Differential chromatin structure within a tandem array 100 kb upstream of the maize b1 locus is associated with paramutation

Abstract

Recombination mapping defined a 6-kb region, 100 kb upstream of the transcription start site, that is required for B-I enhancer activity and paramutation-a stable, heritable change in transcription caused by allele interactions in maize (Zea mays). In this region, B-I and B (the only b1 alleles that participate in paramutation) have seven tandem repeats of an 853-bp sequence otherwise unique in the genome; other alleles have one. Examination of recombinant alleles with different numbers of tandem repeats indicates that the repeats are required for both paramutation and enhancer function. The 6-kb region is identical in B-I and B, showing that epigenetic mechanisms mediate the stable silencing associated with paramutation. This is the first endogenous gene for which sequences required for paramutation have been defined and examined for methylation and chromatin structure. The tandem repeat sequences are more methylated in B-I (high expressing) relative to B (low expressing), opposite of the typical correlation. Furthermore, the change in repeat methylation follows establishment of the B epigenetic state. B-I has a more open chromatin structure in the repeats relative to B. The nuclease hypersensitivity differences developmentally precede transcription, suggesting that the repeat chromatin structure could be the heritable imprint distinguishing the two transcription states.

Repeat elements and the Arabidopsis DNA methylation landscape

“…Moreover, whereas B-I reverts spontaneously to B 0 at high frequency (1-10%) and can thus be considered a metastable epiallele, B 0 is highly stable and only becomes more active in RNAi mutant backgrounds (Dorweiler et al, 2000;Alleman et al, 2006;Woodhouse et al, 2006). These findings suggest that the tandem repeats of B-I and B 0 are, respectively, just below and well above the threshold required for RNAi-dependent chromatin targeting, presumably as a consequence of differences in chromatin states (Stam et al, 2002;Louwers et al, 2009). Although the available evidence seems to indicate otherwise (Arteaga-Vazquez and Chandler, 2010), it is also reasonable to assume that the tandem repeats of B 0 and B-I produce distinct amount of siRNAs, at least during the reproductive phase, when the RNAi-dependent chromatin targeting pathway could be most active, as in Arabidopsis (Figure 2).…”

“…This allele exists in two epiallelic forms, B-I and B 0 , which are strongly and weakly active, respectively. Difference in expression is associated with differential DNA methylation and chromatin accessibility of a set of seven tandem repeats that act as enhancers and that are located 100 kb upstream of the b1 transcription start site (Stam et al, 2002;Louwers et al, 2009). These seven tandem repeats are responsible for mediating in F1 heterozygotes the transfer of the expression state of paramutagenic B 0 to paramutable B-I with 100% penetrance and in an RNAi-dependent manner.…”

The Birth of a Black Rice Gene and Its Local Spread by Introgression

“…These epialleles have strong genetic linkages to changes in grain color and the DNA methylation status in the regulatory sequences of the genes (Walker, 1998;Stam et al, 2002). These results suggest that alteration of the DNA methylation status in these genes can change the activities of the anthocyanin biosynthetic pathway.…”

Paramutation: The Chromatin Connection

“…To identify cis-linked elements regulating paramutation, recombination mapping between B' and neutral b alleles was used (Stam et al, 2002a). A regulatory element, termed an enhancer, was located ;100 kb upstream of the b coding region.…”

“…Brink described a heritable alteration of the r locus that defied principles of Mendelian inheritance (Brink, 1956). A recent publication on paramutation in maize now provides convincing evidence that chromatin-level regulation underlies the phenotypic differences between alleles that participate in paramutation (Stam et al, 2002a). Two additional articles-one detailing paramutation-like effects associated with mammalian imprinting and the other describing paramutation after a change in ploidy in Arabidopsis-challenge us to understand how these cases fit into the developing paradigm explaining the molecular basis for paramutation (Herman et al, 2003;Mittelsten Scheid et al, 2003).…”