Publications

2017

Huang C, Su T, Xue Y, Cheng C, Lay F, McKee R, Li M., Vashisht A, Wohlschlegel J, Novitch B, Plath K, Kurdistani S, Carey M

Cbx3 maintains lineage specificity during neural differentiation
Genes Dev. 2017 31: 241-246. 10.1101/gad.292169.116

Chronis C, Fiziev P, Papp B, Butz S, Bonora G, Sabri S, Ernst J, Plath K

Cooperating Binding of Transcription Factors Orchestrates Reprogramming
Cell. 2017 Jan 19; 168; 1-18. doi: 10.1016/j.cell.2016.12.016

2016

Sahakyan A, Rachel K, Chronis C, Sabri S, Bonora G, Theunissen T, 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 Dec 15; 20: 1-15. doi: 10.1016/j.stem.2016.10.006

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 Dec 15; 18:1-14. doi: 10.1016/j.celrep.2016.11.054

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 Oct 6; 19(4):476-490. doi: 10.1016/j.stem.2016.08.008

Sahakyan A, Plath K.

Transcriptome Encyclopedia of Early Human Development
Cell. 2016 May 5; 165(4):777-9. doi: 10.1016/j.cell.2016.04.042

Pandya-Jones A, Plath K.

The “Inc” between 3D Chromatin Structure and X Chromosome Inactivation. 
Semin Cell Dev Biol. 2016 Apr 5. pii: S1084-9521(16)30087-8. doi: 10.1016/j.semcdb.2016.04.002.

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 Feb 2. pii: S1934-5909(16)00020-5. doi: 10.1016/j.stem.2016.01.019

2015

Pasque V, Plath K.

X chromosome reactivation in reprogramming and in development
Curr Opin Cell Biol. 2015 Dec; 37: 75-83. doi: 10.1016/j.ceb.2015.10.006. Epub 2015 Nov 11.

Minkovsky A, Sahakyan A, Bonora G, Damoiseaux R, Dimitrova E, Rubbi L, Pellegrini M, Radu C, 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.

McHugh CA, Chen CK, Chow A, Surka CF, Tran C, McDonel P, Pandya-Jones A, Blanco MR, Burghard C, Moradian A, Sweredoski MJ, Shishkin AA, Su J, Lander ES, Hess S, Plath K, and Guttman M

The Xist lncRNA directly interacts with SHARP to silence transcription through HDAC3
Nature doi:10.1038/nature14443

2014

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.  *authors contributed equally

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.** Corresponding authors.

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 Jun 26;7:12.

2013

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 7;13(5):602-16. *authors contributed equally; ** Corresponding authors.

Trounson A, Daley GQ, Pasque V, Plath K.

A new route to human embryonic stem cells.
Nature Medicine. 2013 19(7):820-821.

Britton, L.P., Newhart, A., Bhanu, N.V., Sridharan, R., Gonzales-Cope, M., Plath, K., Janicki, S.M., and Garcia, B.A.

Initial Characterization of Histone H3 Serine 10 O-Acetylation
Epigenetics. 2013 8:1101-1113.

Papp, B. and Plath, K.

Epigenetics of Reprogramming to Induced Pluripotency.
Cell. 2013 152:1324-1343.

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.** Corresponding authors. (also see Perspective in Science)

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. *authors contributed equally; ** Corresponding authors.

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. *authors contributed equally; ** Corresponding authors.

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.

2012

Denholtz M, Plath K.

Pluripotency in 3D: genome organization in pluripotent cells.
Curr Opin Cell Biol. 2012 Dec;24(6):793-801.

Papp B, Plath K.

Pluripotency re-centered around Esrrb.
EMBO J. 2012, Nov 14;31(22):4255-7.

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.

Diaz-Perez, S.V., Kim, R., Li, Z., Marquez, V.E., Patel, S., Plath, K., Clark, A.T.

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, 21(4):751-764.

Pera, M.F., and Plath, K.

Cell reprogramming.
Current Opinion Genet Dev. 2012, 22(5):401-402.

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, G.M., Plath, K., Goldhaber, J., Mikkola, H.K., and MacLellan, W.R.

Characterization and therapeutic potential of induced pluripotent stem cell-derived cardiovascular progenitor cells.
Plos One. 2012, 7(10):e45603.

Chen, X.F., Lehmann, L., Lin, J.J., Vashisht, A., Schmidt, R., Ferrari, R., Huang, C., McKee, R., Mosley, A., Plath, K., Kurdistani, S.K., Wohlschlegel, J., and Carey, M.

Mediator and SAGA have distinct roles in Pol II preinitiation complex assembly and function.
Cell Reports. 2012 2:1061-1067.

Plath, K., Srivastava, D., Alvarez-Buylla, A., Tanaka, E.M., Kriegstein, A.R.

Stem cells in the land of the rising sun: ISSCR 2012.
Cell Stem Cell. 2012, 11(5):607-614.

Karumbayaram, S., Lee, P., Azghadi, S.F., Cooper, A.R., Patterson, M., Kohn, D.B., Pyle, A., Clark, A., Byrne, J., Zack, J.A., Plath, K., and Lowry, W.E.

From skin biopsy to neurons through a pluripotent intermediate under Good Manufacturing Practice protocols.
Stem Cells Transl Med. 2012, 1(1):36-43.

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.

2011

Plath, K. and Lowry, W.E.

Progress in understanding reprogramming to the induced pluripotent state.
Nature Reviews Genetics. 2011 12:253-265.

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.

Papp, B. and Plath, K.

Reprogramming to pluripotency: stepwise resetting of the epigenetic landscape.
Cell Research. 2011 21:486-501.

Cooper, A.R., Patel, S., Senadheera, S., Plath, K., Kohn, D.B., and Hollis, R.P.

Highly efficient large-scale lentiviral vector concentration by tandem tangential flow filtration.
J Virol Methods. 2011 177:1-9.

Sridharan R, Plath K.

Small RNAs loom large during reprogramming.
Cell Stem Cell. 2011 Jun 3;8(6):599-601.

 

2010

Ho R*, Chronis C*, Plath K.

Mechanistic insights into reprogramming to induced pluripotency.
J Cell Physiol. 2010 Oct 13. * Authors contributed equally to this work.

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 8;7(4):521-31.

Mason MJ, Plath K, Zhou Q.

Identification of Context-Dependent Motifs by Contrasting ChIP Binding Data.
Bioinformatics. 2010 Nov 15;26(22):2826-32.

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 3;7(3):329-42. * Authors contributed equally to this work.

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 6;7(2):263-9. ** Corresponding authors.

 

2009

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.

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.
Genes Dev. 2009 Dec 15;23(24):2824-38.

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.

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.

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 2;5(1):111-23. ** Corresponding authors.

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.

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.

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 6;4(3):200-1

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.

Saxe JP, Tomilin A, Schöler HR, Plath K, Huang J.

Post-translational regulation of Oct4 transcriptional activity.
PLoS ONE. 2009;4(2):e4467.

Hochedlinger K, Plath K.

Epigenetic reprogramming and induced pluripotency.
Development. 2009 Feb;136(4):509-23.

Sridharan R*, Tchieu J*, Mason MJ*, Yachechko R, Kuoy E, Horvath S, Zhou Q and Plath K.

Role of the murine reprogramming factors in inducing pluripotency.
Cell 2009 Jan 23;136(2):364-77. * Authors contributed equally to this work.

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. ** Corresponding authors.

2008

Lowry WE, Plath K.

The many ways to make an iPS cell.
Nat Biotechnol. 2008 Nov;26(11):1246-8.

Schenke-Layland K, Rhodes K, Angelis E, Butylkova Y, Heydarkhan-Hagvall S, Gekas C, Zhang R, Goldhaber J, Mikkola HK, Plath K and MacLellan WR.

Reprogrammed fibroblasts differentiate into cells of

the cardiovascular and hematopoietic lineages.
Stem Cells 2008 Jun;26(6):1537-46.

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 USA. 2008 Feb 26;105(8):2883-8. * Both authors contributed equally to this work. ** Corresponding authors.

Sridharan, R. and Plath, K.

Illuminating the black box of reprogramming.
Cell Stem Cell. 2008 2:295-297

 

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.
J Mol Biol. 2007 Aug 3;271(1):11-8.

Maherali N*, Sridharan R*, Xie W, Utikal J, Eminli S, Arnold K, Stadtfeld K, 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 June 7;1(1):55-70 * Authors contributed equally to this work. ** Corresponding authors

 

2006 and earlier

Boyer LA*, Plath K*, Zeitlinger J, Brambrink T, Medeiros L, Lee TI, Levine SS, Wernig M, Tajonar A, Ray MK, Bell GW, Otte AP, Vidal M, Gifford DK, Young RA and Jaenisch R.

Polycomb complexes repress developmental regulators in murine embryonic stem cells.
Nature 2006, May 18;441(7091):349-53 * Authors contributed equally to this work.

Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, Fry B, Meissner A, Wernig M, Plath K, Jaenisch R, Waqschal 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

Beard C, Hochedlinger K, Plath K, Wutz A and Jaenisch R.

An efficient method to generate single-copy transgenic mice by site specific integrationin embryonic stem cells.
Genesis 2006, Jan;44(1):23-8.

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.

de la Cruz CC, Fang J, Plath K, Worringer KA, Nusinow DA, Zhang Y and Panning B.

Developmental regulation of Suz12 localization.
Chromosoma 2005;114(3):183-92.

Plath K, Talbot D, Hamer KM, Otte AP, Yang TP, Jaenisch R and Panning B.

Developmentally regulated alterations in polycomb repressive complex 1 proteins on the inactive X chromosome.
J. Cell Biol. 2004;167(6):1025-35.

Plath K, Wilkinson BM, Stirling CJ and Rapoport TA.

Interactions between Sec-complex and perpro-a-factor during posttranslational protein transport into the ER.
Mol. Biol. Cell, 2004;15(1):1-10.

Plath K, Fang J, Mlynarczyk-Evans SK, Cao R, Worringer KA, Wang H, de la Cruz CC, Otte AP, Panning B and Zhang Y.

Role of histone H3 lysine 27 methylation in X inactivation.
Science 2003;300(1):131-135.

Plath K, Mlynarczyk-Evans SK, Nusinow DA and Panning B.

Xist RNA and the mechanism of X chromosome inactivation.
Annu. Rev. Genet. 2002;36(1):233-78.

Plath K, Rapoport TA.

Spontaneous release of cytosolic proteins from posttranslational substrates before their transport into the endoplasmic reticulum.
J. Cell Biol. 2000;151(1):167-178.

Menetret JF, Neuhof A, Morgan DG, Plath K, Radermacher M, Rapoport TA and Akey CW.

The structure of ribosome-channel complexes engaged in protein translocation.
Mol. Cell. 2000;6:1219-1232.

Plath K.

Protein transport into the endoplasmic reticulum.
Biospektrum. 2000;6:466-467.

Rapoport TA, Matlack KES, Plath K, Misselwitz B and Staeck O.

Posttranslational protein translocations across the membrane of the endoplasmic reticulum.
Biol. Chem 1999;380:1143-1150.

Plath, K., Mothes, W., Wilkinson, B.M., Stirling, C.J., Rapoport, T.A.

Signal sequence recognition in posttranslational protein transport across the yeast ER membrane. Cell 1998;94:795-807.

Matlack KES, Misselwitz B, Plath K and Rapoport TA.

BiP acts as a molecular ratchet during posttranslational transport of prepro-factor across the ER membrane.
Cell 1999;97:553-564.

Hanein D, Matlack KE, Jungnickel B, Plath K, Kalies KU, Miller KR, Rapoport TA and Akey CW.

Oligomeric rings of the Sec61p complex induced by ligands required for protein translocation.
Cell 1996;87:721-732.

Matlack, K.E., Plath, K., Misselwitz, B., Rapoport, T.A.

Protein transport by purified yeast Sec complex and Kar2p without membranes.
Science 1997; 277:938-941.

Finke K*, Plath K*, Panzer S, Prehn S, Rapoport TA, Hartmann and 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;15:1482-1494. * Authors contributed equally to this work.

Engel K, Schultz H, Martin F, Kotlyarov A, Plath K, Hahn M, Heinemann U and 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;270:27213-21.

Plath K, Engel K, Schwedersky G and 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;203:1188-1194.

Engel K, Plath K and Gaestel M.

The MAP kinase-activated protein kinase 2 contains a proline-rich SH3-binding domain.
FEBS Lett. 1993;336:143-147.