Kathrin Plath
Professor, Biological Chemistry, University of California Los Angeles
Laboratory Address:
615 Charles E. Young Drive South
BSRB 35410-14
Los Angeles, CA 90095
Lab Number:
(310) 267-0087
Mailing Address:
615 Charles E. Young Drive South
Department of Biological Chemistry
BSRB 390D
Los Angeles, CA 90095
Affiliations
Research Interests
The Plath lab aims to understand molecular mechanisms that control genome organization, chromatin states, and gene expression during cell fate changes, with a particular focus on the pluripotent state and pluripotent stem cells, the differentiation of pluripotent stem cells, and reprogramming of somatic cells to pluripotent stem cells. Our team of experimental and computational biologists uses embryonic stem cell (ESC) and induced pluripotent stem cell (iPSC) model systems, state-of-the-art microscopy, biochemistry and mass spectrometry, high throughput screening approaches, gene editing and transgenic/knockout mouse models, genomic approaches (to map patterns of RNA expression at the single cell and population level, open chromatin, DNA methylation, histone modifications, transcription factor binding, three dimensional genome organization, RNA-protein and RNA-chromatin interactions), and computational modelling.
To understand basic principles of gene regulation during cell fate changes and in diseases, we focus on four fundamental problems of mammalian biology that are intimately connected and inform each other:
1. Our lab is studying how one of the two X chromosomes in female mammalian cells is transcriptionally silenced. This chromosome-wide silencing process, called X-inactivation, is initiated when female pluripotent cells differentiate, and represents the most dramatic example of developmentally regulated heterochromatin formation in mammalian cells. X-inactivation is essential for development and equalizes the dose of X-linked genes to that in male cells with their single X chromosome, and leads to cancer if deregulated in the adult. The silencing of the entire X chromosome is orchestrated by Xist, a long non-coding (lnc) RNA. Mammalian genomes encode thousands of lncRNAs, many of which regulate gene expression. While lncRNAs are clearly functionally important, the mechanisms by which they act are still largely elusive. We systematically identify the proteins that interact with Xist, define how Xist RNA spreads along the X chromosome, modifies chromatin states, the three-dimensional architecture of the chromosome and gene expression, and recruits regulatory complexes. Most of our studies are done in the mouse system. Another exciting finding is that the epigenetic regulation of X chromosome dosage differs between mouse and human development. To this end, we have recently established a cell system that allows us to model the human-specific aspects of X chromosome dosage compensation, which also offers insights into early human development. Our findings on Xist RNA and X chromosome dosage compensation are influential for the general understanding of lncRNA function, and guide us in the study of other lncRNAs.
2. We have been among the first to reprogram human differentiated cells to an embryonic stem cell-like state, known as induced pluripotent stem cells (iPSCs), by simply overexpressing four pluripotency-related transcription factors following a strategy first proposed by Shinya Yamanaka in 2006. While it is now clear that differentiated cells can be reprogrammed to iPSCs, the mechanisms by which this occurs are currently largely unknown. An important goal of our lab is to systematically define how the reprogramming factors reset cell identity and determine their interplay with somatic chromatin states and signaling pathways, to understand how cell fate decisions can be modulated. We are particuarly interested in uncovering how enhancers are selected and activated by the reprogramming factors and how somatic cell identity is destabilized by the reprogramming factors. Our work has revealed unexpected mechanisms underlying these processes, which we are now studying further.
3. Another main interest in our lab is to understand the role of the three-dimensional organization of the genome in the regulation of gene expression and developmental identity. DNA is stored in a non-random and highly organized fashion in the nucleus and the 3D-architecture of the genome is beginning to be incorportated in studies of gene regulation. The spatial organization of chromosomes is a fascinating problem of metazoan biology, but many questions have remained unanswered. A particular challenge has been to decipher the mechanisms driving the co-localization of genetic loci and the importance of co-localization. Our goals are to understand how higher-order genome organization is established and dynamically regulated, and how it influences transcriptional networks, chromatin states, and the function of lncRNAs.
4. Finally, we are also interested in understanding how disease states develop. To this end, we are using patient and disease-specific iPSCs to model human diseases and define where deregulation occurs. We are also studying cancer models by defining the cellular heterogeneity and how it develops.
updated 2017
Biography:
Kathrin Plath earned her doctorate degree in cell biology from Humboldt University (Berlin, Germany) for her work with Dr. Tom Rapoport at Harvard Medical School on how the signal sequence of a secretory protein is recognized by the translocation channel in the endoplasmic reticulum membrane. She did her post-doctoral training at the University of California San Francisco and the Whitehead Institute at MIT with Drs. Barbara Panning and Rudolf Jaenisch and support from fellowships of the Life Sciences Research Foundation and the Leukemia and Lymphoma Foundation. In her postdoctoral research, she uncovered that Polycomb proteins can be recruited to their site of action by long non-coding RNAs, and that this group of transcriptional repressors is important for the maintenance of pluripotency and developmental plasticity through the repression of developmental pathways. She joined the faculty of the Department of Biological Chemistry at the University of California Los Angeles in 2006, where her laboratory studies the gene expression controls that operate during cell fate changes. To decode the genetic instructions that orchestrate the conversion of the single cell zygote into a complex organism and uncover broad principles underlying gene regulation, the Plath lab is focusing on cis-regulatory DNA sequences (such as enhancers), long-noncoding RNAs (lncRNAs), and the three-dimensional organization of the genome. Research in her lab in the past few years has focused on four fundamental problems: (a) Differentiation and reprogramming processes as mean to understand how transcription factors interpret cis-regulatory elements in the context of cellular state and signaling milieu. (b) The function of long-noncoding (lnc) RNAs in the regulation of chromatin and gene expression by understanding how lncRNA-protein complexes form, localize to regulatory targets, and give rise to phenotypic states. To achieve this goal, we currently focus on the X-inactivation process and its regulation by the lncRNA Xist, how the X-inactivation process differs between mouse and human pluripotent stem cells, and how the epigenetic state of the X chromosome influences developmental potency. (c) 3D-organization of the genome changes as a means to understand how transcriptional networks regulate genome organization, and how genome organization influences gene expression and chromatin states. (d) The deregulation of gene regulation processes in disease using iPSC disease models. To accomplish these goals, the Plath lab uses a wide range of approaches including proteomics, genomics, genetics, cell biology, and bioinformatics. Dr. Plath serves on the editorial boards of various journals including Science, Cell, Cell Stem Cell, Cell Reports, and is the chair of the publications committee of the International Society for Stem Cell Research. Recently, she was named a Faculty Scholar of the Howard Hughes Medical Institute.
Awards and Honors
- CIRM Young Investigator Award, 2008.
- V Foundation Scholar, 2007.
- Kimmel Foundation Scholar, 2007.
- HHMI Faculty Scholar Award, 2016.
- Byk-Gulden Graduate Thesis Award, German Society of Biochemistry, 2000.
- Postdoctoral Fellowship, Life Sciences Research Foundation, 2001-2004.
- Undergraduate Fellowship, Humboldt University, Germany, 1989-1990.
- Special Fellowship, Leukemia and Lymphoma Society, 2004-2007.
- NIH Director’s New Innovator Award, 2007.
- Graduate Fellowship, Max-Delbrück-Center, Berlin, Germany, 1995-1998.
- Junior Scientist Award of the States Berlin and Brandenburg, Germany, 2001.
- John H. Walsh Young Investigator Research Price, David Geffen School of Medicine, UCLA, 2009.
Publications
- Jacobson EC, Pandya-Jones A, Plath K. A lifelong duty: how Xist maintains the inactive X chromosome.. Current opinion in genetics & development, 2022.
- 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.
- 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.. Science advances, 2022.
- 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.. Frontiers in cell and developmental biology, 2021.
- 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.
- 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.
- 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.
- 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.
- 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.. Nature neuroscience, 2021.
- Deng W, Jacobson EC, Collier AJ, Plath K. The transcription factor code in iPSC reprogramming.. Current opinion in genetics & development, 2021.
- 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.. Nature medicine, 2021.
- 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.. Nature communications, 2021.
- 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.. Molecular & cellular proteomics : MCP, 2021.
- 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.
- 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 reports, 2020.
- Meshorer E, Plath K. Chromatin and Nuclear Architecture in Stem Cells.. Stem cell reports, 2020.
- 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.. Nature cell biology, 2020.
- 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.
- 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.
- 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.
- 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 : the preprint server for biology, 2020.
- 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.
- 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.
- 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.. The Journal of investigative dermatology, 2019.
- 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.
- 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.
- 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.
- 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.
- 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.. Molecular cell, 2018.
- 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.. Nature methods, 2018.
- 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.. Journal of visualized experiments : JoVE, 2018.
- Sahakyan A, Yang Y, Plath K. The Role of Xist in X-Chromosome Dosage Compensation.. Trends in cell biology, 2018.
- 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.
- 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.
- 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.
- 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 (Cambridge, England), 2018.
- 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.. Nature communications, 2018.
- Keegan A, Plath K, Damoiseaux R. High-Throughput Screening of a Luciferase Reporter of Gene Silencing on the Inactive X Chromosome.. Methods in molecular biology (Clifton, N.J.), 2018.
- Sahakyan A, Plath K, Rougeulle C. Regulation of X-chromosome dosage compensation in human: mechanisms and model systems.. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2017.
- 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 (Cambridge, England), 2017.
- 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 & development, 2017.
- 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.
- 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 reports, 2016.
- 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, 2016.
- 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.
- Sahakyan A, Plath K. Transcriptome Encyclopedia of Early Human Development.. Cell, 2016.
- Pandya-Jones A, Plath K. The "lnc" between 3D chromatin structure and X chromosome inactivation.. Seminars in cell & developmental biology, 2016.
- 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.
- Pasque V, Plath K. X chromosome reactivation in reprogramming and in development.. Current opinion in cell biology, 2015.
- 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.
- 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.
- 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.
- Bonora G, Plath K, Denholtz M. A mechanistic link between gene regulation and genome architecture in mammalian development.. Current opinion in genetics & development, 2014.
- 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.
- 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.
- 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.
- 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 (New York, N.Y.), 2013.
- Trounson A, Daley GQ, Pasque V, Plath K. A new route to human embryonic stem cells.. Nature medicine, 2013.
- 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 reports, 2013.
- 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.. Nature cell biology, 2013.
- 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 reports, 2013.
- Papp B, Plath K. Epigenetics of reprogramming to induced pluripotency.. Cell, 2013.
- Denholtz M, Plath K. Pluripotency in 3D: genome organization in pluripotent cells.. Current opinion in cell biology, 2012.
- 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 reports, 2012.
- 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.
- 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 biology, 2012.
- Pera MF, Plath K. Cell reprogramming.. Current opinion in genetics & development, 2012.
- Papp B, Plath K. Pluripotency re-centered around Esrrb.. The EMBO journal, 2012.
- 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.
- Minkovsky A, Patel S, Plath K. Concise review: Pluripotency and the transcriptional inactivation of the female Mammalian X chromosome.. Stem cells (Dayton, Ohio), 2012.
- 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 translational medicine, 2011.
- 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.. Human molecular genetics, 2011.
- 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 & development, 2011.
- Cooper AR, Patel S, Senadheera S, Plath K, Kohn DB, Hollis RP. Highly efficient large-scale lentiviral vector concentration by tandem tangential flow filtration.. Journal of virological methods, 2011.
- Sridharan R, Plath K. Small RNAs loom large during reprogramming.. Cell stem cell, 2011.
- Ho R, Chronis C, Plath K. Mechanistic insights into reprogramming to induced pluripotency.. Journal of cellular physiology, 2011.
- Plath K, Lowry WE. Progress in understanding reprogramming to the induced pluripotent state.. Nature reviews. Genetics, 2011.
- Papp B, Plath K. Reprogramming to pluripotency: stepwise resetting of the epigenetic landscape.. Cell research, 2011.
- 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.
- Mason MJ, Plath K, Zhou Q. Identification of context-dependent motifs by contrasting ChIP binding data.. Bioinformatics (Oxford, England), 2010.
- 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.
- Chin MH, Pellegrini M, Plath K, Lowry WE. Molecular analyses of human induced pluripotent stem cells and embryonic stem cells.. Cell stem cell, 2010.
- 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 & development, 2009.
- 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 research, 2009.
- 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.
- 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.
- 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.
- 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 (Dayton, Ohio), 2009.
- 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 (Dayton, Ohio), 2009.
- 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.
- 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.. Molecular cell, 2009.
- Saxe JP, Tomilin A, Schöler HR, Plath K, Huang J. Post-translational regulation of Oct4 transcriptional activity.. PloS one, 2009.
- Hochedlinger K, Plath K. Epigenetic reprogramming and induced pluripotency.. Development (Cambridge, England), 2009.
- 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.
- Kanellopoulou C, Muljo SA, Dimitrov SD, Chen X, Colin C, Plath K, Livingston DM. X chromosome inactivation in the absence of Dicer.. Proceedings of the National Academy of Sciences of the United States of America, 2009.
- Lowry WE, Plath K. The many ways to make an iPS cell.. Nature biotechnology, 2008.
- 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 (Dayton, Ohio), 2008.
- Sridharan R, Plath K. Illuminating the black box of reprogramming.. Cell stem cell, 2008.
- 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.
- 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.. Journal of molecular biology, 2007.
- 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.
- 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.
- 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 (New York, N.Y. : 2000), 2006.
- 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.. Molecular & cellular proteomics : MCP, 2005.
- de la Cruz CC, Fang J, Plath K, Worringer KA, Nusinow DA, Zhang Y, Panning B. Developmental regulation of Suz 12 localization.. Chromosoma, 2005.
- 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.. The Journal of cell biology, 2004.
- Plath K, Wilkinson BM, Stirling CJ, Rapoport TA. Interactions between Sec complex and prepro-alpha-factor during posttranslational protein transport into the endoplasmic reticulum.. Molecular biology of the cell, 2003.
- 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 (New York, N.Y.), 2003.
- Plath K, Mlynarczyk-Evans S, Nusinow DA, Panning B. Xist RNA and the mechanism of X chromosome inactivation.. Annual review of genetics, 2002.