Kathrin Plath*
The Plath lab has made numerous ground-breaking contributions that have vast impacts on the scientific community. For example, the lab is leading the way in the discovery of mechanisms underlying X-chromosome inactivation by the long non-coding RNA Xist, from identifying how the RNA can target an entire chromosome to defining protein crowding as the mechanism of action by which few Xist molecules can silence the the 1000 genes along the entire X chromosome. The work of the Plath lab on Xist is showing how RNAs can build functional nuclear compartments. The Plath lab also pioneered the understanding of different modes on X-chromosome dosage compensation by XIST RNA in early human development and discovered an unexpected autosomal function for the RNA with implications for understanding the female bias of diseases. The Plath lab also uncovered key mechanisms underlying transcription factor-induced reprogramming of somatic cells to induced pluripotent stem cells that are providing a considerable impetus for understanding and rationally designing cell fate transition. Here we specifically focus on how cis-regulatory enhancer elements are selected and activated by transcription factors. We are also dissecting how genetic variation controls enhancer function. In addition to continuing the work on X-chromosome dosage compensation, lncRNA function, enhancers and gene regulation, the Plath lab is now also aiming to understand how nutrients that vary with diet can regulate stem cell states and cell fate decisions, particularly those during development, with the ultimate goal to define dietary alterations that enable more accurate models of differentiation in the culture dish or lead to new treatments of pregnancy complications and diseases. We are also using embryonic stem cells, induced pluripotent stem cells and new embryo models to understand the gene regulatory networks underlying cellular specification during development and pathophysiologies. Often, we develop new single cell genomics technologies and apply them to our diverse biological model systems. In collaboration with the Gomperts lab, we are, for instance, deciphering the difference between the healthy and disease lung at a mechanistic and omics level applying novel multi-comics approaches.
Websites:
Research Interests:
induced pluripotent stem cells, enhancers, female-specific processes, reprogramming, development, gene regulation, infertility, embryo models, X-chromosome inactivation, Pluripotent Stem Cells, Genomics, lung disease, placenta biology, Epigenetics, Female-disease bias, X-chromosome dosage compensation, transcription factors, long noncoding RNAs, impact of genetic variation on cell function and cell fate change, metabolism, multiomics technologies,Publications:
Freeland J, Muñoz M, O'Donnell E, Langerman J, Darrow M, Bergonio J, Suarez-Navarro J, Thorpe S, Canter R, Randall RL, Plath K, Carraway KL, Witte ON, Graeber TG, Carr-Ascher JR. Genetic Screen in a Preclinical Model of Sarcoma Development Defines Drivers and Therapeutic Vulnerabilities. Clin Cancer Res. 2024 Nov 01; 30(21):4957-4973. view on PubMed
Dror I, Tan T, Plath K. A critical role for X-chromosome architecture in mammalian X-chromosome dosage compensation. Curr Opin Genet Dev. 2024 Aug; 87:102235. view on PubMed
Chandran RR, Vijayaraj P, Garcia-Milian R, King J, Castillo K, Chen L, Kwon Y, William S, Rickabaugh TM, Langerman J, Choi W, Sen C, Lever JEP, Li Q, Pavelkova N, Plosa EJ, Rowe SM, Plath K, Clair G, Gomperts BN. Loss of cell junctional components and matrix alterations drive cell desquamation and fibrotic changes in Idiopathic Pulmonary Fibrosis. bioRxiv. 2024 Jun 22. view on PubMed
Zacco E, Broglia L, Kurihara M, Monti M, Gustincich S, Pastore A, Plath K, Nagakawa S, Cerase A, Sanchez de Groot N, Tartaglia GG. RNA: The Unsuspected Conductor in the Orchestra of Macromolecular Crowding. Chem Rev. 2024 Apr 24; 124(8):4734-4777. view on PubMed
Tang AA, Afasizheva A, Cano CT, Plath K, Black D, Franco E. Optimization of RNA Pepper Sensors for the Detection of Arbitrary RNA Targets. ACS Synth Biol. 2024 02 16; 13(2):498-508. view on PubMed
Dror I, Chitiashvili T, Tan SYX, Cano CT, Sahakyan A, Markaki Y, Chronis C, Collier AJ, Deng W, Liang G, Sun Y, Afasizheva A, Miller J, Xiao W, Black DL, Ding F, Plath K. XIST directly regulates X-linked and autosomal genes in naive human pluripotent cells. Cell. 2024 01 04; 187(1):110-129.e31. view on PubMed
Udani S, Langerman J, Koo D, Baghdasarian S, Cheng B, Kang S, Soemardy C, de Rutte J, Plath K, Di Carlo D. Associating growth factor secretions and transcriptomes of single cells in nanovials using SEC-seq. Nat Nanotechnol. 2024 Mar; 19(3):354-363. view on PubMed
Hoetker MS, Yagi M, Di Stefano B, Langerman J, Cristea S, Wong LP, Huebner AJ, Charlton J, Deng W, Haggerty C, Sadreyev RI, Meissner A, Michor F, Plath K, Hochedlinger K. H3K36 methylation maintains cell identity by regulating opposing lineage programmes. Nat Cell Biol. 2023 Aug; 25(8):1121-1134. view on PubMed
Tu WB, Christofk HR, Plath K. Nutrient regulation of development and cell fate decisions. Development. 2023 10 15; 150(20). view on PubMed
Cicchetto AC, Jacobson EC, Sunshine H, Wilde BR, Krall AS, Jarrett KE, Sedgeman L, Turner M, Plath K, Iruela-Arispe ML, de Aguiar Vallim TQ, Christofk HR. ZFP36-mediated mRNA decay regulates metabolism. Cell Rep. 2023 05 30; 42(5):112411. view on PubMed
Udani S, Langerman J, Koo D, Baghdasarian S, Cheng B, Kang S, Soemardy C, de Rutte J, Plath K, Carlo DD. Secretion encoded single-cell sequencing (SEC-seq) uncovers gene expression signatures associated with high VEGF-A secretion in mesenchymal stromal cells. bioRxiv. 2023 Jan 08. view on PubMed
Deng W, Sha J, Xue F, Jami-Alahmadi Y, Plath K, Wohlschlegel J. High-Field Asymmetric Waveform Ion Mobility Spectrometry Interface Enhances Parallel Reaction Monitoring on an Orbitrap Mass Spectrometer. Anal Chem. 2022 11 22; 94(46):15939-15947. view on PubMed
Lo JH, Edwards M, Langerman J, Sridharan R, Plath K, Smale ST. Oct4:Sox2 binding is essential for establishing but not maintaining active and silent states of dynamically regulated genes in pluripotent cells. Genes Dev. 2022 10 01; 36(19-20):1079-1095. view on PubMed
Watanabe M, Buth JE, Haney JR, Vishlaghi N, Turcios F, Elahi LS, Gu W, Pearson CA, Kurdian A, Baliaouri NV, Collier AJ, Miranda OA, Dunn N, Chen D, Sabri S, Torre-Ubieta L, Clark AT, Plath K, Christofk HR, Kornblum HI, Gandal MJ, Novitch BG. TGFβ superfamily signaling regulates the state of human stem cell pluripotency and capacity to create well-structured telencephalic organoids. Stem Cell Reports. 2022 10 11; 17(10):2220-2238. view on PubMed
Jacobson EC, Pandya-Jones A, Plath K. A lifelong duty: how Xist maintains the inactive X chromosome. Curr Opin Genet Dev. 2022 08; 75:101927. view on PubMed
Chitiashvili T, Hsu FM, Dror I, Plath K, Clark A. FGFR3 is expressed by human primordial germ cells and is repressed after meiotic initiation to form primordial oocytes. Stem Cell Reports. 2022 06 14; 17(6):1268-1278. view on PubMed
Collier AJ, Bendall A, Fabian C, Malcolm AA, Tilgner K, Semprich CI, Wojdyla K, Nisi PS, Kishore K, Roamio Franklin VN, Mirshekar-Syahkal B, D'Santos C, Plath K, Yusa K, Rugg-Gunn PJ. Genome-wide screening identifies Polycomb repressive complex 1.3 as an essential regulator of human naïve pluripotent cell reprogramming. Sci Adv. 2022 03 25; 8(12):eabk0013. view on PubMed
Pezhouman A, Nguyen NB, Sercel AJ, Nguyen TL, Daraei A, Sabri S, Chapski DJ, Zheng M, Patananan AN, Ernst J, Plath K, Vondriska TM, Teitell MA, Ardehali R. Transcriptional, Electrophysiological, and Metabolic Characterizations of hESC-Derived First and Second Heart Fields Demonstrate a Potential Role of TBX5 in Cardiomyocyte Maturation. Front Cell Dev Biol. 2021; 9:787684. view on PubMed
Markaki Y, Chong JG, Wang Y, Jacobson EC, Luong C, Tan SYX, Jachowicz JW, Strehle M, Maestrini D, Banerjee AK, Mistry BA, Dror I, Dossin F, Sch?neberg J, Heard E, Guttman M, Chou T, Plath K. Xist nucleates local protein gradients to propagate silencing across the X chromosome. Cell. 2021 Dec 09; 184(25):6212. view on PubMed
Quinodoz SA, Jachowicz JW, Bhat P, Ollikainen N, Banerjee AK, Goronzy IN, Blanco MR, Chovanec P, Chow A, Markaki Y, Thai J, Plath K, Guttman M. RNA promotes the formation of spatial compartments in the nucleus. Cell. 2021 11 11; 184(23):5775-5790.e30. view on PubMed
Markaki Y, Gan Chong J, Wang Y, Jacobson EC, Luong C, Tan SYX, Jachowicz JW, Strehle M, Maestrini D, Banerjee AK, Mistry BA, Dror I, Dossin F, Schöneberg J, Heard E, Guttman M, Chou T, Plath K. Xist nucleates local protein gradients to propagate silencing across the X chromosome. Cell. 2021 12 09; 184(25):6174-6192.e32. view on PubMed
Allison T, Langerman J, Sabri S, Otero-Garcia M, Lund A, Huang J, Wei X, Samarasinghe RA, Polioudakis D, Mody I, Cobos I, Novitch BG, Geschwind DH, Plath K, Lowry WE. Defining the nature of human pluripotent stem cell-derived interneurons via single-cell analysis. Stem Cell Reports. 2021 10 12; 16(10):2548-2564. view on PubMed
Samarasinghe RA, Miranda OA, Buth JE, Mitchell S, Ferando I, Watanabe M, Allison TF, Kurdian A, Fotion NN, Gandal MJ, Golshani P, Plath K, Lowry WE, Parent JM, Mody I, Novitch BG. Identification of neural oscillations and epileptiform changes in human brain organoids. Nat Neurosci. 2021 10; 24(10):1488-1500. view on PubMed
Hancock GV, Liu W, Peretz L, Chen D, Gell JJ, Collier AJ, Zamudio JR, Plath K, Clark AT. Divergent roles for KLF4 and TFCP2L1 in naive ground state pluripotency and human primordial germ cell development. Stem Cell Res. 2021 08; 55:102493. view on PubMed
Deng W, Jacobson EC, Collier AJ, Plath K. The transcription factor code in iPSC reprogramming. Curr Opin Genet Dev. 2021 10; 70:89-96. view on PubMed
Carraro G, Langerman J, Sabri S, Lorenzana Z, Purkayastha A, Zhang G, Konda B, Aros CJ, Calvert BA, Szymaniak A, Wilson E, Mulligan M, Bhatt P, Lu J, Vijayaraj P, Yao C, Shia DW, Lund AJ, Israely E, Rickabaugh TM, Ernst J, Mense M, Randell SH, Vladar EK, Ryan AL, Plath K, Mahoney JE, Stripp BR, Gomperts BN. Transcriptional analysis of cystic fibrosis airways at single-cell resolution reveals altered epithelial cell states and composition. Nat Med. 2021 05; 27(5):806-814. view on PubMed
Mullen PJ, Garcia G, Purkayastha A, Matulionis N, Schmid EW, Momcilovic M, Sen C, Langerman J, Ramaiah A, Shackelford DB, Damoiseaux R, French SW, Plath K, Gomperts BN, Arumugaswami V, Christofk HR. SARS-CoV-2 infection rewires host cell metabolism and is potentially susceptible to mTORC1 inhibition. Nat Commun. 2021 03 25; 12(1):1876. view on PubMed
Deng W, Sha J, Plath K, Wohlschlegel JA. Carboxylate-Modified Magnetic Bead (CMMB)-Based Isopropanol Gradient Peptide Fractionation (CIF) Enables Rapid and Robust Off-Line Peptide Mixture Fractionation in Bottom-Up Proteomics. Mol Cell Proteomics. 2021; 20:100039. view on PubMed
Guo J, Sosa E, Chitiashvili T, Nie X, Rojas EJ, Oliver E, DonorConnect, Plath K, Hotaling JM, Stukenborg JB, Clark AT, Cairns BR. Single-cell analysis of the developing human testis reveals somatic niche cell specification and fetal germline stem cell establishment. Cell Stem Cell. 2021 04 01; 28(4):764-778.e4. view on PubMed
Patananan AN, Sercel AJ, Wu TH, Ahsan FM, Torres A, Kennedy SAL, Vandiver A, Collier AJ, Mehrabi A, Van Lew J, Zakin L, Rodriguez N, Sixto M, Tadros W, Lazar A, Sieling PA, Nguyen TL, Dawson ER, Braas D, Golovato J, Cisneros L, Vaske C, Plath K, Rabizadeh S, Niazi KR, Chiou PY, Teitell MA. Pressure-Driven Mitochondrial Transfer Pipeline Generates Mammalian Cells of Desired Genetic Combinations and Fates. Cell Rep. 2020 12 29; 33(13):108562. view on PubMed
Meshorer E, Plath K. Chromatin and Nuclear Architecture in Stem Cells. Stem Cell Reports. 2020 12 08; 15(6):1155-1157. view on PubMed
Chitiashvili T, Dror I, Kim R, Hsu FM, Chaudhari R, Pandolfi E, Chen D, Liebscher S, Schenke-Layland K, Plath K, Clark A. Female human primordial germ cells display X-chromosome dosage compensation despite the absence of X-inactivation. Nat Cell Biol. 2020 12; 22(12):1436-1446. view on PubMed
Purkayastha A, Sen C, Garcia G, Langerman J, Shia DW, Meneses LK, Vijayaraj P, Durra A, Koloff CR, Freund DR, Chi J, Rickabaugh TM, Mulay A, Konda B, Sim MS, Stripp BR, Plath K, Arumugaswami V, Gomperts BN. Direct Exposure to SARS-CoV-2 and Cigarette Smoke Increases Infection Severity and Alters the Stem Cell-Derived Airway Repair Response. Cell Stem Cell. 2020 12 03; 27(6):869-875.e4. view on PubMed
Pandya-Jones A, Markaki Y, Serizay J, Chitiashvili T, Leon WRM, Damianov A, Chronis C, Papp B, Chen CK, McKee R, Wang XJ, Chau A, Sabri S, Leonhardt H, Zheng S, Guttman M, Black DL, Plath K. Publisher Correction: A protein assembly mediates Xist localization and gene silencing. Nature. 2020 Oct; 586(7830):E30. view on PubMed
Pandya-Jones A, Markaki Y, Serizay J, Chitiashvili T, Mancia Leon WR, Damianov A, Chronis C, Papp B, Chen CK, McKee R, Wang XJ, Chau A, Sabri S, Leonhardt H, Zheng S, Guttman M, Black DL, Plath K. A protein assembly mediates Xist localization and gene silencing. Nature. 2020 11; 587(7832):145-151. view on PubMed
Purkayastha A, Sen C, Garcia G, Langerman J, Vijayaraj P, Shia DW, Meneses LK, Rickabaugh TM, Mulay A, Konda B, Sim MS, Stripp BR, Plath K, Arumugaswami V, Gomperts BN. Direct exposure to SARS-CoV-2 and cigarette smoke increases infection severity and alters the stem cell-derived airway repair response. bioRxiv. 2020 Jul 29. view on PubMed
Xi H, Langerman J, Sabri S, Chien P, Young CS, Younesi S, Hicks M, Gonzalez K, Fujiwara W, Marzi J, Liebscher S, Spencer M, Van Handel B, Evseenko D, Schenke-Layland K, Plath K, Pyle AD. A Human Skeletal Muscle Atlas Identifies the Trajectories of Stem and Progenitor Cells across Development and from Human Pluripotent Stem Cells. Cell Stem Cell. 2020 Jul 02; 27(1):181-185. view on PubMed
Xi H, Langerman J, Sabri S, Chien P, Young CS, Younesi S, Hicks M, Gonzalez K, Fujiwara W, Marzi J, Liebscher S, Spencer M, Van Handel B, Evseenko D, Schenke-Layland K, Plath K, Pyle AD. A Human Skeletal Muscle Atlas Identifies the Trajectories of Stem and Progenitor Cells across Development and from Human Pluripotent Stem Cells. Cell Stem Cell. 2020 07 02; 27(1):158-176.e10. view on PubMed
Takahashi R, Grzenda A, Allison TF, Rawnsley J, Balin SJ, Sabri S, Plath K, Lowry WE. Defining Transcriptional Signatures of Human Hair Follicle Cell States. J Invest Dermatol. 2020 04; 140(4):764-773.e4. view on PubMed
Polioudakis D, de la Torre-Ubieta L, Langerman J, Elkins AG, Shi X, Stein JL, Vuong CK, Nichterwitz S, Gevorgian M, Opland CK, Lu D, Connell W, Ruzzo EK, Lowe JK, Hadzic T, Hinz FI, Sabri S, Lowry WE, Gerstein MB, Plath K, Geschwind DH. A Single-Cell Transcriptomic Atlas of Human Neocortical Development during Mid-gestation. Neuron. 2019 09 04; 103(5):785-801.e8. view on PubMed
Bonora G, Rubbi L, Morselli M, Ma F, Chronis C, Plath K, Pellegrini M. DNA methylation estimation using methylation-sensitive restriction enzyme bisulfite sequencing (MREBS). PLoS One. 2019; 14(4):e0214368. view on PubMed
Zhang W, Chronis C, Chen X, Zhang H, Spalinskas R, Pardo M, Chen L, Wu G, Zhu Z, Yu Y, Yu L, Choudhary J, Nichols J, Parast MM, Greber B, Sahlén P, Plath K. The BAF and PRC2 Complex Subunits Dpf2 and Eed Antagonistically Converge on Tbx3 to Control ESC Differentiation. Cell Stem Cell. 2019 01 03; 24(1):138-152.e8. view on PubMed
Fu K, Chronis C, Soufi A, Bonora G, Edwards M, Smale ST, Zaret KS, Plath K, Pellegrini M. Comparison of reprogramming factor targets reveals both species-specific and conserved mechanisms in early iPSC reprogramming. BMC Genomics. 2018 Dec 22; 19(1):956. view on PubMed
Sun F, Chronis C, Kronenberg M, Chen XF, Su T, Lay FD, Plath K, Kurdistani SK, Carey MF. Promoter-Enhancer Communication Occurs Primarily within Insulated Neighborhoods. Mol Cell. 2019 01 17; 73(2):250-263.e5. view on PubMed
Di Stefano B, Ueda M, Sabri S, Brumbaugh J, Huebner AJ, Sahakyan A, Clement K, Clowers KJ, Erickson AR, Shioda K, Gygi SP, Gu H, Shioda T, Meissner A, Takashima Y, Plath K, Hochedlinger K. Reduced MEK inhibition preserves genomic stability in naive human embryonic stem cells. Nat Methods. 2018 09; 15(9):732-740. view on PubMed
Jelinek D, Flores A, Uebelhoer M, Pasque V, Plath K, Iruela-Arispe ML, Christofk HR, Lowry WE, Coller HA. Mapping Metabolism: Monitoring Lactate Dehydrogenase Activity Directly in Tissue. J Vis Exp. 2018 06 21; (136). view on PubMed
Sahakyan A, Yang Y, Plath K. The Role of Xist in X-Chromosome Dosage Compensation. Trends Cell Biol. 2018 12; 28(12):999-1013. view on PubMed
Allison TF, Smith AJH, Anastassiadis K, Sloane-Stanley J, Biga V, Stavish D, Hackland J, Sabri S, Langerman J, Jones M, Plath K, Coca D, Barbaric I, Gokhale P, Andrews PW. Identification and Single-Cell Functional Characterization of an Endodermally Biased Pluripotent Substate in Human Embryonic Stem Cells. Stem Cell Reports. 2018 06 05; 10(6):1895-1907. view on PubMed
Ohashi M, Korsakova E, Allen D, Lee P, Fu K, Vargas BS, Cinkornpumin J, Salas C, Park JC, Germanguz I, Langerman J, Chronis C, Kuoy E, Tran S, Xiao X, Pellegrini M, Plath K, Lowry WE. Loss of MECP2 Leads to Activation of P53 and Neuronal Senescence. Stem Cell Reports. 2018 05 08; 10(5):1453-1463. view on PubMed
Pasque V, Karnik R, Chronis C, Petrella P, Langerman J, Bonora G, Song J, Vanheer L, Sadhu Dimashkie A, Meissner A, Plath K. X Chromosome Dosage Influences DNA Methylation Dynamics during Reprogramming to Mouse iPSCs. Stem Cell Reports. 2018 05 08; 10(5):1537-1550. view on PubMed
Guo G, von Meyenn F, Rostovskaya M, Clarke J, Dietmann S, Baker D, Sahakyan A, Myers S, Bertone P, Reik W, Plath K, Smith A. Correction: Epigenetic resetting of human pluripotency (doi:10.1242/dev.146811). Development. 2018 04 18; 145(8). view on PubMed
Sereti KI, Nguyen NB, Kamran P, Zhao P, Ranjbarvaziri S, Park S, Sabri S, Engel JL, Sung K, Kulkarni RP, Ding Y, Hsiai TK, Plath K, Ernst J, Sahoo D, Mikkola HKA, Iruela-Arispe ML, Ardehali R. Analysis of cardiomyocyte clonal expansion during mouse heart development and injury. Nat Commun. 2018 02 21; 9(1):754. view on PubMed
Keegan A, Plath K, Damoiseaux R. High-Throughput Screening of a Luciferase Reporter of Gene Silencing on the Inactive X Chromosome. Methods Mol Biol. 2018; 1755:75-87. view on PubMed
Sahakyan A, Plath K, Rougeulle C. Regulation of X-chromosome dosage compensation in human: mechanisms and model systems. Philos Trans R Soc Lond B Biol Sci. 2017 Nov 05; 372(1733). view on PubMed
Guo G, von Meyenn F, Rostovskaya M, Clarke J, Dietmann S, Baker D, Sahakyan A, Myers S, Bertone P, Reik W, Plath K, Smith A. Epigenetic resetting of human pluripotency. Development. 2017 08 01; 144(15):2748-2763. view on PubMed
Huang C, Su T, Xue Y, Cheng C, Lay FD, McKee RA, Li M, Vashisht A, Wohlschlegel J, Novitch BG, Plath K, Kurdistani SK, Carey M. Cbx3 maintains lineage specificity during neural differentiation. Genes Dev. 2017 02 01; 31(3):241-246. view on PubMed
Chronis C, Fiziev P, Papp B, Butz S, Bonora G, Sabri S, Ernst J, Plath K. Cooperative Binding of Transcription Factors Orchestrates Reprogramming. Cell. 2017 01 26; 168(3):442-459.e20. view on PubMed
Patel S, Bonora G, Sahakyan A, Kim R, Chronis C, Langerman J, Fitz-Gibbon S, Rubbi L, Skelton RJP, Ardehali R, Pellegrini M, Lowry WE, Clark AT, Plath K. Human Embryonic Stem Cells Do Not Change Their X Inactivation Status during Differentiation. Cell Rep. 2017 01 03; 18(1):54-67. view on PubMed
Sahakyan A, Kim R, Chronis C, Sabri S, Bonora G, Theunissen TW, Kuoy E, Langerman J, Clark AT, Jaenisch R, Plath K. Human Naive Pluripotent Stem Cells Model X Chromosome Dampening and X Inactivation. Cell Stem Cell. 2017 01 05; 20(1):87-101. view on PubMed
Gu W, Gaeta X, Sahakyan A, Chan AB, Hong CS, Kim R, Braas D, Plath K, Lowry WE, Christofk HR. Glycolytic Metabolism Plays a Functional Role in Regulating Human Pluripotent Stem Cell State. Cell Stem Cell. 2016 10 06; 19(4):476-490. view on PubMed
Sahakyan A, Plath K. Transcriptome Encyclopedia of Early Human Development. Cell. 2016 May 05; 165(4):777-9. view on PubMed
Pandya-Jones A, Plath K. The "lnc" between 3D chromatin structure and X chromosome inactivation. Semin Cell Dev Biol. 2016 08; 56:35-47. view on PubMed
Pastor WA, Chen D, Liu W, Kim R, Sahakyan A, Lukianchikov A, Plath K, Jacobsen SE, Clark AT. Naive Human Pluripotent Cells Feature a Methylation Landscape Devoid of Blastocyst or Germline Memory. Cell Stem Cell. 2016 Mar 03; 18(3):323-329. view on PubMed
Pasque V, Plath K. X chromosome reactivation in reprogramming and in development. Curr Opin Cell Biol. 2015 Dec; 37:75-83. view on PubMed
Minkovsky A, Sahakyan A, Bonora G, Damoiseaux R, Dimitrova E, Rubbi L, Pellegrini M, Radu CG, Plath K. A high-throughput screen of inactive X chromosome reactivation identifies the enhancement of DNA demethylation by 5-aza-2'-dC upon inhibition of ribonucleotide reductase. Epigenetics Chromatin. 2015; 8:42. view on PubMed
McHugh CA, Chen CK, Chow A, Surka CF, Tran C, McDonel P, Pandya-Jones A, Blanco M, Burghard C, Moradian A, Sweredoski MJ, Shishkin AA, Su J, Lander ES, Hess S, Plath K, Guttman M. The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3. Nature. 2015 May 14; 521(7551):232-6. view on PubMed
Pasque V, Tchieu J, Karnik R, Uyeda M, Sadhu Dimashkie A, Case D, Papp B, Bonora G, Patel S, Ho R, Schmidt R, McKee R, Sado T, Tada T, Meissner A, Plath K. X chromosome reactivation dynamics reveal stages of reprogramming to pluripotency. Cell. 2014 Dec 18; 159(7):1681-97. view on PubMed
Bonora G, Plath K, Denholtz M. A mechanistic link between gene regulation and genome architecture in mammalian development. Curr Opin Genet Dev. 2014 Aug; 27:92-101. view on PubMed
Minkovsky A, Sahakyan A, Rankin-Gee E, Bonora G, Patel S, Plath K. The Mbd1-Atf7ip-Setdb1 pathway contributes to the maintenance of X chromosome inactivation. Epigenetics Chromatin. 2014; 7:12. view on PubMed
Denholtz M, Bonora G, Chronis C, Splinter E, de Laat W, Ernst J, Pellegrini M, Plath K. Long-range chromatin contacts in embryonic stem cells reveal a role for pluripotency factors and polycomb proteins in genome organization. Cell Stem Cell. 2013 Nov 07; 13(5):602-16. view on PubMed
Britton LM, Newhart A, Bhanu NV, Sridharan R, Gonzales-Cope M, Plath K, Janicki SM, Garcia BA. Initial characterization of histone H3 serine 10 O-acetylation. Epigenetics. 2013 Oct; 8(10):1101-13. view on PubMed
Engreitz JM, Pandya-Jones A, McDonel P, Shishkin A, Sirokman K, Surka C, Kadri S, Xing J, Goren A, Lander ES, Plath K, Guttman M. The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome. Science. 2013 Aug 16; 341(6147):1237973. view on PubMed
Trounson A, Daley GQ, Pasque V, Plath K. A new route to human embryonic stem cells. Nat Med. 2013 Jul; 19(7):820-1. view on PubMed
Ho R, Papp B, Hoffman JA, Merrill BJ, Plath K. Stage-specific regulation of reprogramming to induced pluripotent stem cells by Wnt signaling and T cell factor proteins. Cell Rep. 2013 Jun 27; 3(6):2113-26. view on PubMed
Sridharan R, Gonzales-Cope M, Chronis C, Bonora G, McKee R, Huang C, Patel S, Lopez D, Mishra N, Pellegrini M, Carey M, Garcia BA, Plath K. Proteomic and genomic approaches reveal critical functions of H3K9 methylation and heterochromatin protein-1γ in reprogramming to pluripotency. Nat Cell Biol. 2013 Jul; 15(7):872-82. view on PubMed
Minkovsky A, Barakat TS, Sellami N, Chin MH, Gunhanlar N, Gribnau J, Plath K. The pluripotency factor-bound intron 1 of Xist is dispensable for X chromosome inactivation and reactivation in vitro and in vivo. Cell Rep. 2013 Mar 28; 3(3):905-18. view on PubMed
Papp B, Plath K. Epigenetics of reprogramming to induced pluripotency. Cell. 2013 Mar 14; 152(6):1324-43. view on PubMed
Denholtz M, Plath K. Pluripotency in 3D: genome organization in pluripotent cells. Curr Opin Cell Biol. 2012 Dec; 24(6):793-801. view on PubMed
Chen XF, Lehmann L, Lin JJ, Vashisht A, Schmidt R, Ferrari R, Huang C, McKee R, Mosley A, Plath K, Kurdistani SK, Wohlschlegel J, Carey M. Mediator and SAGA have distinct roles in Pol II preinitiation complex assembly and function. Cell Rep. 2012 Nov 29; 2(5):1061-7. view on PubMed
Plath K, Srivastava D, Alvarez-Buylla A, Tanaka EM, Kriegstein AR. Stem cells in the land of the rising sun: ISSCR 2012. Cell Stem Cell. 2012 Nov 02; 11(5):607-14. view on PubMed
Schmidt R, Plath K. The roles of the reprogramming factors Oct4, Sox2 and Klf4 in resetting the somatic cell epigenome during induced pluripotent stem cell generation. Genome Biol. 2012 Oct 22; 13(10):251. view on PubMed
Pera MF, Plath K. Cell reprogramming. Curr Opin Genet Dev. 2012 Oct; 22(5):401-2. view on PubMed
Papp B, Plath K. Pluripotency re-centered around Esrrb. EMBO J. 2012 Nov 14; 31(22):4255-7. view on PubMed
Nsair A, Schenke-Layland K, Van Handel B, Evseenko D, Kahn M, Zhao P, Mendelis J, Heydarkhan S, Awaji O, Vottler M, Geist S, Chyu J, Gago-Lopez N, Crooks GM, Plath K, Goldhaber J, Mikkola HK, MacLellan WR. Characterization and therapeutic potential of induced pluripotent stem cell-derived cardiovascular progenitor cells. PLoS One. 2012; 7(10):e45603. view on PubMed
Minkovsky A, Patel S, Plath K. Concise review: Pluripotency and the transcriptional inactivation of the female Mammalian X chromosome. Stem Cells. 2012 Jan; 30(1):48-54. view on PubMed
Karumbayaram S, Lee P, Azghadi SF, Cooper AR, Patterson M, Kohn DB, Pyle A, Clark A, Byrne J, Zack JA, Plath K, Lowry WE. From skin biopsy to neurons through a pluripotent intermediate under Good Manufacturing Practice protocols. Stem Cells Transl Med. 2012 Jan; 1(1):36-43. view on PubMed
Diaz Perez SV, Kim R, Li Z, Marquez VE, Patel S, Plath K, Clark AT. Derivation of new human embryonic stem cell lines reveals rapid epigenetic progression in vitro that can be prevented by chemical modification of chromatin. Hum Mol Genet. 2012 Feb 15; 21(4):751-64. view on PubMed
Lin JJ, Lehmann LW, Bonora G, Sridharan R, Vashisht AA, Tran N, Plath K, Wohlschlegel JA, Carey M. Mediator coordinates PIC assembly with recruitment of CHD1. Genes Dev. 2011 Oct 15; 25(20):2198-209. view on PubMed
Cooper AR, Patel S, Senadheera S, Plath K, Kohn DB, Hollis RP. Highly efficient large-scale lentiviral vector concentration by tandem tangential flow filtration. J Virol Methods. 2011 Oct; 177(1):1-9. view on PubMed
Sridharan R, Plath K. Small RNAs loom large during reprogramming. Cell Stem Cell. 2011 Jun 03; 8(6):599-601. view on PubMed
Ho R, Chronis C, Plath K. Mechanistic insights into reprogramming to induced pluripotency. J Cell Physiol. 2011 Apr; 226(4):868-78. view on PubMed
Plath K, Lowry WE. Progress in understanding reprogramming to the induced pluripotent state. Nat Rev Genet. 2011 Apr; 12(4):253-65. view on PubMed
Papp B, Plath K. Reprogramming to pluripotency: stepwise resetting of the epigenetic landscape. Cell Res. 2011 Mar; 21(3):486-501. view on PubMed
Mayshar Y, Ben-David U, Lavon N, Biancotti JC, Yakir B, Clark AT, Plath K, Lowry WE, Benvenisty N. Identification and classification of chromosomal aberrations in human induced pluripotent stem cells. Cell Stem Cell. 2010 Oct 08; 7(4):521-31. view on PubMed
Mason MJ, Plath K, Zhou Q. Identification of context-dependent motifs by contrasting ChIP binding data. Bioinformatics. 2010 Nov 15; 26(22):2826-32. view on PubMed
Tchieu J, Kuoy E, Chin MH, Trinh H, Patterson M, Sherman SP, Aimiuwu O, Lindgren A, Hakimian S, Zack JA, Clark AT, Pyle AD, Lowry WE, Plath K. Female human iPSCs retain an inactive X chromosome. Cell Stem Cell. 2010 Sep 03; 7(3):329-42. view on PubMed
Chin MH, Pellegrini M, Plath K, Lowry WE. Molecular analyses of human induced pluripotent stem cells and embryonic stem cells. Cell Stem Cell. 2010 Aug 06; 7(2):263-9. view on PubMed
Xu J, Watts JA, Pope SD, Gadue P, Kamps M, Plath K, Zaret KS, Smale ST. Transcriptional competence and the active marking of tissue-specific enhancers by defined transcription factors in embryonic and induced pluripotent stem cells. Genes Dev. 2009 Dec 15; 23(24):2824-38. view on PubMed
Hiratani I, Ryba T, Itoh M, Rathjen J, Kulik M, Papp B, Fussner E, Bazett-Jones DP, Plath K, Dalton S, Rathjen PD, Gilbert DM. Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis. Genome Res. 2010 Feb; 20(2):155-69. view on PubMed
Mason MJ, Fan G, Plath K, Zhou Q, Horvath S. Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells. BMC Genomics. 2009 Jul 20; 10:327. view on PubMed
Gaspar-Maia A, Alajem A, Polesso F, Sridharan R, Mason MJ, Heidersbach A, Ramalho-Santos J, McManus MT, Plath K, Meshorer E, Ramalho-Santos M. Chd1 regulates open chromatin and pluripotency of embryonic stem cells. Nature. 2009 Aug 13; 460(7257):863-8. view on PubMed
Chin MH, Mason MJ, Xie W, Volinia S, Singer M, Peterson C, Ambartsumyan G, Aimiuwu O, Richter L, Zhang J, Khvorostov I, Ott V, Grunstein M, Lavon N, Benvenisty N, Croce CM, Clark AT, Baxter T, Pyle AD, Teitell MA, Pelegrini M, Plath K, Lowry WE. Induced pluripotent stem cells and embryonic stem cells are distinguished by gene expression signatures. Cell Stem Cell. 2009 Jul 02; 5(1):111-23. view on PubMed
Park TS, Galic Z, Conway AE, Lindgren A, van Handel BJ, Magnusson M, Richter L, Teitell MA, Mikkola HK, Lowry WE, Plath K, Clark AT. Derivation of primordial germ cells from human embryonic and induced pluripotent stem cells is significantly improved by coculture with human fetal gonadal cells. Stem Cells. 2009 Apr; 27(4):783-95. view on PubMed
Karumbayaram S, Novitch BG, Patterson M, Umbach JA, Richter L, Lindgren A, Conway AE, Clark AT, Goldman SA, Plath K, Wiedau-Pazos M, Kornblum HI, Lowry WE. Directed differentiation of human-induced pluripotent stem cells generates active motor neurons. Stem Cells. 2009 Apr; 27(4):806-11. view on PubMed
Daley GQ, Lensch MW, Jaenisch R, Meissner A, Plath K, Yamanaka S. Broader implications of defining standards for the pluripotency of iPSCs. Cell Stem Cell. 2009 Mar 06; 4(3):200-1; author reply 202. view on PubMed
Xie W, Song C, Young NL, Sperling AS, Xu F, Sridharan R, Conway AE, Garcia BA, Plath K, Clark AT, Grunstein M. Histone h3 lysine 56 acetylation is linked to the core transcriptional network in human embryonic stem cells. Mol Cell. 2009 Feb 27; 33(4):417-27. view on PubMed
Saxe JP, Tomilin A, Schöler HR, Plath K, Huang J. Post-translational regulation of Oct4 transcriptional activity. PLoS One. 2009; 4(2):e4467. view on PubMed
Hochedlinger K, Plath K. Epigenetic reprogramming and induced pluripotency. Development. 2009 Feb; 136(4):509-23. view on PubMed
Sridharan R, Tchieu J, Mason MJ, Yachechko R, Kuoy E, Horvath S, Zhou Q, Plath K. Role of the murine reprogramming factors in the induction of pluripotency. Cell. 2009 Jan 23; 136(2):364-77. view on PubMed
Kanellopoulou C, Muljo SA, Dimitrov SD, Chen X, Colin C, Plath K, Livingston DM. X chromosome inactivation in the absence of Dicer. Proc Natl Acad Sci U S A. 2009 Jan 27; 106(4):1122-7. view on PubMed
Lowry WE, Plath K. The many ways to make an iPS cell. Nat Biotechnol. 2008 Nov; 26(11):1246-8. view on PubMed
Takahashi K, Plath KL, Skodje RT, Vaida V. Dynamics of vibrational overtone excited pyruvic acid in the gas phase: line broadening through hydrogen-atom chattering. J Phys Chem A. 2008 Aug 14; 112(32):7321-31. view on PubMed
Schenke-Layland K, Rhodes KE, Angelis E, Butylkova Y, Heydarkhan-Hagvall S, Gekas C, Zhang R, Goldhaber JI, Mikkola HK, Plath K, MacLellan WR. Reprogrammed mouse fibroblasts differentiate into cells of the cardiovascular and hematopoietic lineages. Stem Cells. 2008 Jun; 26(6):1537-46. view on PubMed
Sridharan R, Plath K. Illuminating the black box of reprogramming. Cell Stem Cell. 2008 Apr 10; 2(4):295-7. view on PubMed
Lowry WE, Richter L, Yachechko R, Pyle AD, Tchieu J, Sridharan R, Clark AT, Plath K. Generation of human induced pluripotent stem cells from dermal fibroblasts. Proc Natl Acad Sci U S A. 2008 Feb 26; 105(8):2883-8. view on PubMed
Maherali N, Sridharan R, Xie W, Utikal J, Eminli S, Arnold K, Stadtfeld M, Yachechko R, Tchieu J, Jaenisch R, Plath K, Hochedlinger K. Directly reprogrammed fibroblasts show global epigenetic remodeling and widespread tissue contribution. Cell Stem Cell. 2007 Jun 07; 1(1):55-70. view on PubMed
Nusinow DA, Sharp JA, Morris A, Salas S, Plath K, Panning B. The histone domain of macroH2A1 contains several dispersed elements that are each sufficient to direct enrichment on the inactive X chromosome. J Mol Biol. 2007 Aug 03; 371(1):11-8. view on PubMed
Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, Fry B, Meissner A, Wernig M, Plath K, Jaenisch R, Wagschal A, Feil R, Schreiber SL, Lander ES. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell. 2006 Apr 21; 125(2):315-26. view on PubMed
Boyer LA, Plath K, Zeitlinger J, Brambrink T, Medeiros LA, Lee TI, Levine SS, Wernig M, Tajonar A, Ray MK, Bell GW, Otte AP, Vidal M, Gifford DK, Young RA, Jaenisch R. Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature. 2006 May 18; 441(7091):349-53. view on PubMed
Beard C, Hochedlinger K, Plath K, Wutz A, Jaenisch R. Efficient method to generate single-copy transgenic mice by site-specific integration in embryonic stem cells. Genesis. 2006 Jan; 44(1):23-8. view on PubMed
Chu F, Nusinow DA, Chalkley RJ, Plath K, Panning B, Burlingame AL. Mapping post-translational modifications of the histone variant MacroH2A1 using tandem mass spectrometry. Mol Cell Proteomics. 2006 Jan; 5(1):194-203. view on PubMed
de la Cruz CC, Fang J, Plath K, Worringer KA, Nusinow DA, Zhang Y, Panning B. Developmental regulation of Suz 12 localization. Chromosoma. 2005 Aug; 114(3):183-92. view on PubMed
Plath K, Talbot D, Hamer KM, Otte AP, Yang TP, Jaenisch R, Panning B. Developmentally regulated alterations in Polycomb repressive complex 1 proteins on the inactive X chromosome. J Cell Biol. 2004 Dec 20; 167(6):1025-35. view on PubMed
Plath K, Wilkinson BM, Stirling CJ, Rapoport TA. Interactions between Sec complex and prepro-alpha-factor during posttranslational protein transport into the endoplasmic reticulum. Mol Biol Cell. 2004 Jan; 15(1):1-10. view on PubMed
Plath K, Fang J, Mlynarczyk-Evans SK, Cao R, Worringer KA, Wang H, de la Cruz CC, Otte AP, Panning B, Zhang Y. Role of histone H3 lysine 27 methylation in X inactivation. Science. 2003 Apr 04; 300(5616):131-5. view on PubMed
Plath K, Mlynarczyk-Evans S, Nusinow DA, Panning B. Xist RNA and the mechanism of X chromosome inactivation. Annu Rev Genet. 2002; 36:233-78. view on PubMed
Menetret JF, Neuhof A, Morgan DG, Plath K, Radermacher M, Rapoport TA, Akey CW. The structure of ribosome-channel complexes engaged in protein translocation. Mol Cell. 2000 Nov; 6(5):1219-32. view on PubMed
Plath K, Rapoport TA. Spontaneous release of cytosolic proteins from posttranslational substrates before their transport into the endoplasmic reticulum. J Cell Biol. 2000 Oct 02; 151(1):167-78. view on PubMed
Rapoport TA, Matlack KE, Plath K, Misselwitz B, Staeck O. Posttranslational protein translocation across the membrane of the endoplasmic reticulum. Biol Chem. 1999 Oct; 380(10):1143-50. view on PubMed
Matlack KE, Misselwitz B, Plath K, Rapoport TA. BiP acts as a molecular ratchet during posttranslational transport of prepro-alpha factor across the ER membrane. Cell. 1999 May 28; 97(5):553-64. view on PubMed
Plath K, Mothes W, Wilkinson BM, Stirling CJ, Rapoport TA. Signal sequence recognition in posttranslational protein transport across the yeast ER membrane. Cell. 1998 Sep 18; 94(6):795-807. view on PubMed
Matlack KE, Plath K, Misselwitz B, Rapoport TA. Protein transport by purified yeast Sec complex and Kar2p without membranes. Science. 1997 Aug 15; 277(5328):938-41. view on PubMed
Hanein D, Matlack KE, Jungnickel B, Plath K, Kalies KU, Miller KR, Rapoport TA, Akey CW. Oligomeric rings of the Sec61p complex induced by ligands required for protein translocation. Cell. 1996 Nov 15; 87(4):721-32. view on PubMed
Finke K, Plath K, Panzner S, Prehn S, Rapoport TA, Hartmann E, Sommer T. A second trimeric complex containing homologs of the Sec61p complex functions in protein transport across the ER membrane of S. cerevisiae. EMBO J. 1996 Apr 01; 15(7):1482-94. view on PubMed
Engel K, Schultz H, Martin F, Kotlyarov A, Plath K, Hahn M, Heinemann U, Gaestel M. Constitutive activation of mitogen-activated protein kinase-activated protein kinase 2 by mutation of phosphorylation sites and an A-helix motif. J Biol Chem. 1995 Nov 10; 270(45):27213-21. view on PubMed
Plath K, Engel K, Schwedersky G, Gaestel M. Characterization of the proline-rich region of mouse MAPKAP kinase 2: influence on catalytic properties and binding to the c-abl SH3 domain in vitro. Biochem Biophys Res Commun. 1994 Sep 15; 203(2):1188-94. view on PubMed
Engel K, Plath K, Gaestel M. The MAP kinase-activated protein kinase 2 contains a proline-rich SH3-binding domain. FEBS Lett. 1993 Dec 20; 336(1):143-7. view on PubMed
