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Paramutation Alters Regulatory Control of the Maize Pl Locus

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Paramutation Alters Regulatory Control of the Maize Pl Locus Copyright 2000 by the Genetics Society of America Paramutation Alters Regulatory Control of the Maize pl Locus Jay B. Hollick,*,1 Garth I. Patterson,*,2 Ingrid M. Asmundsson*,3 and Vicki L. Chandler² *Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403-1229 and ²Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721 Manuscript received October 14, 1999 Accepted for publication December 10, 1999 ABSTRACT The maize purple plant (pl) locus encodes a transcription factor required for anthocyanin pigment synthesis in vegetative and ¯oral tissues. The strongly expressed Pl-Rhoades (Pl-Rh) allele is unstable, spontaneously changing to weaker expression states (PlЈ) at low frequencies and exclusively changing to PlЈ in PlЈ/Pl-Rh heterozygotes. The weakly expressed PlЈ state is mitotically and meiotically stable, yet reversible. This type of allele-dependent, heritable alteration of gene control is called paramutation. Expression studies herein demonstrate that visible differences in anthocyanin pigment levels mirror pl RNA abundance and that pl paramutation is associated with reduced transcription of the pl gene. This transcriptional alteration is accompanied by acquisition of light-dependent regulation. Restriction endonu- clease mapping indicates that these changes in pl gene regulation are not associated with detectable DNA alterations or with extensive changes in cytosine methylation patterns. Genetic tests show that Pl-Blotched (Pl-Bh), a structurally similar pl allele encoding an identical pl RNA and PL protein, does not participate in pl paramutation. This result suggests that if cis-acting sequences are required for pl paramutation they are distinct from the protein coding and immediately adjacent regions. A model is discussed in which pl paramutation results in heritable changes of chromatin structure that fundamentally alter regulatory interactions occurring during plant development. ARAMUTATION describes a process whereby ex- from paramutable r alleles (Eggleston et al. 1995; Ker- Ppression of one allele is heritably altered by another micle et al. 1995). In contrast, paramutagenic alleles of (Hollick et al. 1997). The best-characterized examples the b and pl loci consist of single coding regions and they of paramutation interactions occur in Zea mays between arise spontaneously from corresponding paramutable alleles of three genes encoding transcriptional regula- alleles (Coe 1966; Patterson et al. 1993; Hollick et tors of the anthocyanin pigment biosynthetic pathway al. 1995). (Brink 1956; Coe 1966; Hollick et al. 1995). The r In addition to structural differences between paramu- (red) and b (booster) loci encode functionally duplicate table and paramutagenic alleles of the r, b, and pl loci, basic helix-loop-helix (b-HLH) proteins (Ludwig et al. speci®c details of spontaneous paramutation, paramuta- 1989; Goff et al. 1990; Radicella et al. 1991) and the genic strength, and stability of the paramutant state pl locus encodes a myb-like protein (Cone et al. 1993a). have led to considerable debate about whether or not In plant tissues, purple anthocyanin pigmentation re- these examples are mechanistically related (Coe 1966; quires combined action of PL and one or the other Brink 1973; Hollick et al. 1995). For instance, the b-HLH factors encoded by either r or b (reviewed in paramutable B-Intense (B-I) and Pl-Rhoades (Pl-Rh) alleles Dooner et al. 1991; Goff et al. 1992). can spontaneously change to weaker expression states Alleles susceptible to changes in gene expression by (BЈ and PlЈ) that are strongly paramutagenic; 100% of allelic interactions are termed ªparamutableº while al- the alleles transmitted from B-I/BЈ and Pl-Rh/PlЈ individ- leles that promote this instability are termed ªparamuta- uals are BЈ or PlЈ, respectively (Coe 1966; Hollick et genic.º Alleles that are neither paramutable nor para- al. 1995). In contrast, the paramutable R-r:standard mutagenic are termed ªneutral.º Most paramutagenic r (R-r) allele is relatively stable; its expression is strongly alleles are structurally complex and clearly different reduced only following exposure to strongly paramuta- genic, structurally distinct r alleles such as R-stippled (R-st) or R-marbled (R-mb; Brink 1956; Brink and Weyers Corresponding author: Vicki L. Chandler, Department of Plant Sci- Ј ences, 303 Forbes Hall, University of Arizona, Tucson, AZ 85721. 1957). Paramutant R-r is only weakly paramutagenic; E-mail: [email protected] it is weakly effective in causing reduced expression of 1 Present address: Department of Plant and Microbial Biology, Univer- another paramutable R-r allele in a R-r/R-rЈ heterozy- sity of California, Berkeley, CA 94720-3102. gote (Brown and Brink 1960). 2 Present address: Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854. In contrast to the differences listed above between pl 3 Present address: Department of Biology, University of New Mexico, and r paramutation, the two examples share the ability Albuquerque, NM 87131-1091. of paramutant PlЈ and R-rЈ to revert to fully active, non- Genetics 154: 1827±1838 (April 2000) 1828 J. B. Hollick et al. paramutagenic Pl-Rh and R-r alleles. Paramutant BЈ al- are not within the coding and immediate ¯anking re- leles are extremely stable and have never been observed gions. to change back to a fully active, nonparamutagenic state (Coe 1966; Patterson et al. 1995; G. Patterson, K. Kubo, J. Dorweiler, J. Hollick and V. Chandler, MATERIALS AND METHODS unpublished observations). Both PlЈ and R-rЈ can show Genetic stocks: The Pl-Rhoades (herein designated Pl-Rh) increased pigment and change back to Pl-Rh and R-r in and PlЈ (previously described as PlЈ-mahogany; PlЈ-mah) alleles subsequent generations if they are carried heterozygous were maintained in a W23 inbred background and in four other genetic backgrounds of mixed parentage. The PlЈ allele with neutral pl or r alleles, respectively (Styles and originally isolated as a spontaneous derivative of the Pl-Rh Brink 1966; Hollick and Chandler 1998). A further allele (Hollick et al. 1995) was used for the initial set of in similarity between pl and r is that the amount of pig- vitro transcription assays, sunlight exposure experiments, DNA ment expressed is inversely related to paramutagenic comparisons, and Pl-Bh paramutation tests. Additional PlЈ al- strength; weaker pigmenting states are more paramuta- leles obtained from spontaneous paramutation of Pl-Rh alleles were used for all subsequent experiments. Anthocyanin and genic (Styles 1967; Hollick et al. 1995). Both PlЈ and RNA extractions from anthers were carried out with a single R-rЈ alleles can exist in quantitatively distinct expression family of W23 material displaying a high frequency of sponta- states, and in the PlЈ case these expression states appear neous paramutation. Material for in vitro transcription experi- to be ®xed early in development and maintained ments was produced by backcrossing related Pl-Rh/Pl-Rh and PlЈ/Pl-Rh plants to B-I/B-I; Pl-Rh/Pl-Rh; R-r/R-r testers. Mate- throughout somatic development (Chandler et al. rial for sunlight exposure experiments and restriction endonu- 1996). clease comparisons was obtained from Pl-Rh/Pl-Rh and PlЈ/ Given the phenomenological differences and similari- Pl-Rh plants derived by crosses of Pl-Rh/Pl-Rh and PlЈ/Pl-Rh ties between these various examples of maize paramuta- plants to a common Pl-Rh/Pl-Rh stock. The pl-sunred (pl-sr) tion it remains an open question as to whether they stock used for the Pl-Bh paramutagenicity tests has been pre- viously described (Hollick et al. 1995). The Pl-Bh stocks were share a common molecular mechanism. Somehow, in- provided by the Maize Genetics Cooperation Stock Center, teracting alleles recognize each other and effect some accession no. 607A (Urbana, IL) and by Karen Cone (Univer- type of regulatory change. Following this initial estab- sity of Missouri, Columbia). Material for the r paramutation lishment event, the altered allele is maintained in a tests was in either K55 or K55/W23 hybrid backgrounds. Un- repressed expression state by a mitotically and meioti- less otherwise stated, all stocks were also homozygous for the B-I allele and a functional allele of the r locus required for cally heritable mechanism. Cytosine methylation is ar- anther pigmentation (R-r or r-r). guably the best-characterized example of a heritable Anthocyanin measurements: For each measurement, a total epigenetic change. However, meiotic inheritance of of 12 freshly extruded anthers (3 from each of four primary epigenetic information in organisms lacking cytosine ¯orets) for each anther color score (ACS) were ground in 1-ml aliquots of 70% ethanol, 1% HCl solution in 1.5-ml microfuge methylation (Schizosaccharomyces pombe and Drosophila tubes using disposable plastic pestles (Kontes). Absorbance at melanogaster) is clearly due to a distinct mechanism, hy- 530 nm was measured for extracts from ACS 1±4 and dilutions pothesized to be chromatin based (Grewal and Klar (1:10) of extracts from ACS 5±7. The number of plants sam- 1996; Cavalli and Paro 1998). Increased cytosine pled for each ACS is in parentheses: ACS1 (2); 2 (3); 3 (3); methylation is correlated with decreased expression of 4 (2); 5 (3); 6 (2); 7 (2). DNA materials: DNA was isolated from immature cobs and paramutant r alleles (Walker 1998) and also paramuta- puri®ed by CsCl-density centrifugation (Rivin et al. 1982). tion-like transcriptional silencing of certain transgenes Most of the maize clones (Patterson et al. 1993) and the 1.1- in Petunia hybrida (Meyer et al. 1993) and Nicotiana kb XhoI, pl-speci®c 3Ј clone have been previously described tobacum (Park et al. 1996). In sharp contrast, one of (Cocciolone and Cone 1993). The 5Ј pl-speci®c clone (pJH1) is a 850-bp HindIII subclone from a Pl-Rh genomic clone the strongest repressions of transcriptional activity, that (Cone et al.
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