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DOI: 10.1126/science.1255885 , 826 (2014); 345 Science et al. Steven Zuryn transdifferentiation Sequential histone-modifying activities determine the robustness of This copy is for your personal, non-commercial use only. clicking here. colleagues, clients, or customers by , you can order high-quality copies for your If you wish to distribute this article to others here. following the guidelines can be obtained by Permission to republish or repurpose articles or portions of articles ): October 1, 2014 www.sciencemag.org (this information is current as of The following resources related to this article are available online at http://www.sciencemag.org/content/345/6198/826.full.html version of this article at: including high-resolution figures, can be found in the online Updated information and services, http://www.sciencemag.org/content/suppl/2014/08/13/345.6198.826.DC1.html can be found at: Supporting Online Material http://www.sciencemag.org/content/345/6198/826.full.html#ref-list-1 , 15 of which can be accessed free: cites 42 articles This article http://www.sciencemag.org/cgi/collection/development Development subject collections: This article appears in the following registered trademark of AAAS. is a Science 2014 by the American Association for the Advancement of Science; all rights reserved. The title Copyright American Association for the Advancement of Science, 1200 New York Avenue NW, Washington, DC 20005. (print ISSN 0036-8075; online ISSN 1095-9203) is published weekly, except the last week in December, by the Science on October 1, 2014 www.sciencemag.org Downloaded from on October 1, 2014 www.sciencemag.org Downloaded from on October 1, 2014 www.sciencemag.org Downloaded from on October 1, 2014 www.sciencemag.org Downloaded from on October 1, 2014 www.sciencemag.org Downloaded from

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Page 1: Sequential histone-modifying activities determine …genetics.wustl.edu/bio5491/files/2015/01/Science-2014-Zuryn-826-9.pdf · Sequential histone-modifying activities determine the

DOI: 10.1126/science.1255885, 826 (2014);345 Science et al.Steven Zuryn

transdifferentiationSequential histone-modifying activities determine the robustness of

This copy is for your personal, non-commercial use only.

clicking here.colleagues, clients, or customers by , you can order high-quality copies for yourIf you wish to distribute this article to others

  here.following the guidelines

can be obtained byPermission to republish or repurpose articles or portions of articles

  ): October 1, 2014 www.sciencemag.org (this information is current as of

The following resources related to this article are available online at

http://www.sciencemag.org/content/345/6198/826.full.htmlversion of this article at:

including high-resolution figures, can be found in the onlineUpdated information and services,

http://www.sciencemag.org/content/suppl/2014/08/13/345.6198.826.DC1.html can be found at: Supporting Online Material

http://www.sciencemag.org/content/345/6198/826.full.html#ref-list-1, 15 of which can be accessed free:cites 42 articlesThis article

http://www.sciencemag.org/cgi/collection/developmentDevelopment

subject collections:This article appears in the following

registered trademark of AAAS. is aScience2014 by the American Association for the Advancement of Science; all rights reserved. The title

CopyrightAmerican Association for the Advancement of Science, 1200 New York Avenue NW, Washington, DC 20005. (print ISSN 0036-8075; online ISSN 1095-9203) is published weekly, except the last week in December, by theScience

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TRANSDIFFERENTIATION

Sequential histone-modifyingactivities determine the robustnessof transdifferentiationSteven Zuryn,1 Arnaud Ahier,1 Manuela Portoso,2 Esther Redhouse White,1*Marie-Charlotte Morin,1 Raphaël Margueron,2 Sophie Jarriault1†

Natural interconversions between distinct somatic cell types have been reported inspecies as diverse as jellyfish and mice. The efficiency and reproducibility of somereprogramming events represent unexploited avenues in which to probe mechanisms thatensure robust cell conversion. We report that a conserved H3K27me3/me2 demethylase,JMJD-3.1, and the H3K4 methyltransferase Set1 complex cooperate to ensure invarianttransdifferentiation (Td) of postmitotic Caenorhabditis elegans hindgut cells into motorneurons. At single-cell resolution, robust conversion requires stepwise histone-modifyingactivities, functionally partitioned into discrete phases of Td through nuclear degradation ofJMJD-3.1 and phase-specific interactions with transcription factors that have conserved rolesin cell plasticity and terminal fate selection. Our results draw parallels between epigeneticmechanisms underlying robust Td in nature and efficient cell reprogramming in vitro.

Tissue and organ regeneration occurs inmultiple animal species and can originatefrom transdifferentiation (Td) of surround-ing cell populations (1, 2). Understandinghow individual cells interconvert efficiently

and precisely to contribute to or result in therobust regeneration of whole tissues is a majorgoal of regenerative medicine. To characterizethese mechanisms in a physiological setting, weinvestigated a traceable and predictable Td eventin Caenorhabditis elegans. The Y cell is a post-mitotic hindgut cell that constitutes the half sec-tion of the third ring of the rectal tube. This cellexhibits a remarkable behavior by which it dis-engages from the tube and changes into a motorneuron called PDA during normal development(Fig. 1A) (3). We found that conversion betweenthe two specialized cell types occurred with vir-tually invariant precision in each animal (100%,n = 2209 animals). To identify those factors thatendowed such precision, we chemically mu-tagenized worms, screened for low-penetrancemutants in which Td was no longer invariant(Td–), and isolated several mutant alleles (fp11,fp13, fp15, and fp25) (Fig. 1B and fig. S1, A andB). Using deep-sequencing–based mapping (4),we cloned and confirmed that the causal ge-netic lesions of all mutants affected jmjd-3.1(fig. S1, C and D).jmjd-3.1 encodes an ortholog of human Jmjd3,

which displays specificity for demethylating tri-and dimethylated histone H3 lysine 27 (H3K27)via a highly conserved Jumonji C terminus (JmjC)

domain (5, 6). In each jmjd-3.1mutant, the JmjCdomain is either mutated, truncated, or absent,suggesting that H3K27me3/me2 demethylase ac-tivity mediates its Td role (Fig. 1C). Generatingjmjd-3.1(fp15) strains harboring Cherry-taggedJMJD-3.1 forms, we found that nuclear JMJD-3.1acted cell-autonomously [as well as nonredun-

dantly (fig. S2)] and that disrupting its ability todemethylate lysine residues or recognize histoneH3 tails abolished its activity during Td (Fig. 1Cand figs. S3 and S4). Moreover, expressed andpurified JMJD-3.1 mutant proteins mimickingfp11, fp15, and fp25 had completely lost theircapacity to demethylate H3K27me3 (fig. S5).This correlated with the Td– phenotypes and sug-gested that each allele encoded enzymaticallynull products. Last, deficiencies in the worm Poly-comb Repressive Complex 1 component SPAT-3(Ring1B) (7), which acts to fortify gene repressionupon recruitment to trimethylatedH3K27 residues(8), partially restored Td in jmjd-3.1(fp15) mu-tants (fig. S6). These data indicated that jmjd-3.1acts antagonistically toH3K27me3-mediated tran-scriptional repression during Td by demethylatingH3K27me3.Alongside H3K27, other histone tail residues

can exist in several states of methylation, eachof which can be modulated by specific enzymes.We performedRNA interference (RNAi) screensto determine whether other histone methyltrans-ferases or demethylases, and hence other spe-cific histone modifications, performed a rolesimilar to jmjd-3.1 in ensuring precise Td (fig. S7and table S1). Only RNAi of the mammalianSET1A/SET1B ortholog, set-2, disrupted invariantTd. SET-2 is the catalytic subunit of the Set1 com-plex, a highly conserved multi-subunit ensem-ble that methylates H3K4 (9). Null deficienciesin set-2, as well as other Set1 complex subunits(wdr-5.1/WDR5, ash-2/ASH2L, rbbp-5/RbBP5,

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1Department of Development and Stem Cells, Institut deGénétique et de Biologie Moléculaire et Cellulaire, CNRSUMR 7104/INSERM U964, Université de Strasbourg, 67404Illkirch CU Strasbourg, France. 2Institut Curie, INSERM U934,CNRS UMR3215, 26, Rue d’Ulm, 75005 Paris, France.*Present address: Department of Cell and Developmental Biology,University College London, Gower Street, London WC1E 6BT, UK.†Corresponding author. E-mail: [email protected]

Fig. 1. jmjd-3.1 and the Set1 complex determine invariant Td. (A) Schematic of Y-to-PDA Td. (B) jmjd-3.1mutations cause defects in Td. (C) Schematic of the JMJD-3.1 protein. NLS, nuclear localization signal;JmjC, Jumonji catalytic domain; ZnB, zinc-binding, H3 tail recognition domain. Amino acids highlightedin gray boxes were mutated in order to disrupt either lysine demethylation (blue) or H3 tail recognition(red). (D) Effect of deficiencies in Set1 complex subunits on Td.

RESEARCH | REPORTS

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dpy-30/DPY30, and cfp-1/CFP1), resulted in alow-penetrance Td– phenotype, which again isnot attributable to hypomorphism or redundan-cy (Fig. 1D and fig. S8). Set1 deficiencies couldbe phenocopied by overexpressing several func-tionally antagonistic enzymes (H3K4me3/me2demethylases) in the Y cell in a demethylase-activity–dependent manner (fig. S9). The sameeffect was observed by overexpressing a K4 un-methylable replication-independent H3.3K4Ain Y (fig. S9). Further implicating Set1H3K4methyl-transferase activity in Td, only a catalyticallyactive set-2 transgene expressed in Y could res-cue the defect in set-2mutants (discussed below).Thus, multiple specific histone-modifying activitiesacting on distinct lysines of histone H3 mediateinvariant cell conversion in a natural setting.How do specific histone methylation states

elicit these effects? To answer this question, weinvestigated the progression of Td at the single-cell level in live mutant animals. Td– cells in Set1mutants, and in transgenic animals overexpress-ing Set1 antagonists or H3K4A in Y, could bebroken into two distinct classes: Approximatelyhalf displayed a characteristic, hindgut fried-egg–shaped nuclear morphology, whereas the restdisplayed speckled nuclear morphology (Fig. 2Aand fig. S10A). In contrast, Td– cells in jmjd-3.1mutants had exclusively speckled nuclei. Theseinitial observations hinted that specific K4 and

K27 methylation states mediated different tran-sitions through successive stages of cell conver-sion, which became blocked in the absence oftheir respective modifiers. We have previouslyshown that Y-to-PDA proceeds through discretephases: dedifferentiation and then redifferen-tiation into the new cell type (10), as observed invertebrate examples of Td, such as newt lens re-generation (1). We thus tested whether jmjd-3.1and Set1 mediated distinct Td phases. Indeed,those Td– cells with hindgut morphology in Set1mutants persistently expressed hindgut molecu-lar markers and remained attached to the rectaltube via intercellular adherens junctions (fig. S10,B and C), indicating a failure in dedifferentiation.In Td– cells with speckledmorphology in eitherjmjd-3.1 or Set1 backgrounds, hindgut markerswere correctly extinguished, and the cells dis-engaged from the rectal tube, but they did notproperly activate a range of PDA neural markers(fig. S10B), indicating a failure to properly redif-ferentiate. In addition, timely rescue of wdr-5.1and jmjd-3.1 mutant strains by heat shock–inducible rescue constructs demonstrated thatthe temporal requirements of each factor cor-related precisely with their successive cellularroles (Fig. 2B). Therefore, Set1 acts dichotomous-ly, mediating both dedifferentiation and redif-ferentiation, whereas jmjd-3.1 mediates onlyredifferentiation. This suggests that stepwise

modifications to distinct lysine residues on H3mediate precise transition through distinct cel-lular phases of Td (Fig. 2C).The model above implies a mechanism for ef-

ficient partitioning (temporally and functionally)of K4- and K27-modifying activities within a post-mitotic cell. To determine the mechanisms atplay, we first addressed how each distinct re-quirement was established. Consistent with Set1’saction at different steps of the process, func-tional, green fluorescent protein (GFP)–taggedSet1 subunits were nuclear-localized in Y/PDAthroughout Td (fig. S11A). Contrastingly, Cherry-tagged JMJD-3.1 and a jmjd-3.1 fosmid-basedGFP construct were dynamically localized duringTd (fig. S11, A to C). Both JMJD-3.1 reporters weredetectable in the nucleus at all stages during,before, and after Td, except for a precise windowwhen Y dedifferentiated. This pattern matchedjmjd-3.1’s temporal requirements and exclusiveredifferentiation role, suggesting that regulationof JMJD-3.1 levels may provide a mechanism toensure stepwiseK4andK27modification.Throughthe use of a photoconvertible JMJD-3.1::Dendra2fusion protein, as well as artificial modulation ofJMJD-3.1’s nuclear localization, we determinedthat JMJD-3.1 levels were dynamically regulatedthrough nuclear-dependent degradation duringdedifferentiation (Fig. 2, D and E, and figs. S12).Moreover, precise temporal regulation of JMJD-3.1 levels, and hence stepwise histone modifica-tion, was critical for precise Y-to-PDA conversionbecause forced ectopic JMJD-3.1 expression dur-ing Y dedifferentiation induced a Td– phenotypeand resulted in cells displaying a mixture of ab-normal identities (fig. S13). Catalytic inactivationof JMJD-3.1 largely mitigated these effects (fig.S13D). We conclude that regulation of nuclearJMJD-3.1 protein levels ensures partitioning ofK27 demethylase activity into the redifferentia-tion phase of Td and that such control is criticalfor invariant Td.We next turned our attention to the mecha-

nism (or mechanisms) that partitioned Set1’sK4 methylase activity into temporally separable,seemingly opposite cellular functions (dediffer-entiation and redifferentiation). We reasonedthat each distinct role might be segregated func-tionally through discrete temporal associationswith coregulators. Using coimmunoprecipita-tion, we found that the core Set1 componentWDR-5.1 associates with several subunits of theNanog and Oct4 Deacetylase (NODE)–like com-plex (Fig. 3A) (11). We have previously found thatthe NODE-like complex is required for Y dedif-ferentiation (12) and is composed of factors thathave conserved roles in the maintenance and in-duction of cell plasticity in a variety of species (13).Using Set1;NODE double mutants carrying cat-alytically active or inactive set-2 rescue constructs,we found that the two complexes functionallycooperated—in a Set1-H3K4 methyltransferase–dependent manner—to specifically mediate Ydedifferentiation (Fig. 3B). This suggested thatthe NODE-like complex, which can bind DNAtargets directly (11), provides dedifferentiationfunctional specificity to Set1.

SCIENCE sciencemag.org 15 AUGUST 2014 • VOL 345 ISSUE 6198 827

Fig. 2. Set1 and jmjd-3.1 mediate different Td phases. (A) Fluorescent micrographs of cell fatemarkers in Td– cells in live animals. Asterisk indicates signal from adjacent cell. (B) Timed heat shockpulses show that wdr-5.1 and jmjd-3.1 have distinct temporal requirements matching their successivecellular roles. Ø, no heat-shock. (C) Schematic showing requirements for histone-modifying activities.(D) Photoconversion of Dendra2 fused to JMJD-3.1 indicates that photoconverted protein is degradedduring dedifferentiation and resynthesized during redifferentiation. (E) Modulation of JMJD-3.1 nuclearlocalization indicates that degradation is nuclear-dependent and that removal from the nucleus is suf-ficient for eliminating its activity. **P < 0.01, *P < 0.05; n > 100 animals.

RESEARCH | REPORTS

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Next, we uncovered an alternative functionalinteraction network between WDR-5.1, JMJD-3.1,and the phylogenetically conserved COE (Collier,Olf, EBF)–type transcription factor (TF) UNC-3that appeared to specify Set1’s redifferentiationrole. UNC-3 transcriptionally regulates batteriesof genes that specify terminal features of motorneurons in C. elegans as well as chordates (14).Weshowed that UNC-3, which is required for PDAredifferentiation (10), interacts with a function-ally important N-terminal region of JMJD-3.1.JMJD-3.1 in turn associates withWDR-5.1 (Fig. 3,C and D, and fig. S14), providing a mechanisticrationale for the precise regulation of JMJD-3.1protein levels that we unraveled, one that mayserve to prevent interaction with Set1 until re-differentiation, for which both activities areneeded. Moreover, double unc-3;jmjd-3.1 andunc-3;wdr-5.1mutants suggested that these threefactors functionally cooperate specifically duringthe redifferentiation phase of Td and not duringdedifferentiation (Fig. 3E). Thus, UNC-3 appearsto act as an important regulatory hub for the re-differentiation phase of Td onto which chroma-tin modifiers may log their activities.To gain deeper insight into SET1 and JMJD-3.1’s

mode of action, we analyzed double Set1;jmjd-3.1mutant strains carrying active or inactive set-2or jmjd-3.1 transgenes, or jmjd-3.1(fp15)mutantsoverexpressing H3.3K4A (Fig. 4A). Our resultssuggested that K4 methylation and K27 demeth-ylation (i) acted inparallel, rather than in amutuallydependent manner, and (ii) ultimately convergedon a common downstream target (or targets)to specifically promote redifferentiation. Onepossibility—suggested by their physical associationas well as data presented earlier indicating thatSet1 and JMJD-3.1 cellular localizations and activ-ities intersectedpreciselyduring redifferentiation—is that both activities act in a bifunctional K4/K27–modifying complex. Such complexes have beenshown in other species (6, 15–17) and have beenpredicted to resolve bivalent domains: nucleosomescontaining both H3K4me3 and H3K27me3 signa-tures (18). Evidence suggests that such domains actto poise developmental loci for timely and efficientactivation, representing an attractive mechanismfor ensuring precise PDA redifferentiation (19).However, bivalency has only been reported thus farin vertebrates (20). Here, we demonstrate the co-occurrence of H3K4me3 andH3K27me3marks onmononucleosomes purified from worms, pointingto the existence of bivalent domains in C. elegans(fig. S15) andopening thepossibility that targets ofSet1 and JMJD-3.1 may be bivalently marked.Our results suggest a model in which Set1 and

jmjd-3.1’s role is to ensure precise Td, whereaskey TFs, which exhibit complete penetrance innull mutants (3, 10, 12), act as drivers. We foundthat histone modifications additionally are crit-ically needed when the worm is exposed to ad-verse conditions. In absence of jmjd-3.1 or Set1,Y-to-PDA Td was hypersensitive to a variety ofstressful treatments, whereas Td remained un-affected in wild-type animals (Fig. 4, B to E). Thissuggests that both Set1-dependant H3K4 meth-ylation and jmjd-3.1–dependent H3K27me3/me2

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Fig. 3. Phase-specific interactions specify Set1 and JMJD-3.1’s Td roles. (A) WDR-5.1 immuno-precipitates members of the C. elegans NODE complex, CEH-6(OCT), SOX-2(SOX2), SEM-4(SALL),and EGL-27(MTA). (B) Set1 functionally cooperates with the NODE-like complex to mediate hindgutdedifferentiation. m, mutant; wt, wild type. (C and D) JMJD-3.1 immunoprecipitates WDR-5.1 andUNC-3 via an N-terminal domain. (E) unc-3 cooperates with jmjd-3.1 and Set1 to mediate PDA re-differentiation. Red and blue P values correspond to dedifferentiation and redifferentiation, respec-tively. Error bars indicate SEM. ND, not determined; ns, not significant. Statistical significance wasdetermined by using two-way analysis of variance.

Fig. 4. jmjd-3.1 and Set1 cooperate to ensure robust Td against stress. (A) jmjd-3.1 and Set1components exhibit synergistic genetic interactions in a H3K27 demethylase and H3K4 methyl-transferase activity–dependent manner during redifferentiation. m, null mutant; wt, wild type. (B toE) Stressful environmental conditions enhance Td defects in jmjd-3.1 and Set1 null mutants. Error barsindicate SEM. ND, not determined; ns, not significant. n > 100 animals; ***P < 0.001, **P < 0.01, *P <0.05; n > 100 animals.

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demethylation provide protection against varia-tions that may be encountered in the worm’snatural environment. These roles in ensuring therobustness of cell conversion in stressful circum-stances may underlie invariant Td under normalconditions. Last, our in vivo results suggest thatSet1 and jmjd-3.1 perform highly conserved rolesacross phyla and cell types to reinforce TF-drivenchanges in identity. Indeed, modulation of H3K4and H3K27 methylation state has been shownto regulate somatic reprogramming (21–23).Specifically, the core Set1 subunit, Wdr5, was re-cently shown to interact with and potentiateOct4’s roles in the initial phases of mammalianinduced pluripotent stem (iPS) cell induction (22).Furthermore, Jmjd3 was found to specificallyinhibit the initial stages of iPS reprogramming(23), drawing a distinct parallel to its disrup-tion of the initial stages of Td we observed.

REFERENCES AND NOTES

1. C. Jopling, S. Boue, J. C. Izpisua Belmonte, Nat. Rev. Mol. CellBiol. 12, 79–89 (2011).

2. E. M. Tanaka, P. W. Reddien, Dev. Cell 21, 172–185 (2011).3. S. Jarriault, Y. Schwab, I. Greenwald, Proc. Natl. Acad. Sci. U.S.A.

105, 3790–3795 (2008).4. S. Zuryn, S. Le Gras, K. Jamet, S. Jarriault, Genetics 186,

427–430 (2010).5. K. Agger et al., Nature 449, 731–734 (2007).6. F. De Santa et al., Cell 130, 1083–1094 (2007).7. O. Karakuzu, D. P. Wang, S. Cameron, Development 136,

943–953 (2009).8. N. J. Francis, R. E. Kingston, C. L. Woodcock, Science 306,

1574–1577 (2004).9. A. Shilatifard, Annu. Rev. Biochem. 81, 65–95 (2012).10. J. P. Richard et al., Development 138, 1483–1492 (2011).11. J. Liang et al., Nat. Cell Biol. 10, 731–739 (2008).12. K. Kagias, A. Ahier, N. Fischer, S. Jarriault, Proc. Natl. Acad. Sci.

U.S.A. 109, 6596–6601 (2012).13. I. Chambers, S. R. Tomlinson, Development 136, 2311–2322

(2009).14. P. Kratsios, A. Stolfi, M. Levine, O. Hobert, Nat. Neurosci. 15,

205–214 (2012).15. I. Issaeva et al., Mol. Cell. Biol. 27, 1889–1903 (2007).16. Y. W. Cho et al., J. Biol. Chem. 282, 20395–20406 (2007).17. S. A. Miller, A. C. Huang, M. M. Miazgowicz, M. M. Brassil,

A. S. Weinmann, Genes Dev. 22, 2980–2993 (2008).18. B. E. Bernstein et al., Cell 125, 315–326 (2006).19. P. Voigt, W. W. Tee, D. Reinberg, Genes Dev. 27, 1318–1338

(2013).20. P. Voigt et al., Cell 151, 181–193 (2012).21. A. A. Mansour et al., Nature 488, 409–413 (2012).22. Y. S. Ang et al., Cell 145, 183–197 (2011).23. W. Zhao et al., Cell 152, 1037–1050 (2013).

ACKNOWLEDGMENTS

We are grateful to S. Gasser, R. Klose, M. Labouesse, B. Prud’homme,and R. Schneider for their comments on the manuscript. Workin R.M.’s laboratory is funded by a European Research Council–Stg(REPODDID) grant, an ATIP-Avenir grant, and a Fondation pourla Recherche Medicale (FRM) grant. Work in S.J.’s laboratoryis funded by grants from FRM, the Fondation ARC pour larecherche sur le cancer, the Association Française contre lesMyopathies (AFM), the Fondation Schlumberger pourl’Enseignement et la Recherche (FSER), and the EuropeanMolecular Biology Organization Young Investigator program (EMBOYIP). S.Z. is a FRM and ARC postdoctoral fellow, and S.J. is aCentre National de la Recherche Scientifique research director.

SUPPLEMENTARY MATERIALS

www.sciencemag.org/content/345/6198/826/suppl/DC1Materials and MethodsFigs. S1 to S16Table S1References (24–42)

12 May 2014; accepted 17 July 201410.1126/science.1255885

SYNTHETIC BIOLOGY

Programmable on-chip DNAcompartments as artificial cellsEyal Karzbrun,1* Alexandra M. Tayar,1* Vincent Noireaux,2 Roy H. Bar-Ziv1†

The assembly of artificial cells capable of executing synthetic DNA programs has beenan important goal for basic research and biotechnology. We assembled two-dimensionalDNA compartments fabricated in silicon as artificial cells capable of metabolism,programmable protein synthesis, and communication. Metabolism is maintained bycontinuous diffusion of nutrients and products through a thin capillary, connecting proteinsynthesis in the DNA compartment with the environment. We programmed proteinexpression cycles, autoregulated protein levels, and a signaling expression gradient,equivalent to a morphogen, in an array of interconnected compartments at the scale ofan embryo. Gene expression in the DNA compartment reveals a rich, dynamic system thatis controlled by geometry, offering a means for studying biological networks outside aliving cell.

In the past decade, cell-free gene expressionreactions have been used to design synthet-ic biological systems, including droplets formolecular evolution (1), a vesicle bioreactortoward an artificial cell (2), regulatory (3–6)

and morphogenetic-like genetic circuits (7), aswell as assembly of protein complexes (8–10).Thus far, the lack of efficient protein turnoverhas prevented the emergence of expression dy-namic patterns, such as oscillations, in a con-tinuous expression bioreactor or vesicle (2, 11).Microfluidic chips containing switching valvesand addressable fluidic chambers (12, 13) havesucceeded in implementing steady-state anddynamic protein synthesis reactions (14). How-ever, micrometer-scale positional informationencoded in diffusive concentration gradients ofproteins and mRNA, as in a morphogenetic sce-nario (15), is washed away in flow-driven expres-sion compartments. Here, we present a solid-statebiochip approach for the assembly of an artificialcell, which enables protein turnover, materialsexchange with the environment, a capacity to en-code and express genes at high surface densitywithin a controlled geometry, and the ability tomaintain micrometer-scale positional informa-tion in diffusive molecular gradients.Dense phases of end-attached, linear double-

stranded DNA templates (DNA brushes) wereassembled by chemical photolithography (16, 17)on the surface of circular compartments carvedin silicon with radius R = 50 mm and depth h = 1to 3 mm (Fig. 1, A and B, and figs. S1 to S3). TheDNA compartments were connected to a 30-mm-deep flow channel through thin capillaries ofwidthW = 20 mm and length L = 50 to 300 mm.The device was sealed, and Escherichia colicell extract (18, 19) was continuously flown inthe main channel. Reaction components weretransported by diffusion into the DNA compart-

ment because of the high resistance to flowthrough the capillary (fig. S4). Proteins weresynthesized in the DNA compartment anddiffused out to the flow channel through thecapillary. A linear protein concentration gra-dient formed along the capillary, decaying fromamaximal value in theDNA compartment,whereits distribution was homogenous, down to zero atthe channel junction (Fig. 1C). The protein lineargradient persisted throughout the duration ofexpression, which reached a steady-state concen-tration (fig. S5). The dilution through the capillaryleads to an emergent effective protein lifetime,t ¼ pR2

WD L, that is obtained by solving the diffu-sion equation in the compartment geometry,where D is the protein diffusion constant (sup-plementary materials).The effective protein lifetime enabled us to

observe gene expression dynamics, includingsteady states (Fig. 1D) and oscillations (Fig. 1E).Figure 1D shows expression of green fluorescentprotein (GFP) through a positive feedback geneconstruct, which is self-activated by the AraC pro-tein dimer in the presence of arabinose (20) (fig.S6). The kinetics was characterized by a sharponset after a 2-hour delay and reached a steady-state level for over 8 hours. To implement an os-cillatory gene expression dynamics, we used anactivator-repressor network with sigma factors28 for activation and the lambda phage cI re-pressor (fig. S6 and tables S1 to S3). The net-work exhibited emergent oscillations for manyhours with a period of ~2.5 hours (Fig. 1E). Fur-thermore, the high concentration of regulatoryproteins near the DNA brush enabled direct im-aging of transcription regulation. We imagedrepression of transcription by using a negative-feedback construct that codes for a fusion of aCro repressor dimer and GFP, expressed undera Cro-regulated promoter (fig. S6). The synthe-sized fusion protein bound the repressor site ad-jacent to the promoter, thereby localized theGFP signal to the DNA brush (Fig. 1F) and ledto a reduced self-regulated expression levels insteady state.

SCIENCE sciencemag.org 15 AUGUST 2014 • VOL 345 ISSUE 6198 829

1Department of Materials and Interfaces, Weizmann Instituteof Science, Rehovot 76100, Israel. 2Department of Physics,University of Minnesota, Minneapolis, MN 55455, USA.*These authors contributed equally to this work. †Correspondingauthor. E-mail: [email protected]

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