Kenneth S Zaret

Fox Chase Cancer Center, Filadelfia, Pennsylvania, United States

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Publications (152)

  • Makiko Iwafuchi-Doi · Kenneth S. Zaret
    [Show abstract] [Hide abstract] ABSTRACT: Distinct combinations of transcription factors are necessary to elicit cell fate changes in embryonic development. Yet within each group of fate-changing transcription factors, a subset called ‘pioneer factors’ are dominant in their ability to engage silent, unmarked chromatin and initiate the recruitment of other factors, thereby imparting new function to regulatory DNA sequences. Recent studies have shown that pioneer factors are also crucial for cellular reprogramming and that they are implicated in the marked changes in gene regulatory networks that occur in various cancers. Here, we provide an overview of the contexts in which pioneer factors function, how they can target silent genes, and their limitations at regions of heterochromatin. Understanding how pioneer factors regulate gene expression greatly enhances our understanding of how specific developmental lineages are established as well as how cell fates can be manipulated.
    Article · Jun 2016 · Development
  • Kenneth S. Zaret · Jonathan Lerner · Makiko Iwafuchi-Doi
    [Show abstract] [Hide abstract] ABSTRACT: Pioneer factors such as FoxA target nucleosomal DNA and initiate cooperative interactions at silent genes during development, cellular reprogramming, and steroid hormone induction. Biophysical studies previously showed that the nuclear mobility of FoxA1 is slower than for many other transcription factors, whereas a new single molecule study (Swinstead et al., 2016, Cell) shows comparable chromatin residence times for FoxA1 and steroid receptors. Despite that steroid receptors engage nucleosome-remodeling complexes, the vast majority of co-bound sites with FoxA are dependent upon FoxA, not vice versa. Taken together, the distinguishing feature of pioneer factors remains nucleosomal access rather than an exceptional residence time in chromatin.
    Article · Jun 2016 · Molecular cell
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    Kenneth S Zaret · Susan E Mango
    [Show abstract] [Hide abstract] ABSTRACT: Among the diverse transcription factors that are necessary to elicit changes in cell fate, both in embryonic development and in cellular reprogramming, a subset of factors are capable of binding to their target sequences on nucleosomal DNA and initiating regulatory events in silent chromatin. Such 'pioneer transcription factors' initiate cooperative interactions with other regulatory proteins to elicit changes in local chromatin structure. As a consequence of pioneer factor binding, the local chromatin can either become open and competent for activation, closed and repressed, or transcriptionally active. Understanding how pioneer factors initiate chromatin dynamics and how such can be blocked at heterochromatic sites provides insights into controlling cell fate transitions at will.
    Full-text Article · Apr 2016 · Current opinion in genetics & development
  • Makiko Iwafuchi-Doi · Greg Donahue · Akshay Kakumanu · [...] · Kenneth S. Zaret
    [Show abstract] [Hide abstract] ABSTRACT: Nuclear DNA wraps around core histones to form nucleosomes, which restricts the binding of transcription factors to gene regulatory sequences. Pioneer transcription factors can bind DNA sites on nucleosomes and initiate gene regulatory events, often leading to the local opening of chromatin. However, the nucleosomal configuration of open chromatin and the basis for its regulation is unclear. We combined low and high levels of micrococcal nuclease (MNase) digestion along with core histone mapping to assess the nucleosomal configuration at enhancers and promoters in mouse liver. We find that MNase-accessible nucleosomes, bound by transcription factors, are retained more at liver-specific enhancers than at promoters and ubiquitous enhancers. The pioneer factor FoxA displaces linker histone H1, thereby keeping enhancer nucleosomes accessible in chromatin and allowing other liver-specific transcription factors to bind and stimulate transcription. Thus, nucleosomes are not exclusively repressive to gene regulation when they are retained with, and exposed by, pioneer factors.
    Article · Apr 2016 · Molecular cell
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    [Show abstract] [Hide abstract] ABSTRACT: Statement of significance: Cellular microarrays can provide the capability to perform high-throughput investigations into the role of microenvironmental signals in a variety of cell functions. This study demonstrates the utility of a high-throughput cellular microarray approach for analyzing the effects of extracellular matrix (ECM) in liver and pancreas differentiation of endoderm progenitor cells. Despite an appreciation that ECM is likely involved in these processes, the influence of ECM, particularly combinations of matrix proteins, had not been systematically explored. In addition to the identification of relevant ECM compositions, this study illustrates the capability of the cellular microarray platform to be integrated with a diverse range of cell fate measurements, which could be broadly applied towards the investigation of cell fate regulation in other tissue development and disease contexts.
    Full-text Article · Feb 2016 · Acta biomaterialia
  • Kenneth S Zaret
    [Show abstract] [Hide abstract] ABSTRACT: The early specification, rapid growth and morphogenesis, and conserved functions of the embryonic liver across diverse model organisms have made the system an experimentally facile paradigm for understanding basic regulatory mechanisms that govern cell differentiation and organogenesis. This essay highlights concepts that have emerged from studies of the discrete steps of foregut endoderm development into the liver bud, as well as from modeling the steps via embryonic stem cell differentiation. Such concepts include understanding the chromatin basis for the competence of progenitor cells to develop into specific lineages; the importance of combinatorial signaling from different sources to induce cell fates; the impact of inductive signaling on preexisting chromatin states; the ability of separately specified domains of cells to merge into a common tissue; and the marked cell biological dynamics, including interactions with the developing vasculature, which establish the initial morphogenesis and patterning of a tissue. The principles gleaned from these studies, focusing on the 2 days it takes for the endoderm to develop into a liver bud, should be instructive for many other organogenic systems and for manipulating tissues in regenerative contexts for biomedical purposes.
    Article · Jan 2016 · Current Topics in Developmental Biology
  • Justin S. Becker · Dario Nicetto · Kenneth S. Zaret
    [Show abstract] [Hide abstract] ABSTRACT: Establishing and maintaining cell identity depends on the proper regulation of gene expression, as specified by transcription factors and reinforced by epigenetic mechanisms. Among the epigenetic mechanisms, heterochromatin formation is crucial for the preservation of genome stability and the cell type-specific silencing of genes. The heterochromatin-associated histone mark H3K9me3, although traditionally associated with the noncoding portions of the genome, has emerged as a key player in repressing lineage-inappropriate genes and shielding them from activation by transcription factors. Here we describe the role of H3K9me3 heterochromatin in impeding the reprogramming of cell identity and the mechanisms by which H3K9me3 is reorganized during development and cell fate determination.
    Article · Dec 2015 · Trends in Genetics
  • Kenneth S Zaret
    Article · Aug 2015 · Nature
  • Jungsun Kim · Kenneth S. Zaret
    Article · Jul 2015 · Cancer Research
  • H-T Hsu · H-M Chen · Z Yang · [...] · S E Mango
    [Show abstract] [Hide abstract] ABSTRACT: Pioneer transcription factors initiate cell-fate changes by binding to silent target genes. They are among the first factors to bind key regulatory sites and facilitate chromatin opening. Here, we identify an additional role for pioneer factors. In early Caenorhabditis elegans foregut development, the pioneer factor PHA-4/FoxA binds promoters and recruits RNA polymerase II (Pol II), often in a poised configuration in which Pol II accumulates near transcription start sites. At a later developmental stage, PHA-4 promotes chromatin opening. We found many more genes with poised RNA polymerase than had been observed previously in unstaged embryos, revealing that early embryos accumulate poised Pol II and that poising is dynamic. Our results suggest that Pol II recruitment, in addition to chromatin opening, is an important feature of PHA-4 pioneer factor activity. Copyright © 2015, American Association for the Advancement of Science.
    Article · Jun 2015 · Science
  • Abdenour Soufi · Meilin Fernandez Garcia · Artur Jaroszewicz · [...] · Kenneth S Zaret
    [Show abstract] [Hide abstract] ABSTRACT: Pioneer transcription factors (TFs) access silent chromatin and initiate cell-fate changes, using diverse types of DNA binding domains (DBDs). FoxA, the paradigm pioneer TF, has a winged helix DBD that resembles linker histone and thereby binds its target sites on nucleosomes and in compacted chromatin. Herein, we compare the nucleosome and chromatin targeting activities of Oct4 (POU DBD), Sox2 (HMG box DBD), Klf4 (zinc finger DBD), and c-Myc (bHLH DBD), which together reprogram somatic cells to pluripotency. Purified Oct4, Sox2, and Klf4 proteins can bind nucleosomes in vitro, and in vivo they preferentially target silent sites enriched for nucleosomes. Pioneer activity relates simply to the ability of a given DBD to target partial motifs displayed on the nucleosome surface. Such partial motif recognition can occur by coordinate binding between factors. Our findings provide insight into how pioneer factors can target naive chromatin sites. Copyright © 2015 Elsevier Inc. All rights reserved.
    Article · Apr 2015 · Cell
  • Jungsun Kim · Kenneth S Zaret
    [Show abstract] [Hide abstract] ABSTRACT: The ability to study live cells as they progress through the stages of cancer provides the opportunity to discover dynamic networks underlying pathology, markers of early stages, and ways to assess therapeutics. Genetically engineered animal models of cancer, where it is possible to study the consequences of temporal-specific induction of oncogenes or deletion of tumor suppressors, have yielded major insights into cancer progression. Yet differences exist between animal and human cancers, such as in markers of progression and response to therapeutics. Thus, there is a need for human cell models of cancer progression. Most human cell models of cancer are based on tumor cell lines and xenografts of primary tumor cells that resemble the advanced tumor state, from which the cells were derived, and thus do not recapitulate disease progression. Yet a subset of cancer types have been reprogrammed to pluripotency or near-pluripotency by blastocyst injection, by somatic cell nuclear transfer and by induced pluripotent stem cell (iPS) technology. The reprogrammed cancer cells show that pluripotency can transiently dominate over the cancer phenotype. Diverse studies show that reprogrammed cancer cells can, in some cases, exhibit early-stage phenotypes reflective of only partial expression of the cancer genome. In one case, reprogrammed human pancreatic cancer cells have been shown to recapitulate stages of cancer progression, from early to late stages, thus providing a model for studying pancreatic cancer development in human cells where previously such could only be discerned from mouse models. We discuss these findings, the challenges in developing such models and their current limitations, and ways that iPS reprogramming may be enhanced to develop human cell models of cancer progression. © 2015 The Authors.
    Article · Feb 2015 · The EMBO Journal
  • Makiko Iwafuchi-Doi · Kenneth S Zaret
    [Show abstract] [Hide abstract] ABSTRACT: A subset of eukaryotic transcription factors possesses the remarkable ability to reprogram one type of cell into another. The transcription factors that reprogram cell fate are invariably those that are crucial for the initial cell programming in embryonic development. To elicit cell programming or reprogramming, transcription factors must be able to engage genes that are developmentally silenced and inappropriate for expression in the original cell. Developmentally silenced genes are typically embedded in "closed" chromatin that is covered by nucleosomes and not hypersensitive to nuclease probes such as DNase I. Biochemical and genomic studies have shown that transcription factors with the highest reprogramming activity often have the special ability to engage their target sites on nucleosomal DNA, thus behaving as "pioneer factors" to initiate events in closed chromatin. Other reprogramming factors appear dependent on pioneer factors for engaging nucleosomes and closed chromatin. However, certain genomic domains in which nucleosomes are occluded by higher-order chromatin structures, such as in heterochromatin, are resistant to pioneer factor binding. Understanding the means by which pioneer factors can engage closed chromatin and how heterochromatin can prevent such binding promises to advance our ability to reprogram cell fates at will and is the topic of this review. © 2014 Iwafuchi-Doi and Zaret; Published by Cold Spring Harbor Laboratory Press.
    Article · Dec 2014 · Genes & Development
  • Jungsun Kim · John P. Hoffman · Maximilian Reichert · [...] · Kenneth S. Zaret
    Article · Nov 2014 · Molecular Cancer Research
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    [Show abstract] [Hide abstract] ABSTRACT: These studies show that miR-122, a 22-nucleotide microRNA, is derived from a liver-specificnon-coding polyadenylated RNA transcribed from the gene hcr. The exact sequence of miR-122as well as the adjacent secondary structure within the hcr mRNA are conserved from mammalianspecies back to fish. Levels of miR-122 in the mouse liver increase to half maximal valuesaround day 17 of embryogenesis, and reach near maximal levels of 50,000 copies per averagecell before birth. Lewis et al (2003) predicted the cationic amino acid transporter (CAT-1 orSLC7A1) as a miR-122 target. CAT-1 protein and its mRNA are expressed in all mammaliantissues but with lower levels in adult liver. Furthermore, during mouse liver development CAT-1mRNA decreases in an almost inverse correlation with miR-122. Eight potential miR-122 targetsites were predicted within the human CAT-1 mRNA, with six in the 3’-untranslated region.Using a reporter construct it was found that just three of the predicted sites, linked in a 400-nucleotide sequence from human CAT-1, acted with synergy and were sufficient to stronglyinhibit protein synthesis and reduce mRNA levels. In summary, these studies followed theaccumulation during development of miR-122 from its mRNA precursor, hcr, through toidentification of what may be a specific mRNA target, CAT-1.
    Full-text Article · Oct 2014 · RNA Biology
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    Cheng‐Ran Xu · Lin‐Chen Li · Greg Donahue · [...] · Kenneth S Zaret
    [Show abstract] [Hide abstract] ABSTRACT: Endoderm cells undergo sequential fate choices to generate insulin-secreting beta cells. Ezh2 of the PRC2 complex, which generates H3K27me3, modulates the transition from endoderm to pancreas progenitors, but the role of Ezh2 and H3K27me3 in the next transition to endocrine progenitors is unknown. We isolated endoderm cells, pancreas progenitors, and endocrine progenitors from different staged mouse embryos and analyzed H3K27me3 genome-wide. Unlike the decline in H3K27me3 domains reported during embryonic stem cell differentiation in vitro, we find that H3K27me3 domains increase in number during endocrine progenitor development in vivo. Genes that lose the H3K27me3 mark typically encode transcriptional regulators, including those for pro-endocrine fates, whereas genes that acquire the mark typically are involved in cell biology and morphogenesis. Deletion of Ezh2 at the pancreas progenitor stage enhanced the production of endocrine progenitors and beta cells. Inhibition of EZH2 in embryonic pancreas explants and in human embryonic stem cell cultures increased endocrine progenitors in vitro. Our studies reveal distinct dynamics in H3K27me3 targets in vivo and a means to modulate beta cell development from stem cells.
    Full-text Article · Aug 2014 · The EMBO Journal
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    [Show abstract] [Hide abstract] ABSTRACT: Despite the tremendous hurdles presented by the complexity of the liver's structure and function, advances in liver physiology, stem cell biology and reprogramming, and the engineering of tissues and devices are accelerating the development of cell-based therapies for treating liver disease and liver failure. This State of the Art Review discusses both the near- and long-term prospects for such cell-based therapies and the unique challenges for clinical translation.
    Full-text Article · Jul 2014 · Science translational medicine
  • Kenneth S Zaret
    [Show abstract] [Hide abstract] ABSTRACT: Transcription is silenced during mitosis and reactivated at mitotic exit. The dynamics and identities of "bookmarking" transcription factors and chromatin marks that mediate reactivation often recapitulate those observed during cell identity establishment in development. Thus, features of postmitotic gene reactivation can provide insights into mechanisms of developmental cell fate establishment.
    Article · Apr 2014 · Developmental Cell
  • David E Metzger · Chengyan Liu · Amin Sam Ziaie · [...] · Kenneth S Zaret
    [Show abstract] [Hide abstract] ABSTRACT: In the pancreas, α and β cells possess a degree of plasticity. In vitro differentiation of pluripotent cells yields mostly α and polyhormonal β-like cells, indicating a gap in understanding of how functional monohormonal β cells are formed and the endogenous repressive mechanisms used to maintain β cell identity. Here, we show that the corepressor Grg3 is expressed in almost all β cells throughout embryogenesis to adulthood. However, Grg3 is expressed in fewer nascent α cells and is progressively lost from α cells as endocrine cells mature into adulthood. We show that mouse Grg3+/- β cells have increased α-specific gene expression, and Grg3+/- pancreata have more α cells and more polyhormonal cells indicating that Grg3 is required for the physiologic maintenance of monohormonal β cell identity. Ectopic expression of Grg3 in α cells represses Glucagon and Arx, and the further addition of Pdx1 induces Glut2 expression and glucose-responsive insulin secretion. Furthermore, we found that Grg1 is the predominant Groucho expressed in human β cells but acts functionally similar to Grg3. Overall, we find that Grg3 and Grg1 establish a monohormonal β cell identity and Groucho-family members may be useful tools or markers for making functional β cells.
    Article · Jan 2014 · Diabetes
  • Kenneth S Zaret
    [Show abstract] [Hide abstract] ABSTRACT: Fred Sherman was a prominent yeast geneticist and my mentor in graduate school. Fred passed away in September 2013 at the age of 81. In this minireview, I describe what it was like to know Fred and be in his lab from 1977 to 1982, the extraordinarily exciting time when the recombinant DNA revolution hit yeast genetics.
    Article · Dec 2013 · Molecular and Cellular Biology