Zachary Smith, PhD
Research & Publications
Biography
News
Research Summary
Our overarching goal is to understand moments in developmental time where the genome undergoes dramatic changes in regulation, as well as their purpose and underlying molecular machinery. We are specifically interested in how covalent modifications to chromatin are coordinated to control organismal phenotype epigenetically, including possible impacts of the fetal environment. To study these phenomena, we apply a variety of cutting-edge technological approaches to measure changes in genome regulation as well as advanced micromanipulation techniques to perturb native processes within the early mouse embryo. Our efforts are focused on the first three major transitions in mammalian embryogenesis: fertilization, implantation, and gastrulation.
Extensive Research Description
During fertilization, a full meter of genetic material is delivered by sperm as a highly dense, protamine-compacted particle and rapidly outfitted with chromatin over the first cell cycle. During this period, this formerly inert genome must be activated and made competent for essentially every life process, including transcription, replication, and mitosis. Simultaneously, pre-existing epigenetic modifications within the paternal genome, primarily cytosine methylation, are globally erased. Failure to appropriately reconstruct a functioning genome may also have downstream consequences that affect embryo viability or long term phenotypes. Nonetheless, the exact sequences and molecular pathways that govern these processes are still only minimally understood and hampered by the delicacy and transience of the single cell embryo. We seek to apply a suite of next generation sequencing approaches and advanced micromanipulation techniques to specifically measure and perturb the fertilization process to understand the very first moments of life.
The maternal-fetal interface is established during implantation. During this process, mammalian genomes undergo two distinct waves of global genome reprogramming depending upon their ultimate developmental lineage. Within the embryonic lineage, the pre-implantation inner cell mass (ICM) matures to form the epiblast, which remains capable of forming all subsequent tissues but appears to have fundamentally different genome regulation. This transition (frequently referred to as “naïve to primed”) includes the initial establishment of a chromatin landscape that resembles all subsequent somatic cells in the body and is characterized by high global levels of cytosine methylation and regulation of developmnental gene promoters by the Polycomb Repressive Complexes.
Simultaneously, the pre-implantation trophectodermal lineage matures to form the Extraembryonic Ectoderm (ExE) which will go on to invade maternal tissues and form the placenta. As it develops, the ExE aquires a highly unusual mode of genome regulation characterized by an erratic, highly dynamic DNA methylation landscape that includes terminal silencing of Polycomb targets. While unobserved within the embryonic lineage, a highly similar mode of genome regulation emerges in nearly every observed mammalian cancer, regardless of its mutational profile or tissue of origin. We are interested in understanding how these two highly distinct modes of genome regulation are established and employ a variety of approaches to study the epigenetics and genome biology of implantation in vivo and in vitro. For example, we employ Cas9-mediated genome editing to perturb key epigenetic regulators in zygotes and examine changes to the epigenome or transcriptome in early post-implantation tissues. Similarly, we hope to develop novel massive parallel reporter assays (MPRA) to identify how specific epigenetic states are initiated and maintained.
After implantation, the pluripotent epiblast is triggered to differentiate by ExE-supported morphogen-gradients to initiate gastrulation. Although the initial waves of mammalian development require approximately one week, the establishment of the three germ layers (ectoderm, mesoderm, and endoderm) and foundational embryonic body axes is comparatively rapid. Within two days, the mouse embryo proceeds from a fairly rudimentary conceptus comprised of several hundred cells to a highly sophisticated structure with dozens of unique cell types and well over 100,000 cells. Notably, many chromatin regulators are absolutely essential for this process and produce embryonic lethal knockout phenotypes within the gastrulation window. However, it is exceedingly unclear how this class of regulators, which are constitutively expressed and recognize highly generic substrates, help orchestrate such intricate and highly specific developmental outcomes. To study this seeming paradox, we have innovated a novel platform that combines zygotic Cas9-based mutation and single cell transcriptional analysis to examine cohorts of complex mutant embryos. Using this approach, we hope to develop quantitative models that explain the specific roles of epigenetic regulators in gastrulation. Moreover, we hope to expand on these principles to understand sources of phenotypic variation, particularly environmental factors that may alter the epigenome and result in fetal or congenital disorders.
Finally, we are constantly seeking to develop new technological approaches for studying these processes. For example, we recently helped innovate a novel molecular recorder to capture historical information between thousands of single cells within the post-gastrulation embryo. We hope to utilize this strategy to quantify progenitor field dynamics, the coordinated creation and consumption of multipotent progenitor cells to generate embryonic structures. We are continuing to optimize this technology to improve its resolution and reproducibility. In parallel, we hope to apply it to understand complex developmental transitions, as well as to reconstruct cell lineages within normal and experimentally perturbed cell lineages.
Research Interests
Biotechnology; Cell Nucleus; Chromatin; Embryonic and Fetal Development; Genetics; Molecular Biology; Reproduction; Epigenetic Repression
Selected Publications
- Hijacking of transcriptional condensates by endogenous retrovirusesAsimi V, Sampath Kumar A, Niskanen H, Riemenschneider C, Hetzel S, Naderi J, Fasching N, Popitsch N, Du M, Kretzmer H, Smith ZD, Weigert R, Walther M, Mamde S, Meierhofer D, Wittler L, Buschow R, Timmermann B, Cisse II, Ameres SL, Meissner A, Hnisz D. Hijacking of transcriptional condensates by endogenous retroviruses Nature Genetics 2022, 54: 1238-1247. PMID: 35864192, PMCID: PMC9355880, DOI: 10.1038/s41588-022-01132-w.
- Diverse epigenetic mechanisms maintain parental imprints within the embryonic and extraembryonic lineagesAndergassen D, Smith ZD, Kretzmer H, Rinn JL, Meissner A. Diverse epigenetic mechanisms maintain parental imprints within the embryonic and extraembryonic lineages Developmental Cell 2021, 56: 2995-3005.e4. PMID: 34752748, PMCID: PMC9463566, DOI: 10.1016/j.devcel.2021.10.010.
- Smart-RRBS for single-cell methylome and transcriptome analysisGu H, Raman AT, Wang X, Gaiti F, Chaligne R, Mohammad AW, Arczewska A, Smith ZD, Landau DA, Aryee MJ, Meissner A, Gnirke A. Smart-RRBS for single-cell methylome and transcriptome analysis Nature Protocols 2021, 16: 4004-4030. PMID: 34244697, PMCID: PMC8672372, DOI: 10.1038/s41596-021-00571-9.
- Epigenetic regulator function through mouse gastrulationGrosswendt S, Kretzmer H, Smith ZD, Kumar AS, Hetzel S, Wittler L, Klages S, Timmermann B, Mukherji S, Meissner A. Epigenetic regulator function through mouse gastrulation Nature 2020, 584: 102-108. PMID: 32728215, PMCID: PMC7415732, DOI: 10.1038/s41586-020-2552-x.
- TETs compete with DNMT3 activity in pluripotent cells at thousands of methylated somatic enhancersCharlton J, Jung EJ, Mattei AL, Bailly N, Liao J, Martin EJ, Giesselmann P, Brändl B, Stamenova EK, Müller FJ, Kiskinis E, Gnirke A, Smith ZD, Meissner A. TETs compete with DNMT3 activity in pluripotent cells at thousands of methylated somatic enhancers Nature Genetics 2020, 52: 819-827. PMID: 32514123, PMCID: PMC7415576, DOI: 10.1038/s41588-020-0639-9.
- In vivo Firre and Dxz4 deletion elucidates roles for autosomal gene regulationAndergassen D, Smith ZD, Lewandowski JP, Gerhardinger C, Meissner A, Rinn JL. In vivo Firre and Dxz4 deletion elucidates roles for autosomal gene regulation ELife 2019, 8: e47214. PMID: 31738164, PMCID: PMC6860989, DOI: 10.7554/elife.47214.
- Differential regulation of OCT4 targets facilitates reacquisition of pluripotencyThakurela S, Sindhu C, Yurkovsky E, Riemenschneider C, Smith ZD, Nachman I, Meissner A. Differential regulation of OCT4 targets facilitates reacquisition of pluripotency Nature Communications 2019, 10: 4444. PMID: 31570708, PMCID: PMC6768871, DOI: 10.1038/s41467-019-11741-5.
- Loss of DNA methyltransferase activity in primed human ES cells triggers increased cell-cell variability and transcriptional repressionTsankov AM, Wadsworth MH, Akopian V, Charlton J, Allon SJ, Arczewska A, Mead BE, Drake RS, Smith ZD, Mikkelsen TS, Shalek AK, Meissner A. Loss of DNA methyltransferase activity in primed human ES cells triggers increased cell-cell variability and transcriptional repression Development 2019, 146: dev174722. PMID: 31515224, PMCID: PMC6803377, DOI: 10.1242/dev.174722.
- Molecular recording of mammalian embryogenesisChan MM, Smith ZD, Grosswendt S, Kretzmer H, Norman TM, Adamson B, Jost M, Quinn JJ, Yang D, Jones MG, Khodaverdian A, Yosef N, Meissner A, Weissman JS. Molecular recording of mammalian embryogenesis Nature 2019, 570: 77-82. PMID: 31086336, PMCID: PMC7229772, DOI: 10.1038/s41586-019-1184-5.
- Targets and genomic constraints of ectopic Dnmt3b expressionZhang Y, Charlton J, Karnik R, Beerman I, Smith ZD, Gu H, Boyle P, Mi X, Clement K, Pop R, Gnirke A, Rossi DJ, Meissner A. Targets and genomic constraints of ectopic Dnmt3b expression ELife 2018, 7: e40757. PMID: 30468428, PMCID: PMC6251628, DOI: 10.7554/elife.40757.
- Global delay in nascent strand DNA methylationCharlton J, Downing TL, Smith ZD, Gu H, Clement K, Pop R, Akopian V, Klages S, Santos DP, Tsankov AM, Timmermann B, Ziller MJ, Kiskinis E, Gnirke A, Meissner A. Global delay in nascent strand DNA methylation Nature Structural & Molecular Biology 2018, 25: 327-332. PMID: 29531288, PMCID: PMC5889353, DOI: 10.1038/s41594-018-0046-4.
- Genetic determinants and epigenetic effects of pioneer-factor occupancyDonaghey J, Thakurela S, Charlton J, Chen JS, Smith ZD, Gu H, Pop R, Clement K, Stamenova EK, Karnik R, Kelley DR, Gifford CA, Cacchiarelli D, Rinn JL, Gnirke A, Ziller MJ, Meissner A. Genetic determinants and epigenetic effects of pioneer-factor occupancy Nature Genetics 2018, 50: 250-258. PMID: 29358654, PMCID: PMC6517675, DOI: 10.1038/s41588-017-0034-3.
- Epigenetic restriction of extraembryonic lineages mirrors the somatic transition to cancerSmith ZD, Shi J, Gu H, Donaghey J, Clement K, Cacchiarelli D, Gnirke A, Michor F, Meissner A. Epigenetic restriction of extraembryonic lineages mirrors the somatic transition to cancer Nature 2017, 549: 543-547. PMID: 28959968, PMCID: PMC5789792, DOI: 10.1038/nature23891.
- Probabilistic Modeling of Reprogramming to Induced Pluripotent Stem CellsLiu LL, Brumbaugh J, Bar-Nur O, Smith Z, Stadtfeld M, Meissner A, Hochedlinger K, Michor F. Probabilistic Modeling of Reprogramming to Induced Pluripotent Stem Cells Cell Reports 2016, 17: 3395-3406. PMID: 28009305, PMCID: PMC5467646, DOI: 10.1016/j.celrep.2016.11.080.
- Molecular features of cellular reprogramming and developmentSmith ZD, Sindhu C, Meissner A. Molecular features of cellular reprogramming and development Nature Reviews Molecular Cell Biology 2016, 17: 139-154. PMID: 26883001, DOI: 10.1038/nrm.2016.6.
- Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced PluripotencyCacchiarelli D, Trapnell C, Ziller MJ, Soumillon M, Cesana M, Karnik R, Donaghey J, Smith ZD, Ratanasirintrawoot S, Zhang X, Sui S, Wu Z, Akopian V, Gifford CA, Doench J, Rinn JL, Daley GQ, Meissner A, Lander ES, Mikkelsen TS. Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency Cell 2015, 162: 412-424. PMID: 26186193, PMCID: PMC4511597, DOI: 10.1016/j.cell.2015.06.016.
- Epigenetic predisposition to reprogramming fates in somatic cellsPour M, Pilzer I, Rosner R, Smith ZD, Meissner A, Nachman I. Epigenetic predisposition to reprogramming fates in somatic cells EMBO Reports 2015, 16: 370-378. PMID: 25600117, PMCID: PMC4364876, DOI: 10.15252/embr.201439264.
- DNA methylation dynamics of the human preimplantation embryoSmith ZD, Chan MM, Humm KC, Karnik R, Mekhoubad S, Regev A, Eggan K, Meissner A. DNA methylation dynamics of the human preimplantation embryo Nature 2014, 511: 611-615. PMID: 25079558, PMCID: PMC4178976, DOI: 10.1038/nature13581.
- In Vivo and In Vitro Dynamics of Undifferentiated Embryonic Cell Transcription Factor 1Galonska C, Smith ZD, Meissner A. In Vivo and In Vitro Dynamics of Undifferentiated Embryonic Cell Transcription Factor 1 Stem Cell Reports 2014, 2: 245-252. PMID: 24672748, PMCID: PMC3964277, DOI: 10.1016/j.stemcr.2014.01.007.
- Tet1 Regulates Adult Hippocampal Neurogenesis and CognitionZhang RR, Cui QY, Murai K, Lim YC, Smith ZD, Jin S, Ye P, Rosa L, Lee YK, Wu HP, Liu W, Xu ZM, Yang L, Ding YQ, Tang F, Meissner A, Ding C, Shi Y, Xu GL. Tet1 Regulates Adult Hippocampal Neurogenesis and Cognition Cell Stem Cell 2013, 13: 237-245. PMID: 23770080, PMCID: PMC4474382, DOI: 10.1016/j.stem.2013.05.006.
- Proliferation-Dependent Alterations of the DNA Methylation Landscape Underlie Hematopoietic Stem Cell AgingBeerman I, Bock C, Garrison BS, Smith ZD, Gu H, Meissner A, Rossi DJ. Proliferation-Dependent Alterations of the DNA Methylation Landscape Underlie Hematopoietic Stem Cell Aging Cell Stem Cell 2013, 12: 413-425. PMID: 23415915, DOI: 10.1016/j.stem.2013.01.017.
- DNA methylation: roles in mammalian developmentSmith ZD, Meissner A. DNA methylation: roles in mammalian development Nature Reviews Genetics 2013, 14: 204-220. PMID: 23400093, DOI: 10.1038/nrg3354.
- The simplest explanation: passive DNA demethylation in PGCsSmith ZD, Meissner A. The simplest explanation: passive DNA demethylation in PGCs The EMBO Journal 2013, 32: 318-321. PMID: 23299938, PMCID: PMC3567498, DOI: 10.1038/emboj.2012.349.
- Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profilingBoyle P, Clement K, Gu H, Smith ZD, Ziller M, Fostel JL, Holmes L, Meldrim J, Kelley F, Gnirke A, Meissner A. Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling Genome Biology 2012, 13: r92. PMID: 23034176, PMCID: PMC3491420, DOI: 10.1186/gb-2012-13-10-r92.
- Mouse ooplasm confers context-specific reprogramming capacityChan MM, Smith ZD, Egli D, Regev A, Meissner A. Mouse ooplasm confers context-specific reprogramming capacity Nature Genetics 2012, 44: 978-980. PMID: 22902786, PMCID: PMC3432711, DOI: 10.1038/ng.2382.
- DNA Methylation Dynamics during In Vivo Differentiation of Blood and Skin Stem CellsBock C, Beerman I, Lien WH, Smith ZD, Gu H, Boyle P, Gnirke A, Fuchs E, Rossi DJ, Meissner A. DNA Methylation Dynamics during In Vivo Differentiation of Blood and Skin Stem Cells Molecular Cell 2012, 47: 633-647. PMID: 22841485, PMCID: PMC3428428, DOI: 10.1016/j.molcel.2012.06.019.
- A unique regulatory phase of DNA methylation in the early mammalian embryoSmith ZD, Chan MM, Mikkelsen TS, Gu H, Gnirke A, Regev A, Meissner A. A unique regulatory phase of DNA methylation in the early mammalian embryo Nature 2012, 484: 339-344. PMID: 22456710, PMCID: PMC3331945, DOI: 10.1038/nature10960.
- Epigenomics and chromatin dynamicsAkopian V, Chan MM, Clement K, Galonska C, Gifford CA, Lehtola E, Liao J, Samavarchi-Tehrani P, Sindhu C, Smith ZD, Tsankov AM, Webster J, Zhang Y, Ziller MJ, Meissner A. Epigenomics and chromatin dynamics Genome Biology 2012, 13: 313. PMID: 22364154, PMCID: PMC3334565, DOI: 10.1186/gb-2012-13-2-313.
- Lung Stem Cell Self-Renewal Relies on BMI1-Dependent Control of Expression at Imprinted LociZacharek SJ, Fillmore CM, Lau AN, Gludish DW, Chou A, Ho JW, Zamponi R, Gazit R, Bock C, Jäger N, Smith ZD, Kim TM, Saunders AH, Wong J, Lee JH, Roach RR, Rossi DJ, Meissner A, Gimelbrant AA, Park PJ, Kim CF. Lung Stem Cell Self-Renewal Relies on BMI1-Dependent Control of Expression at Imprinted Loci Cell Stem Cell 2011, 9: 272-281. PMID: 21885022, PMCID: PMC3167236, DOI: 10.1016/j.stem.2011.07.007.
- Pluripotency factors in embryonic stem cells regulate differentiation into germ layers.Thomson M, Liu SJ, Zou LN, Smith Z, Meissner A, Ramanathan S. Pluripotency factors in embryonic stem cells regulate differentiation into germ layers. Cell 2011, 145: 875-89. PMID: 21663792, PMCID: PMC5603300, DOI: 10.1016/j.cell.2011.05.017.
- Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profilingGu H, Smith ZD, Bock C, Boyle P, Gnirke A, Meissner A. Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling Nature Protocols 2011, 6: 468-481. PMID: 21412275, DOI: 10.1038/nprot.2010.190.
- Reference Maps of Human ES and iPS Cell Variation Enable High-Throughput Characterization of Pluripotent Cell LinesBock C, Kiskinis E, Verstappen G, Gu H, Boulting G, Smith ZD, Ziller M, Croft GF, Amoroso MW, Oakley DH, Gnirke A, Eggan K, Meissner A. Reference Maps of Human ES and iPS Cell Variation Enable High-Throughput Characterization of Pluripotent Cell Lines Cell 2011, 144: 439-452. PMID: 21295703, PMCID: PMC3063454, DOI: 10.1016/j.cell.2010.12.032.
- Reprogramming Factor Expression Initiates Widespread Targeted Chromatin RemodelingKoche RP, Smith ZD, Adli M, Gu H, Ku M, Gnirke A, Bernstein BE, Meissner A. Reprogramming Factor Expression Initiates Widespread Targeted Chromatin Remodeling Cell Stem Cell 2011, 8: 96-105. PMID: 21211784, PMCID: PMC3220622, DOI: 10.1016/j.stem.2010.12.001.
- Highly Efficient Reprogramming to Pluripotency and Directed Differentiation of Human Cells with Synthetic Modified mRNAWarren L, Manos PD, Ahfeldt T, Loh YH, Li H, Lau F, Ebina W, Mandal PK, Smith ZD, Meissner A, Daley GQ, Brack AS, Collins JJ, Cowan C, Schlaeger TM, Rossi DJ. Highly Efficient Reprogramming to Pluripotency and Directed Differentiation of Human Cells with Synthetic Modified mRNA Cell Stem Cell 2010, 7: 618-630. PMID: 20888316, PMCID: PMC3656821, DOI: 10.1016/j.stem.2010.08.012.
- Dynamic single-cell imaging of direct reprogramming reveals an early specifying eventSmith ZD, Nachman I, Regev A, Meissner A. Dynamic single-cell imaging of direct reprogramming reveals an early specifying event Nature Biotechnology 2010, 28: 521-526. PMID: 20436460, PMCID: PMC2908494, DOI: 10.1038/nbt.1632.
- Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolutionGu H, Bock C, Mikkelsen TS, Jäger N, Smith ZD, Tomazou E, Gnirke A, Lander ES, Meissner A. Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution Nature Methods 2010, 7: 133-136. PMID: 20062050, PMCID: PMC2860480, DOI: 10.1038/nmeth.1414.
- Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen ResponsesAmit I, Garber M, Chevrier N, Leite AP, Donner Y, Eisenhaure T, Guttman M, Grenier JK, Li W, Zuk O, Schubert LA, Birditt B, Shay T, Goren A, Zhang X, Smith Z, Deering R, McDonald RC, Cabili M, Bernstein BE, Rinn JL, Meissner A, Root DE, Hacohen N, Regev A. Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses Science 2009, 326: 257-263. PMID: 19729616, PMCID: PMC2879337, DOI: 10.1126/science.1179050.
- High-throughput bisulfite sequencing in mammalian genomesSmith ZD, Gu H, Bock C, Gnirke A, Meissner A. High-throughput bisulfite sequencing in mammalian genomes Methods 2009, 48: 226-232. PMID: 19442738, PMCID: PMC2864123, DOI: 10.1016/j.ymeth.2009.05.003.
- High-resolution DNA-binding specificity analysis of yeast transcription factors.Zhu C, Byers KJ, McCord RP, Shi Z, Berger MF, Newburger DE, Saulrieta K, Smith Z, Shah MV, Radhakrishnan M, Philippakis AA, Hu Y, De Masi F, Pacek M, Rolfs A, Murthy T, Labaer J, Bulyk ML. High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Research 2009, 19: 556-66. PMID: 19158363, PMCID: PMC2665775, DOI: 10.1101/gr.090233.108.
- Immunocytochemical localization of plasmalemmal proteins in semi-thin sections of epithelial monolayers.Smith ZD, Caplan MJ, Jamieson JD. Immunocytochemical localization of plasmalemmal proteins in semi-thin sections of epithelial monolayers. Journal Of Histochemistry & Cytochemistry 1988, 36: 311-316. PMID: 2449492, DOI: 10.1177/36.3.2449492.
- Monoclonal antibody localization of Na+-K+-ATPase in the exocrine pancreas and parotid of the dogSmith ZD, Caplan MJ, Forbush B, Jamieson JD. Monoclonal antibody localization of Na+-K+-ATPase in the exocrine pancreas and parotid of the dog American Journal Of Physiology 1987, 253: g99-g109. PMID: 2441610, DOI: 10.1152/ajpgi.1987.253.2.g99.