Control of seed dormancy in Arabidopsis by a cis -acting noncoding antisense transcript

Abstract

Seed dormancy is one of the most crucial process transitions in a plant's life cycle. Its timing is tightly controlled by the expression level of the Delay of Germination 1 gene (DOG1). DOG1 is the major quantitative trait locus for seed dormancy in Arabidopsis and has been shown to control dormancy in many other plant species. This is reflected by the evolutionary conservation of the functional short alternatively polyadenylated form of the DOG1 mRNA. Notably, the 3′ region of DOG1, including the last exon that is not included in this transcript isoform, shows a high level of conservation at the DNA level, but the encoded polypeptide is poorly conserved. Here, we demonstrate that this region of DOG1 contains a promoter for the transcription of a noncoding antisense RNA, asDOG1, that is 5′ capped, polyadenylated, and relatively stable. This promoter is autonomous and asDOG1 has an expression profile that is different from known DOG1 transcripts. Using several approaches we show that asDOG1 strongly suppresses DOG1 expression during seed maturation in cis, but is unable to do so in trans. Therefore, the negative regulation of seed dormancy by asDOG1 in cis results in allele-specific suppression of DOG1 expression and promotes germination. Given the evolutionary conservation of the asDOG1 promoter, we propose that this cis-constrained noncoding RNA-mediated mechanism limiting the duration of seed dormancy functions across the Brassicaceae.seed dormancy | DOG1 gene | cis-acting ncRNA | antisense transcript P lants have evolved elaborate adaptation mechanisms to cope with unexpected and rapid changes in their natural environment (1). The division of the plant life cycle into consecutive developmental phases can be viewed as one such mechanism. This compartmentalization allows plants to focus their resources on particular tasks. The most pronounced developmental phases in plant development are seed dormancy, the juvenile phase, vegetative growth, flowering, and senescence (2). The transition between each successive phase has to be tightly controlled and aligned with the plant's internal metabolic state and external conditions.Seeds are characterized by their remarkable ability to withstand harsh environmental conditions (3). This is in part because of a seed dormancy mechanism that imposes a block on the ability of seeds to sense permissive conditions and initiate germination (4, 5). This mechanism allows seeds to temporarily bypass favorable conditions to germinate in an environment that will support the entire plant life cycle. Seed dormancy is under strong evolutionary selection because the improper timing of germination often results in immediate death (6). In addition, from an agronomical point of view, seed dormancy has been a subject of intensive selection, because on the one hand strong dormancy leads to uneven germination, but on the other hand weak dormancy may result in preharvest sprouting because of germination on the mother plant (7).An analysis of seed dormancy variability among Arabidopsis thaliana ac...

Transcriptional read-through of the long non-coding RNA SVALKA governs plant cold acclimation

“…23, 2018; Main RNA Polymerase II (RNAPII) transcription in genomes results in the production of many long noncoding RNAs (lncRNAs) 1 . The functional significance of resulting lncRNA molecules is actively debated even though biological roles are identified for an increasing number of examples [2][3][4] . Expression of lncRNAs is remarkably specific to the environmental condition, tissue or cell type, arguing for roles of lncRNA in regulation [5][6][7] .…”

Multiple alleles at a single locus control seed dormancy in Swedish Arabidopsis

“…SNP2 was strongly, albeit non-significantly, associated with GR21 (−log 10 p  = 5.80) and is located in the promoter region of DOG1 . As DOG1 expression is often correlated with seed dormancy (Bentsink et al, 2006; Chiang et al, 2011; Nakabayashi et al, 2012; Fedak et al, 2016), we hypothesized that SNP2 could contribute to GR21 variation, and used it as starting point for a multi-locus GWAS based on stepwise inclusion of markers (Segura et al, 2012). The optimal model resulting from starting with SNP2 explained 57% of the variation and consisted of two markers in addition to SNP2: SNP3, also in the DOG1 promoter; and SNP4, a rare allele [minor allele frequency (MAF) = 0.018] in the first exon of DOG1 (Figure 2C–D and Figure 2—figure supplement 3B and E).…”

“…If the former, DOG1 emerges as an evolutionary ‘master switch’ for life history variation, perhaps similar in importance to the central flowering regulator FLC (Li et al, 2014). Indeed a recent study has demonstrated that DOG1 may affect both dormancy and flowering (Huo et al, 2016), and it is interesting to note that both genes appear to be regulated through similar mechanisms, with chromatin remodelling and antisense transcripts switching off sense transcription (Swiezewski et al, 2009; Footitt et al, 2015; Fedak et al, 2016). Perhaps such genes play general role in regulating and modulating environmentally dependent life history transitions?…”

“…Analysis of a diallel cross between a highly dormant line from the Cape Verde Islands and a non-dormant line from Poland revealed several quantitative trait loci (QTL), one of which, DELAY OF GERMINATION1 ( DOG1 ), has been cloned and molecularly characterized (Alonso-Blanco et al, 2003; Bentsink et al, 2006), although its function is poorly understood. It appears to be tightly regulated by a complex array of mechanisms that include alternative splicing, alternative polyadenylation, and a cis-acting antisense non-coding transcript ( asDOG1 ) (Bentsink et al, 2006; Nakabayashi et al, 2015; Cyrek et al, 2016; Fedak et al, 2016), but, although DOG1 mRNA and protein abundance generally correlate with seed dormancy, this relationship is not observed in all accessions (Bentsink et al, 2006; Chiang et al, 2011; Nakabayashi et al, 2012; Fedak et al, 2016). In these cases, epistatic interactions with the genetic background, or other mechanisms, such as the critical self-dimerization of the DOG1 protein, might come into play (Nakabayashi et al, 2015).…”

From species to trait evolution in Aethionema (Brassicaceae)

“…They can influence the flowering time of Arabidopsis thaliana (e.g. COOLAIR and COLDAIR, Ietswaart et al 2012), are involved in seed dormancy in A. thaliana (Fedak et al 2016) and can influence male sterility in long day rice accessions (Ding et al 2012a). Although all these studies identified the conservation of long non-coding RNAs by sequence similarity they did not take the positional conservation of sequences into account.…”