NIH ‘Reprogramming’ P01 2011-2016

Project 1: Defining the Logic of Genome Organization in Pluripotent Cells During Reprogramming – Dr. Kathrin Plath (UCLA)

Project 2: Mechanisms of Chromatin Engagement and Remodeling by Pluripotency Factors – Dr. Kenneth Zaret (UPENN)

Project 3: Control of Differentiation and Dedifferentiation in Human Development – Dr. William Lowry (UCLA)

Project 4: Pluripotency and the Making of Tissue-Specific Genes – Dr. Stephen Smale (UCLA)

Shared Resource Core: Bioinformatics Core – Dr. Matteo Pellegrini (UCLA)

Pilot Projects: Mike Carey (UCLA), Ben Garcia (UPENN), Heather Christofk (UCLA)


Publications:

2015

Soufi, A., Jaroszewicz, A., Osman, N., Fernandez Garcia, M., Pellegrini, M., and Zaret, K.S. (2015) Pioneer transcription factors target partial DNA motifs on nucleosomes to initiate reprogramming. Cell 161, 555-568. PMCID: PMC4409934.

Lam J, Carmichael ST, Lowry WE, Segura T. Hydrogel design of experiments methodology to optimize hydrogel for iPSC-NPC culture. Adv Healthc Mater. 2015 Mar 11;4(4):534-9. doi: 10.1002/adhm.201400410. Epub 2014 Nov 5. PMCID: PMC4384641.

2014

Pasque V, Tchieu J, Karnik R, Uyeda M, Dimashkie A, Case D, Papp B, Bonora G, Patel S, Ho R, Schmidt R, McKee R, Sado T, Tada T, Meissner A, and Plath K. (2014) X Chromosome Reactivation Dynamics Reveal Stages of Reprogramming to Pluripotency. Cell, 159:1681-1697. PMCID: PMC4282187.

Bonora G, Plath K, and Denholtz M. (2014) A mechanistic link between gene regulation and genome architecture in mammalian development. Current Opinion Genet Dev. 27: 92-101. PMCID: PMC4125518.

Iwafuchi-Doi, M., and Zaret, K.S. (2014) Pioneer transcription factors in cell reprogramming. Genes and Development 28, 2679-2692. PMCID: PMC3994953.

Soufi, A. (2014) Mechanisms for enhancing cellular reprogramming. Curr. Opin. Genet. Dev. 25, 101-109. PMCID: PMC4109306.

Xie Y, Zhang J, Lin Y, Gaeta X, Meng X, Wisidagama DR, Cinkornpumin J, Koehler CM, Malone CS, Teitell MA, Lowry WE. Defining the role of oxygen tension in human neural progenitor fate. Stem Cell Reports. 2014 Nov 11;3(5):743-57. doi:10.1016/j.stemcr.2014.09.021. Epub 2014 Oct 30. PMCID: PMC4235163

Patterson M, Gaeta X, Loo K, Edwards M, Smale S, Cinkornpumin J, Xie Y, Listgarten J, Azghadi S, Douglass SM, Pellegrini M, Lowry WE. let-7 miRNAs can act through notch to regulate human gliogenesis. Stem Cell Reports. 2014 Nov 11;3(5):758-73. doi: 10.1016/j.stemcr.2014.08.015. Epub 2014 Oct 3. PMCID: PMC4235151

2013

Lowry WE, -Oh no! hiPSCs misplace their 5hmCs, Cell Stem Cell, 2013. Jul 3; 13(1):10-1. PMCID: PMC3753777

Sridharan, R., Gonzales-Cope, M., Chronis, C., Bonora, G., McKee, R., Huang, C., Patel, S., Lopez, D., Mishra, N., Pellegrini, M., Carey, M., Garcia, B.A., Plath, K. (2013) Proteomic and genomic approaches reveal critical functions of H3K9 methylation and Heterochromatin Protein-1γ in reprogramming to pluripotency. Nature Cell Biology, 15: 872-878. PMCID: PMC3733997.

Ho, R., Papp, B., Hoffman, J.A., Merill, B.J., and Plath, K. (2013) Stage-specific regulation of reprograming to iPSCs by Wnt signaling and Tcf proteins. Cell Reports, 3:2113-2126. PMCID: PMC3700671.

Engreitz, J.M., Pandya-Jones, A., McDonel, P. Shishkin, A., Sirokman, K., Surka, C., Kadri, S., Lander. E.S.*, Plath, K.*, and Guttman, M.* (2013) The Xist lncRNA exploits three-dimensional chromosome architecture to spread across the X-chromosome. Science, 341:1237973. *corresponding authors. PMCID: PMC3778663.

Denholtz, M., Bonora, G., Chronis, C., Splinter, E., deLaat, W., Ernst, J., Pellegrini, M., and Plath, K. (2013) Long-range chromatin contacts in embryonic stem cells reveal a role for pluripotency factors and polycomb proteins in genome organization. Cell Stem Cell, 13(5): 602-16. PMCID: PMC3825755.

Britton, L.P., Newhart, A., Bhanu, N.V., Sridharan, R., Gonzales-Cope, M., Plath, K., Janicki, S.M., and Garcia, B.A. (2013) Initial Characterization of Histone H3 Serine 10 O-Acetylation. Epigenetics, 8:1101-13. PMCID: PMC3891691.

Papp, B. and

Plath, K. (2013) Epigenetics of Reprogramming to Induced Pluripotency. Cell, 152: 1324-1343. PMCID: PMC3602907.

Soufi, A., and Zaret, K.S. (2013)  Understanding impediments to cellular conversion to pluripotency by assessing the earliest events in ectopic transcription factor binding to the genome. Cell Cycle 12, 1487-1491. PMCID: PMC3680528.

2012

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., Carey, M. (2012). Mediator and SAGA have distinct roles in Pol II preinitiation complex assembly and function. Cell Reports, 2: 1061-7. PMCID: PMC3513640.

Schmidt, R., and Plath, K. (2012). The roles of the reprogramming factors Oct4, Sox2 and Klf4 in resetting the somatic cell epigenome during induced pluripotent stem cell generation. Genome Biology 13: 251. PMCID: PMC3491406.

Denholtz, M., and Plath, K. (2012). Pluripotency in 3D: genome organization in pluripotent cells. Current Opinion Cell Biol. 24: 793-801. (review article). PMCID: PMC3540188.

Soufi, A., Donahue, G., and Zaret, K.S. (2012) Facilitators and impediments of the pluripotency reprogramming factors’ initial engagement with the genome. Cell 151, 994-1004. PMCID: PMC3508134.

Lowry WE. Does transcription factor induced pluripotency accurately mimic embryo derived pluripotency? Curr Opin Genet Dev. 2012 Oct;22(5):429-34. doi: 10.1016/j.gde.2012.07.003. Epub 2012 Oct 15. Review. PMCID: PMC3753773.