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Smith, Zachary

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Smith

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Zachary

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Smith, Zachary

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2010 - 20189

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Author's Publications: search.filters.isAuthorOfPublication.9ac2df14-3adb-4a3b-bae7-7cefd3489267

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Now showing 1 - 9 of 9
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    Lung Stem Cell Self-Renewal Relies on BMI1-Dependent Control of Expression at Imprinted Loci
    (Elsevier BV, 2011-09-02) Zacharek, Sima J.; Fillmore, Christine M.; Lau, Allison N.; Gludish, David W.; Chou, Alan; Ho, Joshua W.K.; Zamponi, Raffaella; Gazit, Roi; Bock, Christoph; Jäger, Natalie; Smith, Zachary; Kim, Tae-min; Saunders, Arven H.; Wong, Janice; Lee, Joo-Hyeon; Roach, Rebecca R.; Rossi, Derrick; Meissner, Alexander; Gimelbrant, Alexander; Park, Peter; Kim, Carla
    Bmi1 is required for the self-renewal of stem cells in many tissues including the lung epithelial stem cells, Bronchioalveolar Stem Cells (BASCs). Imprinted genes, which exhibit expression from only the maternally- or paternally-inherited allele, are known to regulate developmental processes but their role in adult cells remains a fundamental question. Many imprinted genes were de-repressed in Bmi1 knockout mice, and knockdown of Cdkn1c (p57) and other imprinted genes partially rescued the self-renewal defect of Bmi1 mutant lung cells. Expression of p57 and other imprinted genes was required for lung cell self-renewal in culture and correlated with repair of lung epithelial cell injury in vivo. Our data suggest that Bmi1-dependent regulation of expressed alleles at imprinted loci, distinct from imprinting per se, is required for control of lung stem cells. We anticipate that the regulation and function of imprinted genes is crucial for self-renewal in diverse adult tissue-specific stem cells.
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    Highly Efficient Reprogramming to Pluripotency and Directed Differentiation of Human Cells with Synthetic Modified mRNA
    (Elsevier BV, 2010) Warren, Luigi; Manos, Philip D.; Ahfeldt, Tim; Loh, Yuin-Han; Li, Hualin; Lau, Frank; Ebina, Wataru; Mandal, Pankaj; Smith, Zachary; Meissner, Alexander; Daley, George; Brack, Andrew S; Collins, James; Cowan, Chad; Schlaeger, Thorsten; Rossi, Derrick
    Clinical application of induced pluripotent stem cells (iPSCs) is limited by the low efficiency of iPSC derivation and the fact that most protocols modify the genome to effect cellular reprogramming. Moreover, safe and effective means of directing the fate of patient-specific iPSCs toward clinically useful cell types are lacking. Here we describe a simple, nonintegrating strategy for reprogramming cell fate based on administration of synthetic mRNA modified to overcome innate antiviral responses. We show that this approach can reprogram multiple human cell types to pluripotency with efficiencies that greatly surpass established protocols. We further show that the same technology can be used to efficiently direct the differentiation of RNA-induced pluripotent stem cells (RiPSCs) into terminally differentiated myogenic cells. This technology represents a safe, efficient strategy for somatic cell reprogramming and directing cell fate that has broad applicability for basic research, disease modeling, and regenerative medicine.
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    Genome-Scale DNA Methylation Mapping of Clinical Samples at Single-Nucleotide Resolution
    (Nature Publishing Group, 2010) Gu, Hongcang; Bock, Christoph; Mikkelsen, Tarjei S; Jäger, Natalie; Smith, Zachary; Tomazou, Eleni; Gnirke, Andreas; Lander, Eric; Meissner, Alexander
    Bisulfite sequencing measures absolute levels of DNA methylation at single-nucleotide resolution, providing a robust platform for molecular diagnostics. We optimized bisulfite sequencing for genome-scale analysis of clinical samples: here we outline how restriction digestion targets bisulfite sequencing to hotspots of epigenetic regulation and describe a statistical method for assessing significance of altered DNA methylation patterns. Thirty nanograms of DNA was sufficient for genome-scale analysis and our protocol worked well on formalin-fixed, paraffin-embedded samples.
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    DNA methylation dynamics of the human preimplantation embryo
    (2014) Smith, Zachary; Chan, Michelle M.; Humm, Kathryn C.; Karnik, Rahul; Mekhoubad, Shila; Regev, Aviv; Eggan, Kevin; Meissner, Alexander
    In mammals, cytosine methylation is predominantly restricted to CpG dinucleotides and stably distributed across the genome, with local, cell type-specific regulation directed by DNA binding factors1-3. This comparatively static landscape dramatically contrasts the events of fertilization, where the paternal genome is globally reprogrammed. Paternal genome demethylation includes the majority of CpGs, though methylation is maintained at several notable features4-7. While these dynamics have been extensively characterized in the mouse, only limited observations are available in other mammals, and direct measurements are required to understand the extent to which early embryonic landscapes are conserved8-10. We present genome-scale DNA methylation maps of human preimplantation development and embryonic stem cell (ESC) derivation, confirming a transient state of global hypomethylation that includes most CpGs, while sites of persistent maintenance are primarily restricted to gene bodies. While most features share similar dynamics to mouse, maternally contributed methylation is divergently targeted to species-specific sets of CpG island (CGI) promoters that extend beyond known Imprint Control Regions (ICRs). Retrotransposon regulation is also highly diverse and transitions from maternally to embryonically expressed, species-specific elements. Together, our data confirm that paternal genome demethylation is a general attribute of early mammalian development that is characterized by distinct modes of epigenetic regulation.
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    Mouse Ooplasm Confers Context-Specific Reprogramming Capacity
    (Nature Publishing Group, 2012) Chan, Michelle; Smith, Zachary; Egli, Dieter; Regev, Aviv; Meissner, Alexander
    Enucleated oocytes have the remarkable ability to reprogram somatic nuclei back to totipotency. Here we investigate genome-scale DNA methylation patterns after nuclear transfer and compare them to the dynamics at fertilization. We identify specific targets for DNA demethylation after nuclear transfer such as germ-line associated promoters, as well as unique limitations that include certain repetitive element classes.
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    Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling
    (BioMed Central, 2012) Boyle, Patrick; Clement, Kendell; Gu, Hongcang; Smith, Zachary; Ziller, Michael; Fostel, Jennifer L; Holmes, Laurie; Meldrim, Jim; Kelley, Fontina; Gnirke, Andreas; Meissner, Alexander
    Sequencing-based approaches have led to new insights about DNA methylation. While many different techniques for genome-scale mapping of DNA methylation have been employed, throughput has been a key limitation for most. To further facilitate the mapping of DNA methylation, we describe a protocol for gel-free multiplexed reduced representation bisulfite sequencing (mRRBS) that reduces the workload dramatically and enables processing of 96 or more samples per week. mRRBS achieves similar CpG coverage to the original RRBS protocol, while the higher throughput and lower cost make it better suited for large-scale DNA methylation mapping studies, including cohorts of cancer samples.
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    Epigenomics and Chromatin Dynamics
    (BioMed Central, 2012) Akopian, Veronika; Chan, Michelle; Clement, Kendell; Galonska, Christina; Gifford, Casey; Lehtola, Elizabeth; Liao, Jing; Samavarchi-Tehrani, Payman; Sindhu, Camille; Smith, Zachary; Tsankov, Alexander M.; Webster, Jamie Orme; Zhang, Yingying; Ziller, Michael; Meissner, Alexander
    A report of the 'Joint Keystone Symposium on Epigenomics and Chromatin Dynamics', Keystone, Colorado, 17-22 January 2012. This year's Joint Keystone Symposium on Epigenomics and Chromatin Dynamics was one of the largest Keystone meetings to date, reflecting the excitement and many developments in this area. Richard Young opened the meeting by giving a historic overview before sharing more detailed insights from his recent work in describing the role of the lysine demethylase Lsd1 in mouse embryonic stem (ES) cell differentiation. He also set the broader stage and highlighted the excitement concerning recent advances in epigenetic drugs such as the new bromodomain inhibitors.
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    Epigenetic restriction of extraembryonic lineages mirrors the somatic transition to cancer
    (2017) Smith, Zachary; Shi, Jiantao; Gu, Hongcang; Donaghey, Julie; Clement, Kendell; Cacciarelli, Davide; Gnirke, Andreas; Michor, Franziska; Meissner, Alexander
    In mammals, the canonical somatic DNA methylation landscape is established upon specification of the embryo proper and subsequently disrupted within many cancer types1-4. However, the underlying mechanisms that direct this genome-scale transformation remain elusive, with no clear model for its systematic acquisition or potential developmental utility5,6. Here we analyzed global remethylation from the mouse preimplantation embryo into the early epiblast and extraembryonic ectoderm. We show that these two states acquire highly divergent genomic distributions with substantial disruption of bimodal, CpG density-dependent methylation in the placental progenitor7,8. The extraembryonic epigenome includes specific de novo methylation at hundreds of embryonically-protected CpG island promoters particularly those that are associated with key developmental regulators and orthologously methylated across most human cancer types9. Our data suggest that the evolutionary innovation of extraembryonic tissues may have required cooption of DNA methylation-based suppression as an alternative to the embryonically utilized Polycomb group proteins, which coordinate germlayer formation in response to extraembryonic cues10. Moreover, we establish that this decision is made deterministically downstream of promiscuously utilized, and frequently oncogenic, signaling pathways via a novel combination of epigenetic cofactors. Methylation of developmental gene promoters during tumorigenesis may therefore reflect the misappropriation of an innate trajectory and the spontaneous reacquisition of a latent, developmentally-encoded epigenetic landscape.
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    Molecular Recording of Mammalian Embryogenesis
    (Nature Publishing Group, 2018-08-03) Chan, Michelle M; Smith, Zachary; Grosswendt, Stefanie; Kretzmer, Helene; Norman, Thomas; Adamson, Britt; Jost, Marco; Yang, Dian; Quinn, Jeffrey J; Jones, Matthew G; Khodaverdian, Alex; Yosef, Nir; Meissner, Alexander; Weissman, Jonathan S; Weissman, Jonathan
    Ontogeny describes the emergence of complex multicellular organisms from single totipotent cells. In mammals, this field is particularly challenging due to the indeterminate relationship between self-renewal and differentiation, variation of progenitor field sizes, and internal gestation. Here, we present a flexible, high information, multi-channel molecular recorder with a single cell (sc) readout and apply it as an evolving lineage tracer to define a mouse cell fate map from fertilization through gastrulation. By combining lineage information with scRNA-seq profiles, we recapitulate canonical developmental relationships between different tissue types and reveal the nearly complete transcriptional convergence of endodermal cells from extra-embryonic and embryonic origins. Finally, we apply our cell fate map to estimate the number of embryonic progenitor cells and their degree of asymmetric partitioning during specification. Our approach enables massively parallel, high-resolution recording of lineage and other information in mammalian systems to facilitate a quantitative framework for understanding developmental processes.