OPINION OPINION : Core misconcept

Mark Ptashne1 cific , and encourage (activate) or dis- Ludwig Professor of Molecular , Memorial Sloan–Kettering Center, New courage (repress) into mRNA York, NY 10021 of those genes (2–4). The process is started by transcrip- tion factors, contributed mainly by the A recent issue of PNAS opened with an 50 years a compelling answer has emerged mother, found in the fertilized egg. In the unfortunate Core Concepts article titled from studies in a wide array of organisms. first division these transcription fac- “Epigenetics” (1). The author, a science Curiously, the article ignores this body of tors are distributed asymmetrically to the writer, began promisingly enough: knowledge, and substitutes for it misguided daughter cells. Then, and in subsequent musings presented as facts. cell generations, new patterns of ex- Despite the fact that every cell in a human body Let me begin with a very brief overview pression arise in two ways: as a matter of contains the same genetic material, not every cell of what drives , a process that course (some transcription factors activat- looks or behaves the same….How does each cell retain its unique properties when, in its DNA- unfolds with essentially no changes in DNA ing expression of genes encoding other containing nucleus, it has the same master set of sequence. Development of an organism regulatory , etc.), and in response genes as every other cell? from a fertilized egg is driven primarily by to signals sent by other cells. Signaling used the actions of regulatory proteins called in development affects expression of genes Indeed understanding this problem has transcription factors. In sequential waves encoding yet more transcription factors—it been an overarching goal of research in mo- and combinations, these proteins bind does so by changing activities of transcrip- lecular, developmental, and, increasingly, to specific DNA sequences—called cis- tion factors, already present, which target . And over the past regulatory sequences—associated with spe- those genes (2). Retinoic acid (a small mol- ecule) and growth hormone (a ) are examples of such signaling molecules. The determinative power of transcription factors is illustrated by a 2012 Nobel Prize– winning experiment: Forced expression of four specific DNA binding regulatory pro- teins can “reprogram” fibroblasts to stem cells (5). Many cell- experi- ments have been done in recent years, all of which reflect the action of ectopically expressed transcription factors (6). Patterns of underlying development can be very complex indeed. But the underlying mechanism by which, for example, a transcription acti- vates transcription of a gene is well under- stood: only simple binding interactions are required. These binding interactions posi- tion the regulator near the gene to be regu- lated, and in a second binding reaction, the relevant enzymes, etc., are brought to the gene. The process is called recruitment (3, 4). Two aspects are especially important in the current context: specificity and .

Specificity. Transcription regulators work specifically—activating one gene or set of Fig. 1. Establishment and maintenance of a positive feedback loop in a bacterium. Represented here genes and not another, for example—as de- are a few of the ca 50 phage genes of the bacteriophage lambda. The initial rightwards transcript ex- tends through gene cII. The CII protein, a transcription activator, then activates a leftwards transcript fined by the location(s) of their affined cis- that includes the gene cI. The cI protein, another transcription activator, activates expression of its own regulatory sequences. Thus, for many regu- gene (a positive feedback reaction) as it represses rightwards transcription, including that of cII. This lators and genes, any regulator will work on feedback loop, once established, is stable for very many cell divisions as the continuously produced CI protein (called the lambda ) is distributed to daughter cells. The bacteria are “lysogenic:” exposure to a signal (e.g., UV light) inactivates the repressor, previously silent phage genes are Author contributions: M.P. wrote the paper. expressed, and the cell lyses with the production of many new phage particles. PRE, PRM, and PR des- ignate the “establishment,” “maintenance,” and “rightwards” promoters, respectively. (Reproduced The author declares no conflict of interest. with permission from refs. 3 and 4.) 1E-mail: [email protected].

www.pnas.org/cgi/doi/10.1073/pnas.1305399110 PNAS | April 30, 2013 | vol. 110 | no. 18 | 7101–7103 Downloaded by guest on September 24, 2021 any gene as determined by the locations of its affined cis-. Evolu- tion can thus bring any gene under control of any regulator by apposing the proper cis- regulatory site with the gene. A recruiter (e.g., a transcription activator) is in effect a specificity determinant. In the absence of such a specificity determinant, the relevant enzymes work as background functions, that is, at low levels across the .

Memory (or Lack Thereof). Genes do not automatically stay “on” or “off” once acti- vated or repressed. Rather, those states of gene expression require the continual ac- tivities of the specific regulators to maintain that state of expression. Put another way, continual recruitment of the relevant en- zymes is required to maintain the imposed state of gene regulation (7, 8). Nevertheless, Fig. 2. Establishment and maintenance of expression of terminal differentiation genes required to de- memory effects are important for develop- fine a specific type of sensory in a nematode. A series of gene regulatory events (not shown) produces, transiently, an activator depicted as a blue ball. That activator binds to the establishment ment, and the question will arise as to how cis-regulatory sequence (blue cube), and activates transcription of a terminal selector gene. The lat- they are achieved. ter, another transcription activator, then maintains transcription of its own gene as it activates genes required for specific functions of the neuron. (Reprinted from ref. 16, Copyright 2011, with permission from Elsevier.) The Core Concepts Misconception Curiously, the picture I have just sketched or as , which turn over rapidly the endogenous genes encoding those tran- is absent from the Core Concepts article. compared with the duration of a , scription factors. The differentiated func- Rather, it is said, chemical modifications to are replaced (15). For example, it is simply tions of a nematode sensory neuron are DNA (e.g., ) and to — not true that once put in place such modifi- activated and maintained in that way (16) the components of nucleosomes around cations can, as stated in the Core Concepts (Fig. 2), and positive feedback loops are which DNA is wrapped in higher organ- article, “lock down forever” expression of a found widely in other developmental gene isms—drive gene regulation. This obviously gene (7). regulatory networks as well (17, 18). cannot be true because the enzymes that It is true, however, that during the course There are mechanisms for self-perpetuat- impose such modifications lack the essential of development as well as at its final stages, ing effects other than the one I described. specificity: All nucleosomes, for example, certain genes, once “turned on” by a tran- For example, immunity to a virus evoked in “look alike,” and so these enzymes would siently acting , stay on a nematode by with a virus can be have no way, on their own, of specifying even in the absence of the original activa- transmitted to subsequent generations. The which genes to regulate under any given set tor that triggered expression. But I noted mechanism turns out to be the transmission of conditions. I ignore DNA methylation in above that activation of transcription of small bits of RNA carried in the sperm. the remainder of this article because its pos- quickly decays once the activator is re- In worms these RNA molecules are auto- sible role in development remains unclear, moved or inhibited. And so whence this matically amplified by an enzymatic func- and it does not exist in, for example, flies critical memory effect? tion not present in humans, and are readily and worms—model organisms the study of passed along as the worms mate (19). RNA which has taught us much of what we know Positive Feedback molecules share with specific DNA bind- about development. The answer—where we know it—is positive ing proteins a critical aspect lacking from modifications are called “epigen- feedback, a process understood for years histone modifying enzymes: They bear etic” in the Core Concepts article, a word for bacterial regulatory systems (4). Thus, a specificities in their base sequences, and so that for years has implied memory (see transcriptional activator will maintain (self- whatever effect they have (repressive in this Epigenetic). This is odd: It is true that some perpetuate) transcription of its own gene if case) can be directed to specific targets. In of these modifications are involved in the a copy of its affined cis-regulatory sequence other words, RNA molecules, like regula- process of transcription per se—facilitating is placed in front of its own gene (Fig. 1). tory proteins, can act specifically (20). For removal and replacement of nucleosomes Any other specified activator, working only an example in which a transient inflamma- as the gene is transcribed, for example (9, transiently, can trigger the feedback loop, tory stimulus activates a chronic inflam- 10). And some are needed for certain forms provided the cis-regulatory sequence rec- matory loop involving transcription fac- of repression (11). But all attempts to show ognized by that other activator is properly tors and small (called micro-RNAs) that such modifications are “copied along positioned. There are increasingly many see ref. 21. with the DNA,” as the article states, have, to illustrations of such systems at work in my knowledge, failed (12–14). Just as tran- biological systems. For example, positive Epigenetic scription per se is not “remembered” with- feedback loops facilitate the reprogram- And finally to that dreaded word “epigen- out continual recruitment, so ming of fibroblasts to stem cells referred etic.” For as long as I can remember, the modifications decay as enzymes remove to above. In that case, transient expression word has been used to imply memory: A them (the way phosphatases remove phos- of the added transcription factors triggers transient signal or event triggers a response phates put in place on proteins by kinases), feedback loops that maintain expression of that is then perpetuated in the absence of

7102 | www.pnas.org/cgi/doi/10.1073/pnas.1305399110 Ptashne Downloaded by guest on September 24, 2021 the original signal. I have mentioned im- regulatory changes (i.e., self-perpetuating tone modifications “epigenetic,” moreover, portant examples of such epigenetic effects, changes); and in the older Waddington obscures what we know. The Core Con- and the figures explain two examples in sense we could refer to all developmental cepts article discussed here (1) is a good more detail. The bizarre situation we find gene regulation (including signaling) as example, further muddying the waters. The ourselves in is that, as in the Core Concepts “epigenetic.” But in neither case is it correct important point is to attend to how things article, histone modifications are often to refer to nucleosome modifiers as “epi- actually work. called “epigenetic.” One can only wonder genetic”—they, like the very many proteins why (22, 23). As mentioned above, the en- recruited to genes by specific transcription zymes that impose such modifications lack regulators, are parts of a response, not a ACKNOWLEDGMENTS. I thank Bob Kingston, Thoru Peder- son, Eric Davidson, Gene Bryant, Oliver Hobert, Kevin Struhl, requisite specificity; the modified states cause, and there is no convincing evidence Ann Hochschild, Lucy Gordon, Alex Gann, and Xin Wang for are not self-perpetuating; and the roles they are self-perpetuating. Labeling his- helpful comments. played by the modifications remain for

the most part obscure (10, 24). As point- 1 Williams SCP (2013) Epigenetics. Proc Natl Acad Sci USA 15 Deal RB, Henikoff JG, Henikoff S (2010) Genome-wide ed out by others (25–27), the ENCODE 110(9):3209. kinetics of nucleosome turnover determined by metabolic project got itself into problems by assum- 2 Davidson EH (2006) The Regulatory Genome: Gene Regula- labeling of histones. Science 328(5982):1161–1164. ing that every espied event or modification tory Networks in Development and (Academic, 16 Hobert O (2011) Maintaining a memory by transcriptional is functional without subjecting that sur- Burlington, MA). autoregulation. Curr Biol 21(4):R146–147. mise to further testing. In our case, only by 3 Ptashne M, Gann A (2002) Genes and Signals (Cold Spring 17 Peter IS, Davidson EH (2013) Transcriptional network logic: studying the effects of removing recruiters Harbor Lab Press, Cold Spring Harbor, NY). The of development. Handbook of Systems can one tell whether histone modifications 4 Ptashne M (2004) A Genetic Switch (Third Edition): Phage Biology: Concepts and Insights (Academic, San Diego), pp are self-perpetuating, or whether (as is evi- Lambda Revisited (Cold Spring Harbor Lab Press, Cold Spring 211–228. Harbor, NY). 18 Holmberg J, Perlmann T (2012) Maintaining differentiated dently the case) their continuing presence 5 Takahashi K, Yamanaka S (2006) Induction of pluripotent cellular identity. Nat Rev Genet 13:429–439. requires maintenance. stem cells from mouse embryonic and adult fibroblast cultures 19 Rechavi O, Minevich G, Hobert O (2011) Transgenerational Scholars can be excused for taking the by defined factors. Cell 126(4):663–676. inheritance of an acquired small RNA-based antiviral response word “epigenetic” to have a broader mean- 6 Graf T, Enver T (2009) Forcing cells to change lineages. in C. elegans. Cell 147(6):1248–1256. ing than the one I have so far described. 462(7273):587–594. 20 Moazed D (2009) Small RNAs in transcriptional gene silenc- For example, in 1952 the developmental 7 Cheng TH, Gartenberg MR (2000) is ing and genome defense. Nature 457(7228):413–420. C. H. Waddington used the term a dynamic structure that requires silencers continuously. Genes 21 Iliopoulos D, Hirsch HA, Struhl K (2009) An epigenetic to refer in general to what we now know Dev 14(4):452–463. switch involving NF-kappaB, Lin28, Let-7 MicroRNA, and IL6 to be changing patterns of gene expression 8 Ho SN, Biggar SR, Spencer DM, Schreiber SL, Crabtree GR links inflammation to cell transformation. Cell 139(4):693–706. that underlie development and that are (1996) Dimeric Ligands define a role for transcriptional activa- 22 Ptashne M (2007) On the use of the word ‘epigenetic’. Curr tion domains in reinitiation. Nature 382(6594):822–826. Biol 17(7):R233–R236. often triggered by signals sent from other 9 Smolle M, Workman JL, Venkatesh S (2013) reSETing chro- 23 Ptashne M (2013) Faddish stuff: epigenetics and the inheri- cells. Expanding on the subtitle of his book, matin during transcription elongation. Epigenetics 8(1):10–15. tance of acquired characteristics. FASEB J 27(1):1–2. Epigenetics: The science concerned with 10 Henikoff S, Shilatifard A (2011) Histone modification: cause 24 Rando OJ (2012) Combinatorial complexity in the causal analysis of development, Wad- or cog? Trends Genet 27(10):389–396. structure and : revisiting the . Curr Opin dington, while mentioning memory (self- 11 Grunstein, M (1990) Histone function in transcription. Annu Genet Dev 22(2):148–155. perpetuating) effects as important, was Rev Cell Biol 6:643–678. 25 Graur D, et al. (2013) On the of television sets: largely trying to describe the effects of one 12 Katan-Khaykovich Y, Struhl K (2002) Dynamics of global “function” in the according to the evolution- part of the (the Spemann organizer, histone and deacetylation in vivo: rapid restoration free gospel of ENCODE. Genome Biol Evol, in press. for example) on another. An overarching of normal histone acetylation status upon removal of activators 26 Eddy SR (2013) The ENCODE project: missteps overshadow- theme was to distinguish epigenetic devel- and . Genes Dev 16(6):743–752. ing a success. Curr Biol, in press. 13 Radman-Livaja M, Liu CL, Friedman N, Schreiber SL, Rando 27 Doolittle WF (2013) Is junk DNA bunk? A critique of EN- opment from the alternative Russian doll OJ (2010) Replication and active demethylation represent CODE. Proc Natl Acad Sci USA, 10.1073/pnas.1221376110. model, wherein fully formed adults were partially overlapping mechanisms for erasure of in 28 Waddington CH (1952) The Epigenetics of Birds (Cambridge present in fertilized eggs and merely had to budding yeast. PLoS Genet 6(2):e1000837. University Press, Cambridge, UK). be revealed (28). 14 Ringrose L, Paro R (2007) Polycomb/Trithorax response And so, in the modern parlance we have elements and epigenetic memory of cell identity. Development epigenetic changes as a subset of gene 134(2):223–232.

Ptashne PNAS | April 30, 2013 | vol. 110 | no. 18 | 7103 Downloaded by guest on September 24, 2021