Cel transitions(Honjo et aL., 2005). Somatic hypermutation is ation and are responsive to the external environment. largely(though not entirely) confined to the regions of an- Specifically, subtelomeric genes are highly genetically ibodies that recognize antigens. Hence, somatic hyper- ariable in yeast, presumably because when silenced mutation is regulated both in locus(the antibody gene) they are largely invisible to selection, while a similar argu- and in time(during an infection to which the antibody is re- ment may be made for highly variable 3 untranslated re- sponding). The mechanism increases the diversity of anti- gions that are not translated in the epigenetic [psi-]prion bodies on th e framework of a previously suc- state of yeast. The subtelomeric silencing complex(de- owing the cell to locally explore cribed above)is inactivated by stress(via phosphoryla sequence space in search of improved antigen-binding tion of Sir 3), possibly allowing environmentally regulated affinity. Although the biochemical mechanism for somatic uncovering of the subtelomeric genetic variation in a pop hypermutation appears to restrict the mutagenesis to ulation (Ai et aL, 2002). Similarly, the protein chaperone transcribed sequences, it is otherwise unclear how this Hsp104 modulates the propagation of the [PSI+ prion ctivity is targeted. Somatic hypermutation the clearest example of a physiological role for the envi- hat the [PSI+ phenotype is suppressed, presumably ronmental regulation of local phenotypic variation, due to increased Hsp104 activity that releases functional though in this case the induced variation is only heritable Sup35 from prion aggregates(Eaglestone et al., 1999) in cell lineages within the organism and does not cross Here again, stress-induced change in an epigenetic phe- organismal generations notype provides a mechanism by which the environment A second system in mammals increases mutation rates may influence the uncovering of hidden genetic variation over parasitic DNAelements such as transposons(Garrick (in 3 UTRs), although in this case the seemingly paradoxi- et aL., 1998). In addition to silencing these parasites, meth- cal observation is that stress transiently decreases the ylation of cytosine residues leads to accumulation of mu- readthrough phenotype of [PSi+] yeast. Both of these tations in the relevant sequence because the deamination mechanisms thus provide regulatable bridges betwee of methylcytosine (resulting, after replication, in aC- T epigenetic variation and genetic variation, which alloy transition)occurs an order of magnitude more rapidly certain types of genetic variation to be uncovered in re- than does the deamination of unmodified cytosine (2 x sponse to environmental regulation of epigenetic switches 10 per bp per generation as opposed to 2x 10 per Regulated subtelomeric silencing and prion folding thus bp per generation for unmethylated cytosine: Garrick can be considered part of the hide-and-release class of et al., 1998). Similar mechanisms have been intensively mechanisms that allow hidden genetic variation to accu- studied in the fungal kingdom. In Neurospora crassa, for mulate without phenotypic effect. Each of the hide-and- example, repetitive DNa is inactivated by a DNA methyla- release mechanisms hides a particular type of genetic mu- tion-dependent process known as repeat-induced point tation in signaling genes(Hsp90 clients), in subtelomeric mutation(RIP; Selker et al., 2003). It is therefore conceiv- genes, or in 3 UTRs, which results in regulatable release able that directed methylation could provide organisms of localized variation. However, this releasable variation with another means to locally increase mutation rates at is expected to be largely random(except for its location) selected loci in response to their environmen We now finally turn to the idea that organisms may orches- Localized Uncovering of Hidden Variation selves in response to appropriate conditions Similar to directed mutagenesis, the hide-and-release or buffering mechanisms described above provide examples Environmentally"Directed"Heritable Phenotypes? where variation at only a subset of genomic loci may We have outlined a number of mechanisms by which or respond to specific environmental conditions. Stress- ganisms modulate the timescale over which a phenotype induced decrease in Hsp90 function uncovers previously is stable and mechanisms by which organisms increase silent mutations in Hsp90 client proteins, which tend to seemingly random phenotypic diversity in response to be signaling molecules(Queitsch et aL, 2002; Rutherford stressful environments. Beyond this, organisms may not and Lindquist, 1998). Although it remains unclear whether only randomly increase heritable variation in response to Hsp9o represents atrue robustness factor or a mechanism stress but in fact may inherit environmentally directed for the hide-and-release of phenotypic variability, the re- phenotypes in some cases, with the inherited phenotype sponsiveness of Hsp 90 to environmental conditions al- being determined by the environment. The"inheritance lows organisms to uncover locus-specific phenotypic of acquired phenotypes"is, of course, generally de- variation at stressful times. In other words, the fact that scribed as Lamarck's theory of evolution. In fact, Darwin Hsp90 only interacts with a subset of proteins means also believed that the parental environment influenced that when Hsp90 levels vary due to environmental influ- progeny and incorporated some of Lamarck's basic ideas ences, only a specific set of phenotypes will increase their in his theory. However, the inheritance of acquired pheno- variance in the population types was discredited by August Weismann (Weismann, In addition, many mechanisms of epigenetic inheritance 1893)and all but disappeared from the New Synthesis described above not only make certain phenotypes more the modern theory of evolution that gradually developed variable but also influence selected types of genetic vari- during the first part of the 20 hn century and that has 664 Cell 128, 655-668, February 23, 2007 @2007 Elsevier Indtransitions (Honjo et al., 2005). Somatic hypermutation is largely (though not entirely) confined to the regions of an￾tibodies that recognize antigens. Hence, somatic hyper￾mutation is regulated both in locus (the antibody gene) and in time (during an infection to which the antibody is re￾sponding). The mechanism increases the diversity of anti￾bodies on the sequence framework of a previously suc￾cessful antibody, thus allowing the cell to locally explore sequence space in search of improved antigen-binding affinity. Although the biochemical mechanism for somatic hypermutation appears to restrict the mutagenesis to transcribed sequences, it is otherwise unclear how this activity is targeted. Somatic hypermutation is perhaps the clearest example of a physiological role for the envi￾ronmental regulation of local phenotypic variation, al￾though in this case the induced variation is only heritable in cell lineages within the organism and does not cross organismal generations. A second system in mammals increases mutation rates over parasitic DNA elements such as transposons (Garrick et al., 1998). In addition to silencing these parasites, meth￾ylation of cytosine residues leads to accumulation of mu￾tations in the relevant sequence because the deamination of methylcytosine (resulting, after replication, in a C / T transition) occurs an order of magnitude more rapidly than does the deamination of unmodified cytosine (2 3 107 per bp per generation as opposed to 2 3 108 per bp per generation for unmethylated cytosine; Garrick et al., 1998). Similar mechanisms have been intensively studied in the fungal kingdom. In Neurospora crassa, for example, repetitive DNA is inactivated by a DNA methyla￾tion-dependent process known as repeat-induced point mutation (RIP; Selker et al., 2003). It is therefore conceiv￾able that directed methylation could provide organisms with another means to locally increase mutation rates at selected loci in response to their environment. Localized Uncovering of Hidden Variation Similar to directed mutagenesis, the hide-and-release or buffering mechanisms described above provide examples where variation at only a subset of genomic loci may respond to specific environmental conditions. Stress￾induced decrease in Hsp90 function uncovers previously silent mutations in Hsp90 client proteins, which tend to be signaling molecules (Queitsch et al., 2002; Rutherford and Lindquist, 1998). Although it remains unclear whether Hsp90 represents a true robustness factor or a mechanism for the hide-and-release of phenotypic variability, the re￾sponsiveness of Hsp90 to environmental conditions al￾lows organisms to uncover locus-specific phenotypic variation at stressful times. In other words, the fact that Hsp90 only interacts with a subset of proteins means that when Hsp90 levels vary due to environmental influ￾ences, only a specific set of phenotypes will increase their variance in the population. In addition, many mechanisms of epigenetic inheritance described above not only make certain phenotypes more variable but also influence selected types of genetic vari￾ation and are responsive to the external environment. Specifically, subtelomeric genes are highly genetically variable in yeast, presumably because when silenced they are largely invisible to selection, while a similar argu￾ment may be made for highly variable 30 untranslated re￾gions that are not translated in the epigenetic [psi] prion state of yeast. The subtelomeric silencing complex (de￾scribed above) is inactivated by stress (via phosphoryla￾tion of Sir3), possibly allowing environmentally regulated uncovering of the subtelomeric genetic variation in a pop￾ulation (Ai et al., 2002). Similarly, the protein chaperone Hsp104 modulates the propagation of the [PSI+] prion state, and during heat and chemical stress it is observed that the [PSI+] phenotype is suppressed, presumably due to increased Hsp104 activity that releases functional Sup35 from prion aggregates (Eaglestone et al., 1999). Here again, stress-induced change in an epigenetic phe￾notype provides a mechanism by which the environment may influence the uncovering of hidden genetic variation (in 30 UTRs), although in this case the seemingly paradoxi￾cal observation is that stress transiently decreases the readthrough phenotype of [PSI+] yeast. Both of these mechanisms thus provide regulatable bridges between epigenetic variation and genetic variation, which allows certain types of genetic variation to be uncovered in re￾sponse to environmental regulation of epigenetic switches. Regulated subtelomeric silencing and prion folding thus can be considered part of the hide-and-release class of mechanisms that allow hidden genetic variation to accu￾mulate without phenotypic effect. Each of the hide-and￾release mechanisms hides a particular type of genetic mu￾tation in signaling genes (Hsp90 clients), in subtelomeric genes, or in 30 UTRs, which results in regulatable release of localized variation. However, this releasable variation is expected to be largely random (except for its location). We now finally turn to the idea that organisms may orches￾trate specific, nonrandom heritable changes in them￾selves in response to appropriate conditions. Environmentally ‘‘Directed’’ Heritable Phenotypes? We have outlined a number of mechanisms by which or￾ganisms modulate the timescale over which a phenotype is stable and mechanisms by which organisms increase seemingly random phenotypic diversity in response to stressful environments. Beyond this, organisms may not only randomly increase heritable variation in response to stress but in fact may inherit environmentally directed phenotypes in some cases, with the inherited phenotype being determined by the environment. The ‘‘inheritance of acquired phenotypes’’ is, of course, generally de￾scribed as Lamarck’s theory of evolution. In fact, Darwin also believed that the parental environment influenced progeny and incorporated some of Lamarck’s basic ideas in his theory. However, the inheritance of acquired pheno￾types was discredited by August Weismann (Weismann, 1893) and all but disappeared from the ‘‘New Synthesis,’’ the modern theory of evolution that gradually developed during the first part of the 20th century and that has 664 Cell 128, 655–668, February 23, 2007 ª2007 Elsevier Inc.