Selected Publications from the Zaret Lab

• Frederick, M.A., Williamson, K.E., Fernandez Garcia, M., Ferretti, M.B., McCarthy, R.L., Donahue, G., Luzete Monteiro, E., Takenaka, N., Reynaga, J., Kadoch, C., and Zaret, K.S. (2022) A pioneer factor locally opens compacted chromatin to enable targeted ATP-dependent nucleosome remodeling. Nature Structure Molecular Biology, doi: 10.1038/s41594-022-00886-5. Online ahead of print. PMID: 36536103.
• Ito, K., and Zaret, K.S.  (2022) Maintaining transcriptional specificity through mitosis. Annual Reviews of Genomics and Human Genetics,23:9.1-9.19.
• Kim, J., Ekstrom, T., Yang, W., Donahue, G., Grygoryev, D., Ngo, T., Muschler, J.L., Morgan, T., Zaret, K.S.  (2021) Longitudinal analysis of human pancreatic adenocarcinoma development reveals transient gene expression signatures. Molecular Cancer Research 19, 1854-1867.
• Gimotty, P.A., Till, J.E., Udgata, S., Takenaka, N., Yee, S.S., LaRiviere, M.J., O’Hara, M.H., Reiss, K.A., O’Dwyer, P., Katona, B.W., Herman, D., Carpenter, E.L., Zaret, K.S. (2021)  THBS2 as a prognostic biomarker for patients diagnosed with metastatic pancreatic ductal adenocarcinoma.  Oncotarget 12, 2266-2272
• McCarthy, R.L., Kaeding, K.E., Keller, S.H., Zhong, Y., Xu, L., Hsieh, A., Hou, Y., Donahue, G., Alberto, O., Lim, B., and Zaret, K.S.  (2021) Diverse heterochromatin-associated proteins repress distinct classes of genes and repetitive elements.  Nature Cell Biology 23, 905-914. PMID: 34354237
• Hsieh, A., Pitaressi, J.R., Lerner, J., Donahue, G., Hsiehchen, D., Rustgi, A.K., Zaret, K.S.  (2020) Growth of pancreatic cancers with hemizygous chromosomal 17p loss of MYBBP1A can be preferentially targeted by PARP inhibitors.  Science Advances 6, eabc4517. PMC7821900
• Zaret, K.S. (2020) Pioneer Transcription Factors Initiating Gene Network Changes. Annual Review of Genetics 54,367-385.  PMCID: PMC7900943
• Lerner, J., Gomez-Garcia, P.A., McCarthy, R., Zhe, L., Lakadamyali, M., Zaret, K.S. (2020) Two-Parameter Mobility Assessments Discriminate Diverse Regulatory Factor Behaviors in Chromatin. Molecular Cell 4, 677-688.
• Iwafuchi, M., Cuesta, I., Donahue, G, Takenaka, N. Osipovich, A.B., Magnuson, M. A., Roder, H., Seeholzer, S.H., Santisteban, P., and Zaret, K.S. (2020) Gene network transitions in embryos depend upon interactions between a pioneer transcription factor and core histones.  Nature Genetics 4, 418-427.  PMID:32203463
• Palozola, K., Lerner, J., Zaret, K.S.  (2019) A Changing Paradigm of Transcriptional Memory Propagation Through Mitosis.  Nat Rev Mol Cell Biol 20, 55-64. PMID: 30420736 PMCID: PMC6557398
• Fernandez Garcia M, Moore CD, Schulz KN, Alberto O, Donague G, Harrison MM, Zhu H, Zaret KS. Structural Features of Transcription Factors Associating with Nucleosome Binding. Mol Cell. 2019 Sep 5;75(5):921-932.e6. doi: 10.1016/j.molcel.2019.06.009. Epub 2019 Jul 11. PMID:31303471
• Grindheim JM, Nicetto D, Donahue G, Zaret KS. Polycomb Repressive Complex 2 Proteins EZH1 and EZH2 Regulate Timing of Postnatal Hepatocyte Maturation and Fibrosis by Repressing Genes With Euchromatic Promoters in Mice. Gastroenterology. 2019 May;156(6):1834-1848. doi: 10.1053/j.gastro.2019.01.041. Epub 2019 Jan 25. PMID:30689973
• Nicetto, D., Donahue G., Jain T., Peng T., Sidoli S., Sheng L., Montavon T., Becker J. S., Grindheim J. M., Blahnik K., Garcia B. A., Tan K., Bonasio R., Jenuwein T, Zaret, K.S. (2019) H3K9me3-heterochromatin loss at protein-coding genes enables developmental lineage specification. Science 363, 294-297
• Nicetto, D., McCarthy, R.L., and Zaret, K.S. (2018) Epigenetic mechanisms in liver and pancreas generation and regeneration. Chapter in book: Epigenetics and Regeneration, Elsevier (Academic Press). In press.
• Palozola, K.S., Lerner, J., and Zaret, K.S. A changing paradigm of transcriptional memory propagation through mistosis. (2019) Nature Reviews Molecular Cell Biology, Jan;20(1):55-64. doi: 10.1038/s41580-018-0077-z.
• Young, M.R., Wagner, P.D., Ghosh, S., Rinaudo, J.A., Baker, S.G., Zaret, K.S., Goggins, M, and Srivastava, S. (2018) Validation of biomarkers for early detection of pancreatic cancer: Summary of the alliance of Pancreatic Cancer Consortia for Biomarkers for Early Detection workshop. Pancreas 47, 135-141.
• Palozola, K.C., Liu, H., Nicetto, D., and Zaret, K.S. (2018) Low‐level, global transcription during mitosis and dynamic reactivation during mitotic exit. Cold Spring Harbor Symposium 82, 197‐205.
• Zaret, K.S. (2018) Telomerase and cell renewal in the liver (News and Views). Nature 556, 181-182
• Kaeding, K.E., and Zaret, K.S. (2018) Microsattelite enhancers can be targeted to impair tumorigenesis (Outlook). Genes and Development 32, 991‐992.
• Zaret, K.S. (2018) Pioneering the chromatin landscape (News and Views). Nature Genetics 50, 167-169
• Becker, J.S., McCarthy, R.L., Sidoli, S., Donahue, G., Kaeding, K.E., He, Z., Lin, S, Garcia, B.A., and Zaret, K.S. (2017) Genomic and proteomic resolution of sonication-resistant heterochromatin and its restriction of alternate fate genes. Molecular Cell 68, 1023-1037.
• Palozola, K.C., Donahue, G , Grant, G.R., Becker, J.S., Cote, A., Liu, H., Yu, H., Raj, A., and Zaret, K.S. (2017) Mitotic Transcription and waves of gene reactivation during mitotic exit.       Science 358, 119-122.
• Kim, J. Bamlet, W.R., Oberg, A.L., Chaffee, K.G., Donahue, G. Cao, X.-J., Chari, S., Garcia, B., Petersen, G.M., and Zaret, K.S. (2017)       THBS2 and CA19-9 blood based markers detect early pancreatic ductal adenocarcinoma. Science Translational Medicine 9, eaah5583.
• Moreno, J., Gearhart, J., Zoloth, L., Pyeritz, R., and Zaret, K.S. (2017) Managing Cell and Human Identity. Science 356, 139-140.
• Bhat, N., Park, J., Zoghbi, H.Y., Arthur, J.S.C., and Zaret, K.S. (2016) The chromatin modifier MSK1/2 suppresses endocrine cell fates during mouse pancreatic development. PLoS ONE 11, e0166703.
• Malta, D.F.B., Reticker-Flynn, N.E., da Silva, C.L., Cabral, J.S., Fleming, H.E., Zaret, K.S., Bahatia, S.N., and Underhill, G.H. (2016) Extracellular matrix microarrays to study endoderm specification. Acta Biomaterialia 34, 30-40. PMID: 26883775.
• Iwafuchi-Doi, M., Donahue, G., Watts, J.A., Mahony, S., Pugh, B.F., Lee, D., Kaestner, K.H., and Zaret, K.S.^. (2016) Pioneer transcription factor FoxA maintains an accessible nucleosome configuration at enhancers for tissue-specific gene activation. Molecular Cell 62, 79-91. PMID: 27058788.
• Nicetto, D., and Zaret, K.S. (2016) Role of heterochromatin in establishing and changing cell fate. Atlas of Science [http://atlasofscience.org/role-of-heterochromatin-in-establishing-and-changing-cell-fate/#more-16992]
• Zaret, K.S., Lerner, J., and Iwafuchi-Doi, M. (2016) Chromatin scanning by dynamic binding of pioneer factors. Molecular Cell 62, 665-776. PMCID: 27259199.
• Iwafuchi-Doi, M., and Zaret, K.S. (2016) Cell fate control by pioneer transcription factors. Development 143, 1833-1837. PMID: 27246709
• Zaret, K.S. (2016) From Endoderm to Liver Bud: Paradigms of Cell Type Specification and Tissue Morphogenesis. Current Topics in Developmental Biology 117, 647-669. PMID: 26970006.
• Zaret, K.S., and Mango, S. (2016) Pioneer transcription factors, chromatin dynamics, and cell fate control. Current Opinions in Genetics and Development 37, 76-81. PMID: 26826681
• Becker, J. S., Nicetto, D., and Zaret, K.S. (2016) H3K9me3-dependent heterochromatin: Barrier to cell fate changes. Trends in Genetics 32, 29-41. PMID 26675384
• Soufi, A., Fernandez Garcia, M., Jaroszewicz, A., Osman, N., 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
• Zaret, K.S. (2015) Maintaining liver mass (News and Views). Nature 524, 165-166. PMID: 26245376
• Kim, J. and Zaret, K.S. (2015) Reprogramming of human cancer cells to pluripotency for models of cancer progression EMBO Journal 34, 739-747.
• Xu, C.-R., Li, L.-C., Donahue, G., Ying, L., Zhang, Y.-W., Gadue, P., and Zaret, K.S. (2014) Dynamics of genomic H3K27me3 domains and role of EZH2 during pancreatic endocrine specification. EMBO Journal 33, 2157-2170. PMCID PMC4282504
• Metzger, D.E., Liu, C., Ziaie, A.S., Naji, A., and Zaret, K.S.  (2014)  Grg3/TLE3 and Grg1/TLE1 Induce monohormonal Pancreatic β Cells While Repressing α Cell Functions.  Diabetes 63, 1804-1816.
• Zaret, K.S. (2014) Genome reactivation after the silence in mitosis: Recapitulating mechanisms of development? Developmental Cell 29, 132-134. PMID: 24780732
• Zaret, K.S. (2014)   At the Revolution with Fred Sherman.  Molecular and Cellular Biology 34, 922-925.
• Iwafuchi-Doi, M., and Zaret, K.S. (2014) Pioneer transcription factors in cell reprogramming. Genes and Development 28, 2679-2692. PMCID: PMC3994953
• Kim, J., Hoffman, J.P., Alpaugh, R.K., Rhim, A.D., Reichert, M., Stanger, B.Z., Furth, E.E., Sepulveda, A.R., Yuan, C.S., Won, K.J., Donahue, G., Sands, J., Gumbs, A.A., and Zaret, K.S.  (2013)  An iPSC line from human pancreatic ductal adenocarcinoma undergoes early to invasive stages of pancreatic cancer progression.  Cell Reports 3, 2088-2099.
• Caravaca, J.M., Donahue, G., Becker, J.S., and Zaret, K.S.  (2013)  Bookmarking by specific and nonspecific binding of FoxA1 pioneer factor to mitotic chromosomes.  Genes and Development 27, 251-260.
• 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.
• Metzger, D.E., Gasperowicz, M., Otto, F., Cross, J.C., Gradwohl, G., and Zaret, K.S.  (2012) The transcriptional corepressor Grg3/TLE3 promotes pancreatic endocrine progenitor delamination and beta-cell differentiation.  Development 139, 1447-1456.
• Zaret, K.S., and Carroll, J.S. (2011)  Pioneer transcription factors:  establishing competence for gene expression.  Genes and Development 25, 2227-2241.
• Watts, J.A., Zhang, C. Kormish, J.D., Klein-Szanto, A., Zhang, M.Q., and Zaret, K.S. (2011)  Study of FoxA Pioneer Factor at Silent Genes Reveals Rfx-Repressed Enhancer at Cdx2 and a Potential Indicator of Esophageal Adenocarcinoma Development.  PLoS Genetics 7, E1002277.
• Xu, C.-R., Cole, P.A., Meyers, D.J., Kormish, J., Dent, S., and Zaret, K.S.  (2011) Chromatin “prepattern” and histone modifiers in a fate choice for liver or pancreas.  Science 332, 963-966.
• An interview with Ken Zaret.  Interviewed by Kathryn Senior. (2010) Development 137, 3151-3152.
• Sekiya, T., Muthurajan, U.M., Tulin, A., McPherson, C., Luger, K., and Zaret, K.S.  (2009)  Nucleosome-binding affinity as a primary determinant of the nuclear mobility of pioneer transcription factor FoxA.  Genes and Development 23, 804-809.
• Wandzioch, E., and Zaret, K.S. (2009) Dynamic signaling network for the specification of embryonic pancreas and liver progenitors.  Science 324, 1707-1710.
• Zaret, K.  (2008)  JEEM and my evolution in development.  Development 135, 2341.
• Zaret, K.S., and Grompe, M.  (2008)  Generation and regeneration of cells of the liver and pancreas.  Science 322, 1490-1494.
• Zaret, K.S.  (2008)  Genetic programming of liver and pancreas progenitors:  Lessons for stem cell differentiation.  Nature Reviews Genetics 9, 329-340.
• Sekiya, T., and Zaret, K.S. (2007) Repression by Groucho/TLE/Grg proteins:  Genomic site recruitment generates compacted chromatin in vitro and impairs activator binding in vivo.  Molecular Cell 28, 291-303.
• Zaret, K.S.  (2006)  Stability and evolution of transcriptional regulatory networks.  Molecular Systems Biology 2, 21
• Calmont, A., Wandzioch, E., Tremblay, K.D., Minowada, G., Kaestner, K.H., Martin, G.R., and Zaret, K.S.  (2006)  FGF-response pathways that mediate hepatic gene induction in embryonic endoderm cells.  Developmental Cell 11, 339-348.
• Tremblay, K.D., and Zaret, K.S.  (2005)  Distinct populations of progenitor cells converge to generate the embryonic liver bud and other ventral gut tissues.  Developmental Biology 280, 87-99.
• Yoshitomi, H., and Zaret, K.S.  (2004) Endothelial cell interactions initiate dorsal pancreas development by selectively inducing the transcription factor Ptf1a.  Development 131, 807-817.
• Bort, R., Martinez Barbera, J.P., Beddington, R.S.P., and Zaret, K.S.  (2004) Hex Homeobox gene-dependent tissue positioning is required for organogenesis of the ventral pancreas.  Development 131, 787-806.
• Parviz, F., Matullo, C., Ning, G., Kaestner, K.H., Rossi, J., Zaret, K.S., and Duncan, S.A.  (2003)  Hepatocyte nuclear factors 4alpha controls the development of a hepatic epithelium and liver organogenesis.  Nature Genetics 34, 292-296.
• Cirillo, L.A., Lin, F.R., Cuesta, I., Jarnik, M., and Zaret, K.S.  (2002) Opening of compacted chromatin by early developmental transcription factors HNF3 (FoxA) and GATA-4.  Molecular Cell 9, 279-289.
• Zaret, K.S.  (2002)  Regulatory phases of early liver development:  Paradigms of organogenesis.  Nature Reviews Genetics 3, 499-512.
• Matsumoto, K., Yoshitomi, H., Rossant, J., and Zaret, K.S.  (2001) Liver organogenesis promoted by endothelial cells prior to vascular function.  Science 294, 559-563.
• Rossi, J.M., Dunn, N.R., Hogan, B.L.M., and Zaret, K.S.  (2001)  Distinct mesodermal signals, including BMPs from the septum transversum mesenchyme, are required in combination for hepatogenesis from the endoderm.  Genes and Development 15, 1998-2009.
• Deutsch, G., Jung, J., Zheng, M., Lora, J., and Zaret, K.S.  (2001) Bipotential precursor cell population for liver and pancreas within the embryonic endoderm.  Development 128, 871-881.
• Cirillo, L.A., and Zaret, K.S.   (1999)  An early developmental transcription factor complex that is more stable on nucleosome core particles than on free DNA.  Molecular Cell 4, 961-969.
• Jung, J., Zheng, M., Goldfarb, M., and Zaret, K.S.  (1999)  Initiation of mammalian liver development from endoderm by fibroblast growth factors.  Science 284, 1998-2003.
• Bossard, P., and Zaret, K.S.  (1998)  GATA transcription factors as potentiators of gut endoderm differentiation.  Development 125, 4909-4917.
• Shim, E.Y., Woodcock, C., and Zaret, K.S.  (1998)  Nucleosome positioning by the winged-helix transcription factor HNF3.  Genes and Development 12, 5-10.
• Cirillo, L.A., McPherson, C.E., Bossard, P., Cherian, S., Shim, E.Y., Clark, K., Burley, S., and Zaret, K.S.  (1998)  Nucleosome-specific binding activity of the winged-helix transcription factor HNF3.  EMBO Journal 17, 244-254.
• Gualdi, R., Bossard, P., Zheng, M., Hamada, Y., Coleman, J., and Zaret, K.S.  (1996)  Hepatic specification of the gut endoderm in vitro:  Cell signalling and transcriptional control.  Genes and Development 10, 1670-1682.
• Ang, S.-L, Wierda, A., Wong, D. Stevens, K., Cascio, S., Rossant, J., and Zaret, K.S.  (1993)  The formation and maintenance of the definitive endoderm lineage in the mouse:  Potential role of HNF3/forkhead proteins.  Development 119, 1301-1315.
• McPherson, C.E., Shim, E.-Y., Friedman, D.S., and Zaret, K.S.  (1993)  A tissue-specific enhancer and bound transcription factors existing in a precisely positioned nucleosome array.  Cell 75, 387-398.