Time to Wake Up: Epigenetic and Small-RNA-Mediated Regulation during Seed Germination

Luján-Soto, Eduardo; Dinkova, Tzvetanka D.

doi:10.3390/plants10020236

Cited by 28 publications

(26 citation statements)

References 130 publications

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“…We also noted some well-known and important miRNAs in our predicted network, such as miR156, miR157, miR158, miR161, miR162, miR164, miR172, miR395, and miR396. These miRNAs proved to be involved in many biological and developmental processes such as vegetative growth, flowering, fertility, and fruit ripening [ 87 , 96 , 97 , 98 ]. For example, we found nine circRNAs with binding sites for miR156, seven circRNA with binding sites for miR172, four circRNAs with binding sites for miR396, and three circRNAs with binding sites for miR164, which all are known to regulate flower development in Arabidopsis [ 99 , 100 ], barley [ 101 ], tomato [ 102 ], Brassica napus [ 103 ], and strawberry [ 104 ].…”

Section: Discussionmentioning

confidence: 99%

Circular RNAs Repertoire and Expression Profile during Brassica rapa Pollen Development

Babaei

Singh

Bhalla

2021

IJMS

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Circular RNAs (circRNAs) are covalently closed RNA molecules generated by the back-splicing of exons from linear precursor mRNAs. Though various linear RNAs have been shown to play important regulatory roles in many biological and developmental processes, little is known about the role of their circular counterparts. In this study, we performed high-throughput RNA sequencing to delineate the expression profile and potential function of circRNAs during the five stages of pollen development in Brassica rapa. A total of 1180 circRNAs were detected in pollen development, of which 367 showed stage-specific expression patterns. Functional enrichment and metabolic pathway analysis showed that the parent genes of circRNAs were mainly involved in pollen-related molecular and biological processes such as mitotic and meiotic cell division, DNA processes, protein synthesis, protein modification, and polysaccharide biosynthesis. Moreover, by predicting the circRNA–miRNA network from our differentially expressed circRNAs, we found 88 circRNAs with potential miRNA binding sites, suggesting their role in post-transcriptional regulation of the genes. Finally, we confirmed the back-splicing sites of nine selected circRNAs using divergent primers and Sanger sequencing. Our study presents the systematic analysis of circular RNAs during pollen development and forms the basis of future studies for unlocking complex gene regulatory networks underpinning reproduction in flowering plants.

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Section: Discussionmentioning

confidence: 99%

Circular RNAs Repertoire and Expression Profile during Brassica rapa Pollen Development

Babaei

Singh

Bhalla

2021

IJMS

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“…These miRNAs proved to be involved in many biological and developmental processes such as vegetative growth, flowering, fertility, and fruit ripening (Waititu et al 2020;Luján-Soto and Dinkova 2021;Wu 2013;Li and Zhang 2016). For example, we found nine circRNAs with binding sites for miR156, seven circRNA with binding sites for miR172, four circRNAs with binding sites for miR396, and three circRNAs with binding sites for miR164, which all are known to regulate flower development in Arabidopsis (Wang et al 2009;Jung et al 2014), barley (Nair et al 2010), tomato (Cao et al 2016), Brassica napus (Wang et al 2019a), and strawberry (Zheng et al 2019).…”

Section: Discussionmentioning

confidence: 99%

Non-coding circular RNAs repertoire and expression profile during Brassica rapa pollen development

Babaei

Singh

Bhalla

2021

Preprint

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Circular RNAs (circRNAs) are covalently closed long non-coding RNA (lncRNA) molecules generated by the back-splicing of exons from linear precursor mRNAs. Though linear lncRNAs have been shown to play important regulatory roles in diverse biological and developmental processes, little is known about the role of their circular counterparts. In this study, we have performed high-throughput RNA sequencing to delineate the expression profile and potential function of circRNAs during the five stages of pollen development in Brassica rapa. A total of 1180 circRNAs were detected in pollen development, of which 367 showed stage-specific expression patterns. Functional enrichment and metabolic pathway analysis showed that the parent genes of circRNAs were mainly involved in pollen-related molecular and biological processes such as mitotic and meiosis cell division, DNA processes, protein synthesis, protein modification, and polysaccharide biosynthesis. Moreover, by predicting the circRNA-miRNA network from our differentially expressed circRNAs, we found 88 circRNAs with potential miRNA binding sites suggesting their role in post-transcriptional regulation of the genes. Finally, we confirmed the back-splicing sites of 9 randomly selected circRNAS using divergent primers and Sanger sequencing. Our study presents the first systematic analysis of circular RNAs during pollen development and forms the basis of future studies for unlocking complex gene regulatory networks underpinning reproduction in flowering plants.

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“…DNA methylation patterns have a clearly dynamic character and are continuously changing during plant seed development [ 159 , 160 , 161 , 162 ]. Thus, the occupancy of the CHH methylation sites remarkably increases from the early to the late stages of seed development and gradually decreases later on during germination.…”

Section: Epigenetic Mechanisms Of the Seed-to-seedlings Transitionmentioning

confidence: 99%

“…Among them, the LAFL network of transcription factors is directly involved in the activation of seed maturation, whereas VAL (VP1/ABI3-LIKE) proteins suppress LAFL-related effects, i.e., initiation of germination and vegetative development [ 16 , 183 ]. As was already mentioned above, chromatin remodeling complexes PRC1 and PRC2 [ 17 , 18 ], as well as the PKL and PKR2 proteins [ 21 , 22 ], are involved in repression of the LAFL network of transcription factors during seed germination [ 160 ]. For example, during seed germination, LAFL genes are repressed by the Polycomb machinery via its histone-modifying activities: the histone H3 K27 trimethyltransferase activity of the PRC2 and the histone H2A E3 monoubiquitin ligase activity of the PRC1 [ 184 , 185 , 186 , 187 ] ( Figure 2 B).…”

Section: Epigenetic Mechanisms Of the Seed-to-seedlings Transitionmentioning

confidence: 99%

“…Small non-coding RNAs (sRNAs) are known as important regulators of gene expression, affecting almost all stages of the plant lifecycle [ 195 , 196 ]. The regulatory RNAs of this type act at the transcriptional and post-transcriptional levels and essentially impact on seed development and germination [ 160 , 197 , 198 ].…”

Section: Epigenetic Mechanisms Of the Seed-to-seedlings Transitionmentioning

confidence: 99%

See 1 more Smart Citation

Transition from Seeds to Seedlings: Hormonal and Epigenetic Aspects

Smolikova

Стрыгина

Крылова

et al. 2021

Plants

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Transition from seed to seedling is one of the critical developmental steps, dramatically affecting plant growth and viability. Before plants enter the vegetative phase of their ontogenesis, massive rearrangements of signaling pathways and switching of gene expression programs are required. This results in suppression of the genes controlling seed maturation and activation of those involved in regulation of vegetative growth. At the level of hormonal regulation, these events are controlled by the balance of abscisic acid and gibberellins, although ethylene, auxins, brassinosteroids, cytokinins, and jasmonates are also involved. The key players include the members of the LAFL network—the transcription factors LEAFY COTYLEDON1 and 2 (LEC 1 and 2), ABSCISIC ACID INSENSITIVE3 (ABI3), and FUSCA3 (FUS3), as well as DELAY OF GERMINATION1 (DOG1). They are the negative regulators of seed germination and need to be suppressed before seedling development can be initiated. This repressive signal is mediated by chromatin remodeling complexes—POLYCOMB REPRESSIVE COMPLEX 1 and 2 (PRC1 and PRC2), as well as PICKLE (PKL) and PICKLE-RELATED2 (PKR2) proteins. Finally, epigenetic methylation of cytosine residues in DNA, histone post-translational modifications, and post-transcriptional downregulation of seed maturation genes with miRNA are discussed. Here, we summarize recent updates in the study of hormonal and epigenetic switches involved in regulation of the transition from seed germination to the post-germination stage.

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Time to Wake Up: Epigenetic and Small-RNA-Mediated Regulation during Seed Germination

Cited by 28 publications

References 130 publications

Circular RNAs Repertoire and Expression Profile during Brassica rapa Pollen Development

Circular RNAs Repertoire and Expression Profile during Brassica rapa Pollen Development

Non-coding circular RNAs repertoire and expression profile during Brassica rapa pollen development

Transition from Seeds to Seedlings: Hormonal and Epigenetic Aspects

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