Alternative Polyadenylation of the Sense Transcript Controls Antisense Transcription of DELAY OF GERMINATION 1 in Arabidopsis

Kowalczyk, Justyna; Palusińska, Małgorzata; Wroblewska-Swiniarska, Agata; Pietras, Zbigniew; Szewc, Lukasz; Dolata, Jakub; Jarmołowski, Artur; Świeżewski, Szymon

doi:10.1016/j.molp.2017.07.011

Cited by 25 publications

(29 citation statements)

References 10 publications

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“…Therefore, it is conceivable that the transcription of lgDOG1 and concomitant H2Bubq during sense expression negatively affect the antisense promoter (Figure ). This hypothesis is supported by the drastic upregulation of asDOG1 expression observed in the hub1‐5 mutant (Liu et al ) seeds, which lack the H2Bubq enzyme (Kowalczyk et al ).…”

Section: Seed Dormancymentioning

confidence: 88%

“…The null mutations in C-terminal domain (CTD) phosphatase-like 1 (CPL1) (Koiwa et al 2004) causes preferential selection of pTTS and increases shDOG1 expression. The shDOG1-enriched condition in the cpl1-8 or cpl-9 seeds results in enhanced dormancy (Kowalczyk et al 2017) (Figure 5). In contrast, the mutation in the flowering time control protein FY (fy-2), which is an Arabidopsis ortholog of the yeast RNA 3 0 processing factor Pfs2p and a component of Cleavage and Polyadenylation Specificity Factor (CPSF) (Simpson et al 2003), promotes dTTS selection and increases lgDOG1 expression (Cyrek et al 2016;Kowalczyk et al 2017).…”

Section: Cryptic Mechanisms Of Dog1 Expression and Beyondmentioning

confidence: 99%

“…The shDOG1-enriched condition in the cpl1-8 or cpl-9 seeds results in enhanced dormancy (Kowalczyk et al 2017) (Figure 5). In contrast, the mutation in the flowering time control protein FY (fy-2), which is an Arabidopsis ortholog of the yeast RNA 3 0 processing factor Pfs2p and a component of Cleavage and Polyadenylation Specificity Factor (CPSF) (Simpson et al 2003), promotes dTTS selection and increases lgDOG1 expression (Cyrek et al 2016;Kowalczyk et al 2017). The lgDOG1-enriched condition in the fy-2 seeds results in reduced dormancy (Cyrek et al 2016) ( Figure 5).…”

Section: Cryptic Mechanisms Of Dog1 Expression and Beyondmentioning

confidence: 99%

“…Nonetheless, the latest discovery about the significance of alternative polyadenylation in DOG1 expression (Cyrek et al ; Kowalczyk et al ) explicitly depicts the regulation of antisense expression by sense transcription. More importantly, this discovery, together with the previous discovery of asDOG1 (Fedak et al ), highlights the “reciprocal regulation of the DOG1 ‐ asDOG1 pair” (Kowalczyk et al ), which is an intriguing mechanism not only for seed dormancy control but also as a general mechanism of gene regulation. Thus, the past mysteries about DOG1 regulation have now been integrated into a convincing mechanism, while providing new puzzles for future studies.…”

Section: Seed Dormancymentioning

confidence: 99%

“…It is possible that seed dormancy is determined by the primary mechanism of shDOG1 or lgDOG1 selection and the asDOG1 regulation serves as the secondary mechanism of negative feedback. Based on Simpson et al 2003;Koiwa et al 2004;Liu et al 2007;Cyrek et al 2016;Fedak et al 2016;Kowalczyk et al 2017. See text for details.…”

Section: Cryptic Mechanisms Of Dog1 Expression and Beyondmentioning

confidence: 99%

See 4 more Smart Citations

Seed germination and dormancy: The classic story, new puzzles, and evolution

Nonogaki¹

2019

JIPB

142

141

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This review highlights recent progresses in seed germination and dormancy research. Research on the weakening of the endosperm during germination, which is almost a classic theme in seed biology, was resumed by α‐xylosidase studies. Strong genetic evidence was presented to suggest that the quality control of xyloglucan biosynthesis in the endosperm (and the embryo) plays a critical role in germination. Further analyses on the endosperm and the adjacent layers have suggested that the cutin coat in the endosperm‐testa interphase negatively affects germination while the endosperm‐embryo interphase produces a sheath that facilitates germination. These progresses significantly advanced our understanding of seed germination mechanisms. A breakthrough in dormancy research, on the other hand, revealed the unique abscisic acid signaling pathway that is regulated by DELAY OF GERMINATION1 (DOG1). The detailed analysis of DOG1 expression uncovered the intriguing story of reciprocal regulation of the sense‐antisense pair, which generated new questions. Recent studies also suggested that the DOG1 function is not limited to dormancy but extended through general seed maturation, which provokes questions about the evolution of DOG1 family proteins. Seed biology is becoming more exciting with the classic stories being revitalized and new puzzles emerging from the frontier.

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Section: Seed Dormancymentioning

confidence: 88%

Section: Cryptic Mechanisms Of Dog1 Expression and Beyondmentioning

confidence: 99%

Section: Cryptic Mechanisms Of Dog1 Expression and Beyondmentioning

confidence: 99%

Section: Seed Dormancymentioning

confidence: 99%

Section: Cryptic Mechanisms Of Dog1 Expression and Beyondmentioning

confidence: 99%

See 3 more Smart Citations

Seed germination and dormancy: The classic story, new puzzles, and evolution

Nonogaki¹

2019

JIPB

142

141

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Understanding the evolution of miRNA biogenesis machinery in plants with special focus on rice

Chithung

Kansal

Jajo

et al. 2023

Funct Integr Genomics

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miRNA biogenesis process is an intricate and complex event consisting of many proteins working in a highly coordinated fashion. Most of these proteins have been studied in Arabidopsis; however, their orthologs and functions have not been explored in other plant species. In the present study, we have manually curated all the experimentally verified information present in the literature regarding these proteins and found a total of 98 genes involved in miRNA biogenesis in Arabidopsis. The conservation pattern of these proteins was identified in other plant species ranging from dicots to lower organisms, and we found that a major proportion of proteins involved in the pri-miRNA processing are conserved. However, nearly 20% of the genes, mostly involved in either transcription or functioning of the miRNAs, were absent in the lower organisms. Further, we manually curated a regulatory network of the core components of the biogenesis process and found that nearly half (46%) of the proteins interact with them, indicating that the processing step is perhaps the most under surveillance/regulation. We have subsequently attempted to characterize the orthologs identified in Oryza sativa, on the basis of transcriptome and epigenetic modifications under field drought conditions in order to assess the impact of drought on the process. We found several participating genes to be differentially expressed and/or epigenetically methylated under drought, although the core components like DCL1, SE, and HYL1 remain unaffected by the stress itself. The study enhances our present understanding of the biogenesis process and its regulation.

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Reactive oxygen and nitrogen species (RONS) signalling in seed dormancy release, perception of environmental cues, and heat stress response

Puglia

2023

Plant Growth Regul

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Seed germination is a crucial plant-life process whose success depends largely on the seed's ability to germinate under favourable environmental conditions. Through molecular signalling, a seed is able to perceive environmental information, assimilate it, and transmit signals that determine its destiny. Reactive Oxygen and Nitrogen Species (RONS) function as signalling molecules that influence multiple phases of plant development. In the process of seed germination, their presence generally promotes germination completion, though not to the same extent in all species and environments. As signalling molecules, they participate in the sensing of light and temperature fluctuations as favourable germination cues, but they also play a role in inhibiting germination when temperatures exceed the optimal range, preventing seedling exposure to heat. Depending on environmental conditions, RONS set up crosstalk with the major phytohormones involved in germination, ABA, GA, and even auxin, regulating their biosynthesis and signalling. Here, we show relevant studies on how RONS exert seed germination control on multiple levels, such as through protein oxidation, epigenetic control, promotion of phytohormone key-metabolism genes expression, post-translational protein modifications, and redox interactions with DOG1. This review summarises the current understanding of the role of RONS in the seed, from its maturation to the transduction of environmental conditions. Special consideration is given to the RONS-mediated germination response to favourable stimuli, such as light or temperature fluctuations, and to conditions that inhibit germination, such as high temperatures.

show abstract

Alternative Polyadenylation of the Sense Transcript Controls Antisense Transcription of DELAY OF GERMINATION 1 in Arabidopsis

Cited by 25 publications

References 10 publications

Seed germination and dormancy: The classic story, new puzzles, and evolution

Seed germination and dormancy: The classic story, new puzzles, and evolution

Understanding the evolution of miRNA biogenesis machinery in plants with special focus on rice

Reactive oxygen and nitrogen species (RONS) signalling in seed dormancy release, perception of environmental cues, and heat stress response

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