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Abstract

Doppia (Dop) transposable elements were first identified from element termini found in the upstream portions of certain alleles of the pl1 and r1 loci of maize. At the r1 locus, these Dop end sequences are present in a region called sigma, which functions as the promoter for the S genes of the R-r haplotype, and which is required for efficient epigenetic modification of the S genes during paramutation. In order to better understand the significance of the Dop element sequences at R-r, and to investigate the Dop-encoded products that might regulate r1 genes in this haplotype, we have cloned a more complete Dop element, Dop4. The Dop4 element can encode two proteins that have strong sequence similarity to the TnpA and TnpD proteins of the well characterized maize transposable element En/Spm. The DOPA protein, which is similar to TnpA of En/Spm, is shown to bind to short, subterminal repeat motifs located in the Dop element ends. Like TnpA, DOPA promotes intermolecular associations between DNA molecules. In contrast to the activity of TnpA, which is a transcriptional repressor of En/Spm, DOPA activates expression of reporter genes driven by either the Dop promoter or sigma in transient expression assays.

Transposable element abundance subtly contributes to lower fitness in maize

“…We find that 23 TE families are significantly associated with grain yield; 12 are associated with lower grain yield, while 11 TE families are associated with higher grain yield (Fig 4D), but none of these associations surpass FDR correction. Families associated with negative effects include DTC00048, an En/Spm family originally named Doppia, that was discovered when active transposition generated chromosomal rearrangements and gene duplications at the r1 locus (Walker et al ., 1995; Bercury et al ., 2001). Families associated with positive effects include RLG00017, a Ty3 LTR retrotransposon family originally named Dagaf, that confers salt responsiveness to nearby genes (Makarevitch et al ., 2015).…”

A Novel Snf2 Protein Maintains trans-Generational Regulatory States Established by Paramutation in Maize

“…While it is not clear where RMR1 acts in this pathway it presumably acts coordinately with the maize orthologs of known RdDM components identified in Arabidopsis, namely DCL3 [16,45], the DRM methyltransferases [36], AGO4 [46,47], the RNA polymerase IV subunits, and the maize DRD1 ortholog (Figure 6A). In this model, doppia transcripts, perhaps because of the repetitive nature of the doppia genomic elements and/or the numerous internal subterminal repeats that are present in these elements [32,48], are the source of aberrant RNA that is processed via MOP1 and a DCL3 enzyme into siRNAs. This small RNA production is carried out in a manner that is dependent on RMR1 activity, possibly via direct interaction with a small RNA processing complex or by making the DNA accessible to factors necessary for siRNA precursor generation such as polymerase IVa.…”

Intraspecific violation of genetic colinearity and its implications in maize

“…Alternatively, although retrotransposon blocks are most likely recombinationally inert in present-day maize (15), the deletions could have been generated by unequal crossing over between related retrotransposon sequences in the wild ancestors of maize. The occurrence of DNA transposon sequences, such as MuRB and the CACTA family members Misfit and Doppia4 (22,23,38,39), within and f lanking some retrotransposon blocks, raises the possibility that they, too, could have been involved in the deletion process, because complex DNA transposons are known to induce chromosome breakage (40 -42). The presence of the same Doppia4-related element at the termini of two different retrotransposon blocks in different locations of the McC and B73 bz genomic regions is particularly suggestive.…”