Zachary Smith, PhD
Assistant Professor of GeneticsCards
Appointments
Contact Info
Yale School of Medicine
Yale Stem Cell Center, 10 Amistad Street
New Haven, CT 06519
United States
About
Titles
Assistant Professor of Genetics
Biography
Zachary Smith received his B.S. in Biology from M.I.T. in 2008. Inspired by the recent works of Takahashi and Yamanaka and by the first genome-wide “epigenomes” from the Broad Institute, he joined Dr. Alex Meissner’s new lab at Harvard University’s Department of Stem Cell and Regenerative Biology as its first employee. During his time as a Research Assistant, Zachary published research on direct reprogramming of somatic cells to pluripotency, including early morphological changes by live imaging and chromatin dynamics by Chromatin Immunoprecipitation followed by high throughput sequencing (ChIP-seq). He also optimized emerging genome-scale technologies to study DNA methylation in precious samples and used these to understand its global dynamics during early mouse and human development. After matriculating into Harvard’s Molecules, Cells and Organisms (MCO) program in 2013, Zachary continued applying cutting edge technologies to understand global changes in genome regulation as they contribute to mammalian development, including new strategies to study the roles of chromatin regulators during implantation and gastrulation. Furthermore, he collaborated with Jonathan Weissman’s lab at UCSF to produce a novel Cas9-based molecular recorder, which can recover the historical relationships between single cells and used to construct comprehensive lineage hierarchies. These and other technologies offer new approaches for quantitative ontogeny, the population-level coordination of progenitor fields as they commit to form complex structures. Zachary received his Ph.D. in 2019 and joined the Yale Stem Cell Center and Department of Genetics as an Assistant Professor in September, 2020.
Appointments
Genetics
Assistant ProfessorPrimary
Other Departments & Organizations
Education & Training
- PhD
- Harvard University, Biology (2019)
- BS
- Massachusetts Institute of Technology, Biology (2008)
Research
Overview
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.
Medical Subject Headings (MeSH)
Research at a Glance
Yale Co-Authors
Publications Timeline
Research Interests
Michael Caplan, PhD, MD
Berna Sozen, PhD
Biff Forbush, PhD
Kevin Tse
Liangwen Zhong, PhD
Publications
2024
DNA methylation in mammalian development and disease
Smith Z, Hetzel S, Meissner A. DNA methylation in mammalian development and disease. Nature Reviews Genetics 2024, 1-24. PMID: 39134824, DOI: 10.1038/s41576-024-00760-8.Peer-Reviewed Original ResearchAltmetricConceptsLong-read sequencing technologiesDNA methylation fieldDNA methylation landscapeGenome functionMethylation landscapeSequencing technologiesEpigenetic codeGenomic characterizationRegulatory layerDNA methylationCell physiologyMammalian developmentMammalian lifespanGenetic featuresFunctional understandingSingle-cellDNAMechanistic discoveriesSomatic transitionsPhases of discoveryDevelopmental potentialDiscoveryPhenotypeSenescencePhysiologyReconstructing axial progenitor field dynamics in mouse stem cell-derived embryoids
Bolondi A, Law B, Kretzmer H, Gassaloglu S, Buschow R, Riemenschneider C, Yang D, Walther M, Veenvliet J, Meissner A, Smith Z, Chan M. Reconstructing axial progenitor field dynamics in mouse stem cell-derived embryoids. Developmental Cell 2024, 59: 1489-1505.e14. PMID: 38579718, PMCID: PMC11187653, DOI: 10.1016/j.devcel.2024.03.024.Peer-Reviewed Original ResearchCitationsAltmetricConceptsNeuro-mesodermal progenitorsFate outcomesStem cell-based modelsEmbryonic trunkEnvironmental cuesMorphological phenotypesDownstream lineagesMolecular recordCell-based modelsCell typesTranscriptional signatureComplex tissuesAxial progenitorsLineagesDevelopmental timeNeural lineagesTransient progenitor populationProgenitor populationsDevelopmental windowPhylogenyAutonomous transposons tune their sequences to ensure somatic suppression
Ilık İ, Glažar P, Tse K, Brändl B, Meierhofer D, Müller F, Smith Z, Aktaş T. Autonomous transposons tune their sequences to ensure somatic suppression. Nature 2024, 626: 1116-1124. PMID: 38355802, PMCID: PMC10901741, DOI: 10.1038/s41586-024-07081-0.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsTransposable elementsSAFB proteinsPiwi-interacting RNA pathwayRNA-basedIntronic transposed elementsRNA processing signalsPre-mRNA processingIntronic spaceNested genesPostmeiotic spermatidsAutonomous transposonsDNA transposonsRNA pathwaysCassette exonsSplicing codeSplicing eventsGenome integrityTE exonizationHuman genesL1 elementsRNA synthesisHost genesTissue-specificSAFBSomatic cells
2023
Self-patterning of human stem cells into post-implantation lineages
Pedroza M, Gassaloglu S, Dias N, Zhong L, Hou T, Kretzmer H, Smith Z, Sozen B. Self-patterning of human stem cells into post-implantation lineages. Nature 2023, 622: 574-583. PMID: 37369348, PMCID: PMC10584676, DOI: 10.1038/s41586-023-06354-4.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsStem cellsPlacental cell typesPost-implantation embryonic developmentHuman pluripotent stem cellsPluripotent stem cellsHuman embryonic developmentEmbryonic developmentHuman stem cellsCongenital pathologyPost-implantation epiblastDiverse cell statesSingle-cell transcriptomicsAmniotic ectodermExtra-embryonic endodermSpontaneous differentiationSignaling hubThree-dimensional structureSecreted modulatorsCell types
2022
Hijacking of transcriptional condensates by endogenous retroviruses
Asimi 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.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsTranscriptional condensatesEndogenous retrovirusesMurine embryonic stem cellsSingle-cell RNA-seq analysisKnockout mouse embryosRNA-seq analysisEmbryonic stem cellsMost endogenous retrovirusesERV RNAsPhase-separated dropletsNascent RNAPluripotency genesPluripotent lineageRNA polymeraseTranscription factorsReconstitution systemTriggers dissociationERV lociMouse embryosMediator coactivatorSelective degradationDisease contextsStem cellsRNASpecific depletion
2021
Diverse epigenetic mechanisms maintain parental imprints within the embryonic and extraembryonic lineages
Andergassen 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.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsX-chromosome inactivationGenomic imprintingEpigenetic mechanismsEpigenetic pathwaysIndependent gene clustersPolycomb group repressorsDiverse epigenetic mechanismsDistinct gene setsAllele-specific expressionH3K9 methyltransferase G9aAutosomal imprintingChromosomal scaleExtraembryonic lineagesParental imprintsPlacental lineagesGene clusterChromosome inactivationEutherian mammalsMethyltransferase G9aDNA methylationExtraembryonic ectodermGene setsSingle locusX chromosomeDistinct domainsSmart-RRBS for single-cell methylome and transcriptome analysis
Gu 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.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsSingle cellsProtein-coding genesSingle-cell methylomesSame single cellMulti-omics approachRare cell populationsSmart-seq2Transcriptional statesDNA methylomeTranscriptome analysisImportant mechanistic insightsEpigenetic modificationsDNA methylationDissected tissue samplesGenomic DNAHundreds of cellsCellular heterogeneityFlow sortingRegulatory consequencesMethylomeEpigenetic promoterMechanistic insightsCell populationsCellsTypical single cell
2020
Epigenetic regulator function through mouse gastrulation
Grosswendt 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.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsMutant phenotypePolycomb Repressive Complex 1Single-cell RNA sequencingComplex mutant phenotypesSingle totipotent cellRepressive Complex 1Mutant mouse embryosSpecific transcription factorsMouse gastrulationTranscriptional informationEpigenetic machineryHistone residuesMolecular functionsCellular diversityTotipotent cellsTranscriptional changesTranscription factorsEssential regulatorRNA sequencingDevelopmental roleMouse embryosGenetic templatesRegulator functionSubstantial cooperativityGastrulationTETs compete with DNMT3 activity in pluripotent cells at thousands of methylated somatic enhancers
Charlton 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.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsMeSH KeywordsAnimalsCell DifferentiationCell LineDNA (Cytosine-5-)-MethyltransferasesDNA MethylationDNA Methyltransferase 3AEmbryonic Stem CellsEnhancer Elements, GeneticEpigenesis, GeneticGene Expression Regulation, DevelopmentalGerm LayersHumansMiceMice, KnockoutMixed Function OxygenasesPluripotent Stem CellsProto-Oncogene ProteinsConceptsPluripotent cellsHuman embryonic stem cell linesEmbryonic stem cell linesDNA methylation landscapeEpiblast stem cellsStem cell linesGlobal methylation levelsMethylation landscapeMouse ESCsMammalian cellsRegulatory sequencesDNA methylationSomatic tissuesNegative regulatorTET expressionMethylation levelsDynamic locusStem cellsCell linesLociDemethylationRegulatorEnhancerCellsTet
2019
In vivo Firre and Dxz4 deletion elucidates roles for autosomal gene regulation
Andergassen 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.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsX-chromosome inactivationAutosomal gene regulationGene regulationDouble deletionOrgan-specific mannerChromosome inactivationGene setsX chromosomeTranscriptional effectsExpression signaturesLociCell linesDeletionGenesRegulationVivo contributionRecent evidenceMegadomainsAutosomesFIRREMutantsChromosomesMain driversBiologySuperloops
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Yale School of Medicine
Yale Stem Cell Center, 10 Amistad Street
New Haven, CT 06519
United States