THE STATES OF A GENE LOCUS IN MAIZE Barbara McClintock The locus of a gene whose action is governed by a known system of controlling elements may undergo a change that alters the pattern of ex- pression of the gene in mature tis- sues. The change arises as a single event and thus resembles a mutation. Because the effect is on the gene- control mechanism, the alteration is not termed a mutation but rather a change in “state” of the locus. The states reflect the presence of a mech- anism that is able to modify gene ex- pression during development. The nature of the states and their signifi- cance will be discussed in this report. The distinctiveness of the various states of a gene locus may be illus- trated by selected examples. For this purpose, some of the states of a."° and a,™? will be considered. These symbols were assigned to designate the effects on the Ai (Anthocyanin) locus in maize of two independent in- ceptions of control of the action of its gene by the Spm (Suppressor-muta- tor) system. This action is required for production of anthocyanin pig- ment in both plant and kernel. The states of a.%? differ from those of a, in their modes of regulating gene action. Some aspects of the difference were mentioned in previous Year Books, but its breadth was not em- phasized because knowledge of some of the states of a."? was insufficient for characterization. Recent investi- gations have made it possible to com- pare a number of states of a:”° with those of a,* previously studied. The comparisons demonstrate the manner in which a single control system pro- vides diversity of regulation of gene expression. Although distinctions among states are made apparent in the phenotypes of both plant and ker- nel, only those manifested in the ker- nel will be considered here, as they can be readily illustrated. The States of a.™* The states of a,"" were derived through modifications of the original state that arose when the first in- stance of inception of control of Ay gene action by the Spm system oc- curred in my stocks. Each state was recognized initially by the appearance of an altered type or distribution of anthocyanin pigment in the progeny of a plant carrying the original state, and most often in a single individual] of the progeny. Investigation of the cause of the changed phenotypes was begun with such individuals and con- tinued. with their progeny. The studies indicated that each change was initiated at the A, locus by the element of the control system residing there, and that it represented one type of this element’s response to the Spm element, located elsewhere in the chromosome complement. In the presence of a fully active Spm ele- ment, the states of a,”* are distin- guished from one another by differ- ences in the time of “turning on” of A, gene action during development of a tissue, by the frequency of occur- rence of such action in the cells of a tissue, and by the pigment intensity in those cells in which it is produced. They are also distinguished by the intensity of pigment produced in the GENETICS RESEARCH UNIT absence of an active Spm element. One state produces no pigment when Spm is inactive. Each of the other states does produce pigment, which is uniformly distributed over the aleurone layer of the kernel. The pigment is intense with one state but pale to faint with the others. There is no direct relation between the expres- sion given in the presence of a fully active Spm element and that given in its absence. It should also be men- tioned that when two states are com- bined as alleles in a plant or kernel, gene action is regulated independ- ently by each, and when an active Spm element is present, the pattern of anthocyanin distribution and in- tensity produced by one allele over- laps that produced by the other. Ilus- trations of the phenotypes of kernels produced by the different states of a,"™1, both in the presence and in the absence of a fully active Spm ele- ment, and the overlapping patterns produced by combinations of states as alleles, appear in the Brookhaven Symposia in Biology, Number 18. Analysis of the states of a,”1 was not complicated. Simple rules could be formulated that allowed prediction of the phenotype each state would produce in response to changes in ac- tivity of the components of Spm. These components—component-1, the suppressor, and component-2, the mutator—were considered in Year Book 64. The distinctions among states relate to the gene-associated element of the system, which resides at the A, locus. How this element operates at the level of the gene and within the nucleus to accomplish such diverse modes of regulation of gene action is not yet known. It is im- portant to recognize, nevertheless, that the gene-associated element of a two-element control system does pro- vide a means for directing a broad range of types and patterns of gene expression during development. 665 The States of a”? Some of the states of a,"? are so multifaceted in expression that an understanding of them requires forms of analysis not demanded by any of the states of a,". The infor- mation obtained from the analyses has provided additional evidence of the way in which gene action may be regulated differentially by a single system of controlling elements. The. states of a,"? may be divided into two major classes: those having an Spm element at or close to the A, gene locus, and those that show no evidence of the presence of Spm at the locus but respond to that element in a distinctive manner when it is located elsewhere in the chromosome complement. The original state, from which most of the other states were derived, belongs in the first class. An Spm element is present, either within or just distal to the locus of the struc- tural gene(s). The original state of a,™?. The phenotype produced by the original state of a,”-? depends altogether on the phase of activity of each of the components of Spm. If component-1 is inactive, no pigment is produced in the plant or in the aleurone layer of the kernel. When this component is active, the gene is activated and pig- ment is produced. The type and dis- tribution of the pigment depend on the activity of component-2. If this component is inactive, the aleurone layer is lightly pigmented. If com- ponent-2 acts only late in the develop- ment of a kernel, then smail, deeply pigmented spots appear in a lightly pigmented background. If it is active at all stages of development, both Jarge and small deeply pigmented spots appear in the lighter back- ground. The kernels shown in Plate 1(A)illustrate responses of the initial state of a.-? to these different phases of activity of the components of Spm. 666 The phenotype produced by this state does not depend solely on the action of the Spm element that is situated at or close to the locus. If either com- ponent of that element is inactive, a fully active Spm element located else- where in the chromosome complement will induce the same types of re- sponse. The responses of the original state of a”? to phases of activity of com- ponent-1 of Spm, the suppressor or inhibitor component, are the reverse of those given by most of the states of a,”?. Responses to component-2, the mutator component, are alike. The term “mutator” is applied to this component because it induces re- sponses that modify the organization of the locus and thus the expression of the gene. One such modification is responsible for the origin of the different states that are under dis- cussion in this report. Some states are produced that respond to com- ponent-1 of Spm but not to com- ponent-2. Others show no evidence of a response to component-1 but do respond to component-2. Still others, which respond to neither component, are termed “stable states,” and each of them gives rise to a distinctive phenotype in both plant and kernel. Only a few of the stable states de- rived from the original state of a:”° resemble that of the A: locus before control of its gene action was taken over by the Spm system. They pro- duce deep anthocyanin pigmentation in both plant and kernel, and in the kernel the pigment is uniformly dis- tributed over the aleurone layer. Most of the stable states give rise to a dis- tinctive pattern of pigment distribu- tion and intensity in plant and kernel. In the kernels, clusters of cells with more intense pigment than the sur- rounding cells are distributed over the aleurone layer. The intensity of the background pigmentation ranges from faint with some states to deep CARNEGIE INSTITUTION with others. Three kernels with inter- mediate but differing levels of back- ground pigmentation are shown in Plate 1(B), (C), and (D). Each of the stable states is inherited in the same manner as any stable mutant allele of the gene. Intralocus cross- over studies have shown that the phenotype each produces relates to a component residing at a particular site within the locus. New states, either responding or not responding to Spm, arise only from those states that react to com- ponent-2 of Spm. The event respon- sible for an altered state must occur in a cell of the germ line and the modified state must be included in a gamete. A zygote produced by the functioning of this gamete will give rise to a plant having the new state. The behavior of the state may then be analyzed in this plant and its progeny. With some states of both a? and ai”?, responses to com- ponent-2 of Spm occur only very late in development of a tissue. None may occur in the germ-line cells. Thus these states remain unaltered through successive plant generations even in the presence of an Spm element with an early-acting component-2. All states are inherited unaltered if com- ponent-2 is inactive or if its action is effective only very late in develop- ment. The derived states of a?. The phenotypes produced by four modi- fied states of a,"? appear in Plate 1(E). A fully active Spm element, placed at or close to the A; gene locus, is present in each kernel. No visible evidence of a response to com- ponent-1 of Spm is shown by any of these states. The dark background pigmentation in kernels like the one on the left, and the colorless back- grounds of kernels carrying the other three states, are the same regardless of the phase of activity of compo- nent-1 in the kernel. In the kernel on GENETICS RESEARCH UNIT the left the small deeply pigmented spots represent one response of the state present in the kernel to com- ponent-2. The size of such spots is al- ways small. Another response to com- ponent-2 occurs early enough for the modified locus to be included in a number of gametes produced by a plant carrying this state. The modi- fications give rise to stable states that no longer respond to compo- nent-2. In the kernel, the aleurone layer is uniformly pigmented, and the intensity of color is the same as , the background pigmentation pro- duced by the parent state (the dark kernel in the photograph). The second kernel from the left illustrates one of the.responses of the state present in that kernel to com- ponent-2. The response produces pig- mented areas, within which the pig- ment distribution is similar to that in the kernels shown in (B), (C), and (D). A second type of response is not visibly registered in the kernel but is made apparent by the stable derivatives this state produces. Some of them give rise to phenotypes re- sembling those in (B), (C), and (D). Others, however, produce no pigment in the aleurone layer of the kernel. The state of a,”? present in the second kernel from the right is dis- tinguished by the range of phenotypic expressions brought about by its re- sponses to component-2. Areas in the aleurone layer exhibit phenotypes similar to those produced by several other states. One such area is visible in this kernel; it has many deeply pigmented spots in a pale-pigmented background. Other kernels carrying this state may have sharply defined areas containing a number of deeply pigmented spots in a colorless rather than a pale background. All the spots may be small, or some may be large and some small. The kernel on the right in Plate 1(E) has only very pale spots in a 667 colorless background. Some of the stable derivatives of this state give rise to kernels whose aleurone layer is uniformly pale-pigmented, but most of them produce colorless kernels. Five additional states, each derived from the initial state, have been ex- amined. None of them gives evidence of the presence of an Spm element at the locus of the A, gene. Each re- sponds in a distinctive manner, how- ever, to an active Spm _ element located elsewhere. The phenotypes produced by two of these states in the presence of a fully active Spm are shown in Plate 1(F). The two left-hand kernels have one state. Their deeply pigmented spots are distinguished from those in most of the other kernels illustrated by a near absence of diffusion rims. Usually, when deeply pigmented spots or areas are formed, a product that diffuses from the pigment-producing cells into the surrounding cells, and often through several rows of cells, allows pigment to be formed there even though the A, gene is not functioning in these cells. The common expression given by the other state shown in Plate 1(F) is seen in the second kernel from the right. Small deeply pigmented spots appear in a colorless background. This state gives rise frequently to a new state, characterized by a marked increase in the number of pigmented spots, as in the adjacent kernel on the right. The remaining three states have been examined in greater detail than most of the others, as they provide information about the operation of the Spm system that could not be deduced readily from the behavior of other states. Two of them, although independently isolated, are so much alike that they may be considered jointly. These states (7977B and 7995) furnished the initial evidence of the “presetting” and “erasure” 668 mechanism that was outlined and illustrated in Year Book 63 (pp. 592- 602) and further commented on in Year Book 64 (pp. 527-536). This aspect of their behavior will not be restated here. Another aspect, not discussed earlier, will be considered in conjunction with the behavior of the remaining state, 8004. These three states differ greatly from the original state of a”? in their re- sponses to the changes in activity of the Spm element that can occur in individual cells during development of the endosperm of the kernel. It is recognized that the compo- nents of Spm undergo changes in phase of activity. Control of the time and frequency of their occurrence resides in the Spm element itself, each change regulating in a distinc- tive manner the period when the next will take place. The changes in phase of activity of component-1, from ac- tive to inactive and back to active, are unambiguously registered by each of the states of a.%'. The same unam- biguity applies to the states of some of the other gene loci that have come under the control of the Spm system, and it applies to the original state of a;"-?. The phenotype that will appear after each phase change can be pre- dicted and the predictions validated by tests that accurately determine the phase. Illustrations are given in the Brookhaven Symposium paper men- tioned earlier. The states of a”? designated 7997B, 7995, and 8004, however, respond in a distinctly dif- ferent manner to the alternating phases of activity of Spm. The dif- ference is especially well registered when the changes in phase occur dur- ing development of the kernel. State 8004 will be discussed first. State 8004 of a."-?. Examination of this state was conducted with plants having different constitutions with respect to the Spm element. These CARNEGIE INSTITUTION were: (1) no active Spm element; (2) one Spm element with both components fully active; (8) one Spm element with an active component-l and a late-acting component-2; (4) two Spm elements, both as in (2); (5) two Spm elements, one as in (2) and one as in (3). In addition, some plants had an Spm element whose component-1 was inactive and re- mained inactive in most plants and in their progeny, returning to the active phase only very rarely; the returns could be observed in small regions within individual kernels. Numerous tests were conducted with plants hav- ing these different constitutions. For the purposes of this discussion, the evidence obtained from only a few kinds of test need be mentioned. When state 8004 is propagated in the absence of an active Spm element, the aleurone layer of the kernel is colorless. If, however, an active Spm element is present, pigment is pro- duced. Its type and distribution then depend on the nature of the Spm and the number of elements present. If component-2 of the Spm element (s) is inactive or becomes active only late in development, the aleurone layer is uniformly light-pigmented. If this component is active initially, different phenotypic expressions of the gene appear. When two or more such ele- ments are present, pigment in the aleurone layer may range from nearly colorless in some kernels to dark pale in others, with, in most kernels, one or several very small deeply pig- mented spots. If, however, a kernel starts development with a single ac- tive Spm element that undergoes change in phase of activity in some cells, early in development, then pig- ment intensities in the aleurone layer of the mature kernel are strikingly modified. Examples are seen in the kernels of Plate 2(A)-(D). These kernels have both large and small GENETICS RESEARCH UNIT areas outlined by rims of deep pig- ment. The background pigmentation in all but one kernel is faint: such kernels were purposely selected for clear illustration of the deeply pig- mented borders. The kernel with a darker background (B) is included to suggest the range in intensity of background pigmentation among these kernels. The rimmed areas consist of de- scendants of individual cells in which a change in phase of Spm activity has occurred. The deep pigment outlining an area is produced by the outermost cells of the area. They receive a diffusible substance from the cells surrounding the area, in which Spm is fully active. This substance allows the border cells to make a pigment that is more intense than that in the cells either inside or outside the area. Thus the deep pigment of the rims is the result of a complementation reac- tion. The rims indicate that the prod- uct of action of the A, gene (or genes) differs in the cells within and without the areas. The larger rimmed areas often contain , small areas that also are rimmed with deep pigment. Again, the rims are the product of a complementation reac- tion. Here, however, the diffusible substance comes from cells within the small area and enters the cells surrounding it, where the deep pig- ment is produced, It could be demon- strated that the small rimmed areas within the larger ones are composed of descendants of cells in which Spm has returned to an active phase. Not all returns are made visible in this way. Some are accompanied by a change at the a,” locus that alters its capacity to produce a substance that can complement. In some kernels the pigment with- in a rimmed area is much more in- tense than that outside the area. It is not uniform in intensity, but 669 mottled, as illustrated in Plate 2(C), (D). Some of the mottling is due to very small areas in which a diffus- ible complementing substance is pro- duced. If a number of rimmed areas are present in a kernel, the intensity of the background pigmentation within the areas is often the same. In some kernels, however, it may differ in one or more of the areas; see Plate 2(B) and legend. It is sus- pected that the differences among - kernels in the intensity of pigment within rimmed areas, exclusive of the rims, reflect initial differences in or- ganization of the a,”? locus in the kernels, or differences that may arise during kernel development. That such differences do arise was learned in tests conducted to deter- mine the cause of interruptions of a rim along a segment of an otherwise rimmed area. Such interruptions, ex- pressed as absence of deep pigment, are often noted. Some of them are not continuous but are arranged in sequence along a continuous segment. It was found that the interruptions are due in some instances to loss of ability of the adjacent outer cells to produce a complementing diffusible substance that will allow the border cells of the rimmed area to form deep pigment. The tests were made by introducing wa™® along with state 8004 of a,”? into the primary endo- sperm nucleus. The gene at the Wx (Waxy) locus functions to convert amylopectin into amylose in the starch granules of cells in the endosperm. Changes in action of this gene during develop- ment may be detected in the mature kernel visually and also quite pre- cisely by staining the starch with an iodine—potassium iodide solution. Gene action at the wx locus is under the control of the Spm system, and its responses to Spm result in the production of amylose in the 670 starch granules of the cells. Because all the cells of the endosperm below the aleurone layer—the outermost layer—have starch granules, each change in action of the gene during endosperm development is registered in the mature endosperm. The de- scendants of a cell in which a change has occurred form a well-defined sec- tor in which the altered action of the gene is expressed in every cell. Most of the large sectors terminate in the aleurone layer. Small sectors, pro- duced by changes occurring late in kernel development, also may termi- nate in the aleurone layer. Thus, when state 8004 of aym? and wa™* are both present in a kernel, the cell lineage of the aleurone layer over- lying such a sector, either large or small, is also sharply defined. Parts of some of these sectors are adjacent to parts of a rimmed area, and some- times these adjacent rim-area cells do not form deep pigment. The inter- ruption of the rim is precisely defined by the common region of contact of cells of the sector with those of the rimmed area. It is evident that the sector is formed from descendants of a cell in which changes have occurred coincidentally at the loci of a,™? and wa®, The change at a,”? alters its ability to make a diffusible substance that can be utilized by the adjacent cells in the rimmed area to form in- tense pigment. In Year Book 57 the first evidence of phenotypic change produced by Alternating cycles of activity of Spm was outlined. The studies were con- ducted with a selected state of a.”". (A, is another locus in maize whose gene is involved in the biosynthetic pathway leading to anthocyanin for- mation.) It was learned that the num- ber and size of pigmented areas in a kernel, produced as the consequence of a change of Spm from an active to an inactive phase, depend on the CARNEGIE INSTITUTION number of Sym elements present in the kernel. When one is present, many areas exhibit this change, and many of them are large. With two Spm elements, the areas are all small. With three elements, no areas or only some very small ones are formed. The same relationship governs the produc- tion of the rimmed areas with state 8004 of a,"-?. Few or no rimmed areas are formed if two or more active Spm elements are present in the kernel. Both large and small areas are pro- duced if only one Spm element is present. An additional aspect of the be- havior of state 8004 should be men- tioned. If a plant carrying this state and also one active Spm element is utilized as pollen parent in a cross to a plant that lacks an active Spm ele- ment, the kernels receiving the Spm element from the pollen parent may show large rimmed areas, and in some kernels the pigment within the areas is dark. Kernels that do not receive the Spm element from the pollen parent are colorless. Removal of Spm from the nucleus by meiotic segregation does not induce a setting of the locus that allows pigment of various intensities to be produced subsequently among the kernels, as happens with states 7997B and 7995. States 7997B and 7995 of a,™*. An earlier report (Year Book 63, pp. 592-602) showed that kernels having one of these states and also one or more fully active Spm elements de- velop a number of small, deeply pig- mented spots in a more lightly pig- mented background. Should only one Spm element be present and should this element undergo change in phase of activity during kernel develop- ment, the response of either state to the change results in a darkly pig- mented area in the aleurone layer. Many of these dark areas contain small colorless areas. Examples are GENETICS RESEARCH UNIT seen in the two kernels in Plate 2(E), each of which carries state 7995. Kernels with a faintly pigmented background were chosen for the illus- tration, so that the dark areas might be noted readily. In the parts of the kernels where the Spm element was active, the characteristic pattern of small, deeply pigmented spots ap- pears. Such spots are absent in the darkly pigmented areas. Except for the small colorless spots, the pigment within the dark areas is uniform in intensity. The edges of the areas are not defined by deeply pigmented rims, as are comparable areas in kernels carrying state 8004. Rims will appear if the two states 8004 and 7995 are present as alleles in a kernel. An ex- ample is shown in Plate 2(F). Here the uniformly dark areas, produced by state 7995, are bordered by deeply pigmented rims, produced by state 8004. The small colorless spot within the area on the left is also bordered by a pigmented rim resulting from the action of state 8004. The pigment produced by state 7995 when a change in phase of Spm activity occurs during kernel develop- ment differs markedly both in inten- sity and in pattern of distribution from that produced by this state when Spm is removed by a somati- cally occurring transposition of Spm or by means of meiotic segregation. In a kernel that develops from the functioning of a gamete that has lost the Spm element by such means, the aleurone layer has a distinctively dif- ferent pattern of pigment distribu- tion, as illustrated in Year Book 63 (pp. 592-602 and Plate 2). This review of the states of a gene locus is intended to illustrate the extraordinary diversity in capacity of a single system of controlling ele- ments to regulate the action of a gene during development. It also demon- strates that the distribution and de- 671 gree of expression of the end product of action of a series of genes is mediated through control of the ac- tion of one of these genes. Only the fact that anthocyanin pigment—the end product of such a series—is not vital to the plant makes it possible to learn about the many kinds of reg- ulation such a system can provide. It is well known that the various races and strains of maize are distin- guished from one another by a re- markable diversity with respect to distribution of anthocyanin to parts of the plant and its intensity in any one part. The patterns are so varied that they defy a meaningful classifi- cation. The same is true of the differ- ent distributions of pigment produced by the states of a,” and, especially, the states of a,”?. Studies conducted by maize geneticists have shown that in some instances different alleles of a gene locus involved in anthocyanin production are responsible for the ap- pearance of different patterns of pig- ment distribution. The kind of regu- lation exercised by some of these alleles resembles that afforded by some of the states described here. In the studies of the alleles, with two exceptions, it has not been possible to determine the presence at the gene locus of a control-mechanism compo- nent that could be responsible for the differences in action of the alleles. That is understandable, for a means of detecting such a component usually is not available. It can be suspected, however, that many of these alleles represent different “states” of the loci, in the sense of the term defined in this report. Without a means of distinguishing between a mutant of the structural gene itself and a mutant that is produced by a regula- tory component at the locus, the term “allele” must be retained even though its significance in any one instance will remain ambiguous. 672 Since 1962, the Brookhaven Na- tional Laboratory has provided gar- den space and cultivation facilities for growing my maize plants. I should like to express my apprecia- CARNEGIE INSTITUTION tion of this courtesy, and of the gen- erous attitude and cooperative atten- tion of those persons at Brookhaven who are responsible for the care and maintenance of plant materials. BIBLIOGRAPHY Butler, B., see Skalka, A. Echols, H., see Skalka, A. Goldberg, E. B., The amount of DNA be- tween genetic markers in phage T4. Proce. Natl. Acad. Sci. U.S., 56, 1457-14638, 1966. Mosig, G., Distances separating genetic markers in T4 DNA. Proc. Natl. Acad. Sci. U.S., 56, 1177-11838, 1966. Skalka, A., Multiple units of transcription in phage lambda. Cold Spring Harbor Symp. Quant. Biol., 31, 877-879, 1966. Skalka, A., B. Butler, and H. Echols, Genetic control of transcription during develop- ment of phage a. Proc. Natl. Acad. Sci. U.S., 58, 576-583, 1967. Smith, M. G., A replicating form of \ phage DNA, in IX International Congress for Microbiology, Symposia, Moscow, pp. 483- 492, 1966. Smith, M. G., Isolation of high-molecular- weight DNA from normal and phage- infected E. coli, in Metheds in Enzymol- ogy, vol. 12, part A, L. Grossman and K. Moldave, eds., Academic Press, pp. 545-550, 1967. PERSONNEL Year Ended June 30, 1967 Phyllis D. Bear, Carnegie Institution Fellow Elizabeth M. Bocskay, Chief Clerk Jennie S. Buchanan, Curator of Drosoph- ila Stocks Elizabeth Burgi, Associate in Micro- biclogy Ruth Ehring, Carnegie Institution Fel- low Agnes C. Fisher, Secretary to Director ; Editor Alfred D. Hershey, Director Laura J. Ingraham, Research Assistant Barbara McClintock, Cytogeneticist Shraga Makover, Carnegie Institution ' Fellow Anna Marie Skalka, Carnegie Institu- tion Fellow Carole E. Thomason, Technical Assist- ant Rudolf Werner, Associate in Research Temporary and Part-Time John B. Earl, Technical Assistant