AMutatorTransposon Insertion Is Associated With Ectopic Expression of a Tandemly Repeated MulticopyMybGenepericarp color1of Maize

Abstract

The molecular basis of tissue-specific pigmentation of maize carrying a tandemly repeated multicopy allele of pericarp color1 (p1) was examined using Mutator (Mu) transposon-mediated mutagenesis. The P1-wr allele conditions a white or colorless pericarp and a red cob glumes phenotype. However, a Mu-insertion allele, designated as P1-wr-mum6, displayed an altered phenotype that was first noted as occasional red stripes on pericarp tissue. This gain-of-pericarp-pigmentation phenotype was heritable, yielding families that displayed variable penetrance and expressivity. In one fully penetrant family, deep red pericarp pigmentation was observed. Several reports on Mu suppressible alleles have shown that Mu transposons can affect gene expression by mechanisms that depend on transposase activity. Conversely, the P1-wr-mum6 phenotype is not affected by transposase activity. The increased pigmentation was associated with elevated mRNA expression of P1-wr-mum6 copy (or copies) that was uninterrupted by the transposons. Genomic bisulfite sequencing analysis showed that the elevated expression was associated with hypomethylation of a floral-specific enhancer that is $4.7 kb upstream of the Mu1 insertion site and may be proximal to an adjacent repeated copy. We propose that the Mu1 insertion interferes with the DNA methylation and related chromatin packaging of P1-wr, thereby inducing expression from gene copy (or copies) that is otherwise suppressed.

Pack- Mutator –like transposable elements (Pack-MULEs) induce directional modification of genes through biased insertion and DNA acquisition

“…4). This is consistent with previous reports describing the de novo insertion site preference of Mutator-like elements (17)(18)(19)(20), particularly the recent finding that the highest insertion density of active Mutator elements in maize is found in the regions around the TSS (21). Our data suggest that the insertion preference for sequences flanking the 5′ termini of genes is conserved for Mutator-like elements in all three plants, and a significant negative GC gradient of genes is not required for such targeting specificity.…”

“…Again, this illustrates the observed insertion preference of Pack-MULEs in the 5′ region of genes. It also suggests that some genes are "hot spots" for the insertion of Pack-MULEs, a phenomenon that has also been observed for de novo insertions of Mu elements in maize (17,20,23). The Pack-MULE on chromosome 11 (OsChr11-00120) is located 92 bp upstream of the TSS of ABFH11, according to gene annotation and the FL-cDNA sequence (Fig.…”

“…This might explain why the fraction of expressed Pack-MULEs is much higher than other transposable elements, including the autonomous elements of MULEs (10). It is also interesting to note that a de novo insertion of Mu1 (a GC-rich Pack-MULE) in the 5′ UTR of one of the tandemly duplicated p1 genes in maize induced the expression of other p1 genes in the same cluster, possibly through the alteration of DNA methylation and chromatin structure (20). From this point of view, some of the Pack-MULEs could be favored by selection simply due to their GC content.…”

Progressive Loss of DNA Methylation Releases Epigenetic Gene Silencing From a Tandemly Repeated Maize Myb Gene

“…On the basis of this study and past studies (Chopra et al 2003;Sekhon et al 2007;Robbins et al 2008), it seems that a function of ufo1 (wild type) is to maintain a tissuespecific expression pattern of P1-wr by modulating its chromatin state during development. Disruption of the P1-wr chromatin state in Ufo1 (mutant) background results in ectopic expression in pericarp and other tissues.…”

“…Two regions were chosen for this assay: a 333-bp fragment from a distal enhancer region, and a 312-bp region from the 59 end of intron 2 of P1-wr (see Figure 3A for location of these regions). Both regions undergo significant methylation modifications during P1-wr 3 Ufo1 interaction and have been considered important for upregulation of P1-wr expression (Chopra et al 2003;Sekhon et al 2007;Robbins et al 2008). In the distal enhancer region, overall CG and CNG methylation was very high ($95%) in P1-wr as well as in the F 1 expressers ( Figure 4A).…”