Kathrin Plath*

The Plath lab focuses on the epigenetic mechanisms that maintain pluripotency and control differentiation and reprogramming processes. Within this context, we are studying six fundamental problems: (i) How do long-noncoding (lnc) RNAs build nuclear compartments and regulate chromatin changes during differentiation and reprogramming? This aspect of our work particularly centers on understanding how the X chromosome dosage compensation is regulated by the lncRNA Xist in mouse and human. (ii) We are dissecting the cellular decision-making governing reprogramming to induced pluripotency as a means to understand how transcription factors drive cell fate changes and induce new chromatin and gene expression states. (iii) We are examining how the three-dimensional organization of the genome changes during differentiation and reprogramming processes, how transcriptional networks and lncRNAs regulate 3D genome organization, and how 3D genome organization in turn influences gene expression, chromatin states, and lncRNA function. (iv) We are 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. (v) We are 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. (vi) We aim to develop new single cell genomics technologies and to apply them to diverse biological model systems to, for instance, understand the difference between the healthy and disease lung.

Websites:

Plath Lab

Research Interests:

development, Genomics, Epigenetics, Stem Cells, Female disease bias, long noncoding RNAs,

Publications:

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 05. 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 Feb 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

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

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

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