 857-868.
  4. Anguera, M.C., Sadreyev, R., Zhang, Z., Szanto, A., Payer, B., Sheridan, S.D., Kwok, S., Haggarty, S.J., Sur, M., Alvarez, J., Gimelbrant, A., Mitalipova, M., Kirby, J.E., and Lee, J.T. (2012) Molecular signatures of human induced pluripotent stem cells (hiPSCs) highlight sex differences and cancer genes. Cell Stem Cell. 11:75-90.
  5. Yildirim, E. †, Sadreyev, R.I. †, Pinter, S.F., and Lee, J.T. (2011) X-chromosome hyperactivation in mammals via nonlinear relationships between chromatin states and transcription. Nat Struct Mol Biol ePub 2011 Dec 4. doi: 10.1038/nsmb.2195.
  6. Lee, J.T. (2012) Epigenetic regulation by long noncoding RNAs. Science 338:1435-1439.


2011

  1. Anguera, M.C., Ma, W., Clift, D., Namekawa, S., Kelleher, R.J., and Lee, J.T. (2011) Tsx produces a long noncoding RNA and has general functions in the germline, stem cells, and brain. PLoS-Genet 7:e1002248.
  2. Spencer, R.J., del Rosario, B.C., Pinter, S.F., Lessing, D., Sadreyev, R.I., and Lee, J.T. (2011) A boundary element between Tsix and Xist binds the chromatin insulator Ctcf and contributes to initiation of X-chromosome inactivation. Genetics 189, 441-454.
  3. Jeon, Y. and Lee, J.T. (2011) YY1 tethers Xist RNA to the inactive X nucleation center. Cell 146, 119-133.
  4. Namekawa, S.H., and Lee, J.T. (2011) Detection of nascent RNA, single-copy DNA, and protein localization by immunoFISH in mouse germ cells and preimplantation embryos. Nat Protocols 6, 270-284.
  5. Lee, J.T. (2011) Gracefully ageing at 50, X-chromosome inactivaiton becomes a paradigm for RNA and chromatin control. Nat Rev Mol Cell Biol. 12: 815-826
  6. Payer, B., Lee, J.T., Namekawa, S.H. (2011) X-inactivation and X-reactivation: epigenetic hallmarks of mammalian reproduction and pluripotent stem cells. Hum Genet. 130: 265-280.
  7. Kim, D.H., Jeon, Y., Anguera, M.C., and Lee, J.T. (2011) X-chromosome epigenetic reprogramming in pluripotent stem cells via noncoding genes. Semin Cell Dev Biol. 22, 336-342.


2010

  1. Zhao, J., Ohsumi, T.K., Kung, J.T., Ogawa, Y., Grau, D.J., Sarma, K., Song, J.J., Kingston, R.E., Borowsky, M., Lee, J.T. (2010) Genome-wide identification of Polycomb-associated RNAs by RIP-seq. Molecular Cell 40, 939-953. PMCID3021903
  2. Sarma, K., Levasseur, P., Aristarkhov, A., and Lee, J.T. (2010) Locked nucleic acids (LNAs) reveal sequence requirements and kinetics of Xist RNA localization to the X chromosome. Proc Natl Acad Sci, USA 107(51), 22196-22201. PMCID3009817
  3. Nordstrand, L.M., Svard, J., Larsen, E., Nilsen, A., Ougland, R., Furu, K., Lien, G.F., Rognes, T., Namekawa, S.H., Lee, J.T., and Klungland, A. (2010) Mice lacking Alkbh1 display sex-ratio distortion and unilateral eye defects. PLoS One 3, e13827. PMCID2972218
  4. Tian, D., Sun, S., and Lee, J.T. (2010) The long noncoding RNA, Jpx, is a molecular switch for X chromosome inactivation. Cell 143, 390-403. PMCID2994261
  5. Ahn, J.Y., and Lee, J.T. (2010) Retinoic acid accelerates downregulation of the Xist repressor, Oct4, and increases the likelihood of Xist activation when Tsix is deficient. BMC Dev Biol 10, 90. PMCID2933617
  6. Sun, S. †, Fukue, Y. †, Nolen, L., Sadreyev, R.I., and Lee, J.T. (2010) Characterization of Xpr (Xpct) reveals instability but no effects on X-chromosome pairing or Xist expression. Transcription 1, 46-56. PMCID3035190
  7. Lengner, C.J., Gimelbrant, A.A., Erwin, J.A., Cheng, A.W., Guenther, M.G., Welstead, G.G., Alagappan, R., Frampton, G.M., Xu, P., Muffat, J., Santagata, S., Powers, D., Barrett, C.B., Young, R.A., Lee, J.T., Jaenisch, R., Mitalipova, M. (2010) Derivation of pre-X-inactivation human embryonic stem cells under physiological oxygen concentrations. Cell 141, 872-883. PMC in process
  8. Namekawa, S.H., Payer, B. Huynh, K.D., Jaenisch, R., and Lee, J.T. (2010) Two-step imprinted X-inactivation: Repeat vs genic silencing in the mouse. Mol Cell Biol 30, 3187-3205. PMCID2897575
  9. Lee, J.T. (2010) The X as model for RNA’s niche in epigenomic regulation. CSH Perspectives in Biology 2, a003749.
  10. Paro, R., and Lee, J.T. (2010) Extending the frontiers of epigenetic regulation. Curr Opin Genet Dev 20, 107-109.
  11. Lee, J.T. (2010) The X as model for RNA’s niche in epigenomic regulation. CSH Perspectives in Biology. 2, a1003749. Epub 2010 Mar 31.


2009

  1. Zhou D, Conrad C, Xia F, Park JS, Payer B, Yin Y, Lauwers GY, Thasler W, Lee J.T., Avruch J, Bardeesy N. (2009) Mst1 and Mst2 maintain hepatocyte quiescence and suppress hepatocellular carcinoma development through inactivation of the Yap1 oncogene. Cancer Cell 16, 425-438. PMCID3023165
  2. Lee, J.T. (2009) Lessons from X-chromosome inactivation: long ncRNA as guides and tethers to the epigenome. Genes Dev 23, 1831-1842. PMCID2725936
  3. Donohoe, M.E. †, Silva, S.S. †, Pinter, S.F., Xu, N., and Lee, J.T. (2009) The pluripotency factor Oct4 interacts with Ctcf and also controls X-chromosome pairing and counting. Nature 460, 128-132. PMCID3057664
  4. Zhang, L., Ogawa, Y., Ahn, J., Namekawa, S.H., Silva, S., and Lee, J.T. (2009) Telomeric RNAs mark sex chromosomes in stem cells. Genetics 182, 685-698. PMCID2710151
  5. Lee, J.T. (2009) Lessons from X-chromosome inactivation: long ncRNA as gudes and tethers to the epigenome. Genes Dev 23, 1831-1842.
  6. Namekawa, S.H., and Lee, J.T. (2009) Is meiotic sex chromosome inactivation the rule in evolution? PLoS Genet 5, e1000493. PMCID267206


2008

  1. Zhao, J., Sun, B.K., Erwin, J.A., Song, J.J., and Lee, J.T. (2008) Polycomb proteins targeted by a short repeat RNA to the mouse X-chromosome. Science 322, 750-756. PMCID2748911
  2. Anguera, M., Liu, M., Avruch, J., and Lee, J.T. (2008) Characterization of two Mst1-deficient mouse models. Dev Dynamics 237, 3424-3434. PMCID2596583
  3. Lindroth, A.M., Park, Y.J., MeLean, C.M., Dokshin, G.A., Persson, J.M., Herman, H., Pasini, D., Miro, X., Donohoe, M.E., Lee, J.T., Helin, K., and Soloway, P. (2008) Antagonism between DNA and H3K27 methylation at the imprinted Rasgrf1 locus. PLoS Genet. 4, e1000145. PMCID2475503
  4. Ogawa, Y., Sun, B.K, and Lee, J.T. (2008) Intersection of the RNAi and X-inactivation pathways. Science 320, 1336-1341. PMCID2584363
  5. Tsai, C.L. †, Rowntree, R.K. †, Cohen, D.E., and Lee, J.T. (2008) Higher order chromatin struture at the X-inactivation center via looping DNA. Dev Biol. 319, 416-425. PMCID2567126
  6. Silva, S.S. †, Rowntree, R.K. †, Mekhoubad, S., and Lee, J.T. (2008) X-chromosome inactivation and epigenetic fluidity in human embryonic stem cells. Proc Natl Acad Sci, USA 105, 4820-4825. PMCID2290799
  7. Payer, B., and Lee, J.T. (2008) X-chromosome dosage compensation: How mammals keep the balance. Annual Review of Genetics 42, 633-772.
  8. Erwin, J.A., and Lee, J.T. (2008) New Twists in X-chromosome inactivation. Curr Op Cell Biol, 20(3),349-355.
  9. Shibata, S. and Lee, J.T. (2008) MacroRNAs in the epigenetic control of X-chromosome inactivation. In: Epigenomics Ed. A.C Ferguson-Smith, et al. (Springer, Netherlands), pp 187-214.


2007

  1. Xu, N. †, Donohoe, M.E. †, Silva, S.S., and Lee, J.T. (2007) Evidence for a role of transcription and Ctcf protein in homologous X-chromosome pairing. Nature Genetics 39,1390-1396.
  2. Kim, S., Namekawa, S.H., Niswander, L.M., Ward, J.O., Lee, J.T., Bardwell, V.J., Zarkower, (2007) A mammal-specific Doublesex homolog associates with male sex chromatin and is required for male meiosis. PLoS Genet 3:e62.
  3. Namekawa, S.H., VandeBerg, J.L., McCarrey, J.R.†, and Lee, J.T.† (2007) Sex chromosome silencing in the marsupial male germ line. Proc Natl Acad Sci, USA 104, 9730-9735. PMCID1887598
  4. Zhang, L.F., Huynh, K.D., and Lee, J.T. (2007) Perinculeolar targeting of the inactive X during S phase: evidence for a role in the maintenance of silencing. Cell 129, 693-706.
  5. Mikkelson, T.S., Wakefieldm M.J, Aken, B., Amemiya, C.T., Chang, J.L., Duke, S., Garber, M., Gentles, A.J., Goodstadt, L., Heger, A., Jurka, J., Kamal, M., Mauceli, E., Searle, S.M., Sharpe, T., Baker, M.L., Batzer, M.A., Benos, P.V., Belov, K., Clamp, M., Cook, A., Cuff, J., Das, R., Davidow, L., Deakin, J.E., Fazzari, M.J., Glass, J.L., Grabherr, M., Greally, J.M., Gu, W., Hore, T.A., Huttley, G.A., Kleber, M., Jirtle, R.L., Koina, E., Lee, J.T., Mahony, S., Marra, M.A., Miller, R.D., Nicholls, R.D., Oda, M., Papenfuss, A.T., Parra, Z.E., Pollock, D.D., Ray, D.A., Schein, J.E., Speed, T.P., Thompson, K., VandeBerg, J.L., Wade, C.M., Walker, J.A., Waters, P.D., Webber, C., Weidman, J.R., Xie, X., Zody, M.C; Broad Institute Genome Sequencing Platform; Broad Institute Whole Genome Assembly Team, Graves, J.A., Ponting, C..P, Breen, M., Samollow, P.B., Lander, E.S., Lindblad-Toh, K., (2007) Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature 447, 167-177.
  6. Davidow, L.S., Breen, M., Duke, S.E., Samollow, P.B., McCarrey, J.R., and Lee, J.T. (2007) The search for a marsupial XIC reveals a break with vertebrate synteny. Chromosome Research 15, 137-146.
  7. Donohoe, M.E., Zhang, L.-F., Xu, N., Shi, Y., and Lee, J.T. (2007) Identification of a Ctcf co-factor, Yy1, for the X-chromosome binary switch. Molecular Cell 25, 43-56.
  8. Cohen, D.E.†, Davidow, L.S.†, Erwin, J.A., Xu, N., Warshawsky, D., and Lee, J.T. (2007) The DXPas34 repeat regulates random and imprinted X-inactivation. Developmental Cell 12, 57-71.
  9. Anguera, M.C., Sun, B.K., Xu, N., and Lee, J.T. (2007) X-chromosome kiss and tell: How the Xs go their separate ways. Cold Spring Harbor Symposium on Quantitative Biology 71, 429-437.


2006

  1. Lewis, A., Green, K., Dawson, C., Redrup, L., Dean, W., Huynh, K.D., Lee, J.T., Hemberger, M., Reik W. (2006) Epigenetic dynamics of the Kcnq1 imprinted domain in the early embryo. Development 133, 4203-4210.
  2. Rowntree, R.K., and Lee, J.T. (2006) Mapping of DNA replication origins to non-coding genes of the X-inactivation center. Mol. Cell Biol., 26, 3707-3717.
  3. Namekawa, S., Park, P.J., Zhang, L.F., Shima, J., McCarrey, J.R., Griswold, M., and Lee, J.T. (2006) Post-meiotic sex chromatin in the male germline of mice. Current Biology 16, 660-667.
  4. Sun, B.K., Deaton, A., and Lee, J.T. (2006) A transient heterochromatic state in Xist preempts and predicts X-inactivation choice without RNA stabilization. Molecular Cell 21, 617-628.
  5. Boumil, R.M., Ogawa, Y., Sun, B.K., Huynh, K., and Lee, J.T. (2006) Differential methylation of Xite and CTCF sites in Tsix mirrors the pattern of X-inactivation choice in mice. Mol Cell Biol 26, 2109-2117.
  6. Xu, N., Tsai, C.L., and Lee, J.T. (2006) Transient homologous chromosome pairing marks the onset of X inactivation. Science 311, 1149-1152.
  7. Sun, B.K., and Lee, J.T. (2006) X-chromosome inactivation. Chapter in Encyclopedia Reference of Genomics and Proteomics in Molecular Medicine. Springer-Verlag.


2005

  1. Lee, J.T. (2005) Regulation of X-chromosome counting by Tsix and Xite sequences. Science 29, 768-71.
  2. Huynh, K.D., and Lee, J.T. (2005) The ontogeny and phylogeny of X-chromosome inactivation. Nature Reviews Genetics 6, 410-418. (An original peer-reviewed theoretical treatise).
  3. Stavropoulos.N., Rowntree, R.K., and Lee, J.T. (2005) Identification of developmentally specific enhancers for Tsix in the regulation of X chromosome inactivation. Mol & Cell Biol 25, 2757-2769.
  4. Spencer, R. and Lee, J.T. (2005) Noncoding RNAs in imprinting and dosage compensation. In: RNA World III, 3rd Ed., Eds: R.F.Gesteland, T.R. Cech, J.F. Atkins, Cold Spring Harbor Laboratory Press.
  5. Lee, J.T. (2005) Sex chromosome inactivation: The importance of pairing. Curr Biol 15, R249-R252.


2004

  1. Shibata, S. and Lee, J.T. (2004) Transcription- vs. RNA-mediated mechanisms of Tsix action in Xist repression and epigenetic choice. Current Biology 14, 1747-1754.


2003

  1. Huynh, K.D. and Lee, J.T. (2003) Inheritance of a pre-inactivated paternal X-chromosome in early mouse embryos. Nature 426, 857-862.
  2. O'Neill, L.P., Randall, T.E., Lavender, J., Spotswood, H.T., Lee, J.T., Turner, B.M. (2003) X-linked genes in female embryonic stem cells carry an epigenetic mark prior to the onset of X inactivation. Hum Mole Genet 12, 1783-1790.
  3. Ogawa, Y. and Lee, J.T. (2003) Xite, X-inactivation intergenic transcription elements that regulate the probability of choice. Molecular Cell 11, 731-743.
  4. Shibata, S. and Lee, J.T. (2003) Characterization and quantitation of Tsix transcriptional variants: implications for the mechanism of antisense regulation. Hum Mole Genet 12, 125-136.
  5. Lee, J.T. (2003) Functional intergenic transcription: A case of the X-inactivation center. Philosophical Transactions B 358:,1417-1423.
  6. Ogawa, Y. and Lee, J.T. (2003) Antisense RNA's in autosomal imprinting and X-chromosome inactivation. Review chapter in special volume devoted to "Vertebrate Sex Chromosomes.” Cytogenet Genome Res. 99, 59-65.
  7. Lee, J.T. (2003) News & Views: Complicity of gene and pseudogene. Nature 423, 26-28.
  8. Lee, J.T. (2003) Molecular links between X-chromosome inactivation and autosomal imprinting: dosage compensation as an evolutionary impetus for imprinting. Current Biology 13, R242-R254.


2002

  1. Lee, J.T. (2002) Homozygous Tsix mutant mice reveal a sex-ratio distortion and revert to random X-inactivation. Nature Genetics 32, 195-200.
  2. Chao, W., Huynh, K.D., Spencer, R.J., Davidow, L.S., and Lee, J.T. (2002) CTCF, a candidate trans-acting factor for X-inactivation choice. Science 295, 345-347.
  3. Lee, J.T. (2002) Is X-chromosome inactivation a homology effect? In: Advances in Genetics in Genetics . Ed: J. Dunlap and C.T. Wu, Academic Press.
  4. Cohen, D.E. and Lee, J.T. (2002) X-chromosome inactivation and the search for chromosome-wide silencers. Curr Op Genet Dev 12, 219-224.


1998-2001

  1. Stavropoulos, N., Lu, N., and Lee, J.T. (2001) A functional role for Tsix transcription in blocking Xist RNA accumulation but not in X-chromosome choice. Proc Natl Acad Sci, USA 98, 10, 232-237.
  2. Huynh, K.D. and Lee, J.T. (2001) Imprinted X inactivation in eutherians: a model of gametic execution and zygotic relaxation. Curr Op Genet Dev 12, 219-224..
  3. Boumil, R. M., and Lee, J.T. (2001) Decoding the silence in X-chromosome inactivation. Hum Molec Gent 10, 2225-2232.
  4. Lee, J.T. (2000) Disruption of imprinted X-inactivation by parent-of-origin effects at Tsix. Cell 103, 17-27.
  5. Reizes, B., Lee, J.T., and Leder, P. (2000) Homologous genomic fragments in the mouse pre-T cell receptor alpha (pTa) and Xist loci. Genomics 63, 149-15.
  6. Warshawsky, D., Stavropoulos, N., and Lee, J.T. (1999) Further examination of the Xist promoter switch hypothesis in X-inactivation: Evidence against the existence and function of a Po promoter. Proc Natl Acad Sci, USA 96,424-429.
  7. Lee, J.T., and Lu, N. (1999) Targeted mutagenesis of Tsix leads to nonrandom X-inactivation. Cell 99, 47-57.
  8. Lee, J.T., Davidow, L.S., and Warshawsky, D. (1999) Tsix, a gene antisense to Xist at the X-inactivation centre. Nature Genetics 21, 400-404.
  9. Lee, J.T., Lu, N., and Han, Y. (1999) Genetic analysis of the mouse X-inactivation center defines an 80-kb multifunction domain. Proc Natl Acad Sci, USA 96, 3836-3841.
  10. Lee, J.T. (1998) X-chromosome inactivation in mammals. In: Development: Genetics, Epigenetics and Environmental Regulation. Ed: V.E.A. Russo et al., Springer-Verlag, Heidelberg.
Laboratory of Jeannie T. Lee
Department of Molecular Biology
Massachusetts General Hospital & Department of Genetics
The Blavatnik Institute | Harvard Medical School
​185 Cambridge Street, Boston, MA 02114 USA
Contact: Molly O'Mara Fillmore

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