Resetting of the 24-nt siRNA landscape in rice zygotes

Li, Chenxin; Gent, Jonathan I.; Xu, Hengping; Fu, Hongyong; Russell, Scott D.; Sundaresan, Venkatesan

doi:10.1101/2020.08.31.275958

Cited by 4 publications

(6 citation statements)

References 98 publications

(278 reference statements)

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“…Another point of difference with A. thaliana is that rice endosperm siren loci appear to differ in genomic distribution from similar "siren-like" loci that dominate ovary and egg sRNA populations PLANT BIOLOGY (63). Siren sRNAs in Brassica rapa and A. thaliana are expressed via the canonical RNA POLYMERASE IV (Pol IV)-RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) pathway from the same loci in maternal and seed tissues, relatively highly in ovules and seed coat, moderately in the endosperm, and lowly in embryos and mature seeds (64).…”

Section: Discussionmentioning

confidence: 99%

Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting

Rodrigues

Hsieh

Ruan

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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Parent-of-origin–dependent gene expression in mammals and flowering plants results from differing chromatin imprints (genomic imprinting) between maternally and paternally inherited alleles. Imprinted gene expression in the endosperm of seeds is associated with localized hypomethylation of maternally but not paternally inherited DNA, with certain small RNAs also displaying parent-of-origin–specific expression. To understand the evolution of imprinting mechanisms in Oryza sativa (rice), we analyzed imprinting divergence among four cultivars that span both japonica and indica subspecies: Nipponbare, Kitaake, 93-11, and IR64. Most imprinted genes are imprinted across cultivars and enriched for functions in chromatin and transcriptional regulation, development, and signaling. However, 4 to 11% of imprinted genes display divergent imprinting. Analyses of DNA methylation and small RNAs revealed that endosperm-specific 24-nt small RNA–producing loci show weak RNA-directed DNA methylation, frequently overlap genes, and are imprinted four times more often than genes. However, imprinting divergence most often correlated with local DNA methylation epimutations (9 of 17 assessable loci), which were largely stable within subspecies. Small insertion/deletion events and transposable element insertions accompanied 4 of the 9 locally epimutated loci and associated with imprinting divergence at another 4 of the remaining 8 loci. Correlating epigenetic and genetic variation occurred at key regulatory regions—the promoter and transcription start site of maternally biased genes, and the promoter and gene body of paternally biased genes. Our results reinforce models for the role of maternal-specific DNA hypomethylation in imprinting of both maternally and paternally biased genes, and highlight the role of transposition and epimutation in rice imprinting evolution.

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Section: Discussionmentioning

confidence: 99%

Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting

Rodrigues

Hsieh

Ruan

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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“…Under the condition we set in greehouse for rice growth, the seed set rate is 97%, which told us that, if any, the rate of unfertilized egg cells is lower than 3% in our isolated zygote sample; in contrast, the seed set rate is only 1% in the minus control of emasqulated florets without pollination. In conclusion, the quality of our isolated zygotes from self-pollination is reliable for the transfection for cellular localization and Bimolecular Fluorescent Complementation (BiFC), as it was previously used for the studies of rice gametic and zygotic siRNA (Li et al 2020 and2022).…”

Section: Isolation Of Rice Egg Cells and Zygotesmentioning

confidence: 91%

“…Purity. The isolated rice gametes and zygotes are very pure, as verified by PCR using marker genes (Li et al 2019) and the study of siRNAs (Li et al 2020 and2022). This feature makes it possible to study the epigenetic modifications in rice gametes and zygotes (Khanday and Sundaresan 2021) to reveal the mechanism underlying the zygotic development.…”

Section: Advantageous Features Of Isolated Rice Gametes and Zygotes F...mentioning

confidence: 93%

“…The isolated rice gametes were used for in vitro fusion for artificial zygote (Khalequzzaman and Haq 2005), and detection of specific gene expression (Ohnishi et al 2011). The isolation of rice gametes and zygotes were also systematically optimized for higher purity and quantity in the Russell Lab and the products were applied for a number of studies, including cis -regulatory elements and transcriptomes of rice sperm cells and egg cells (Anderson et al 2013; Russell et al 2012; Sharma et al 2011), large-scale transcriptomic changes in rice zygotes (Anderson et al 2017) and the landscape of small interference RNA (siRNA) in rice gametes and zygotes (Li et al 2020 and 2022).…”

Section: Introductionmentioning

confidence: 99%

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Isolation and Transfection of Rice Egg Cells and Zygotes for Cellular Localization

Bartley

Libault

et al. 2022

Preprint

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Due to the difficulty in accessing to gametes and zygotes in flowering plants, which are controlled in single cells deeply embedded in multiple tissues, little is known about how the initiation of plant embryogenesis may reflect or contrast from such systems in other eukaryotes. In this study we has developed an approach of isolation and transfection of rice egg cells and zygotes for cellular localization of rice cell cycle factors (KRP5, KRP4 and FB3), which opened a pathway to monitor protein expression in rice egg cells and zygotes at different developmental stages. The advantageous feature of isolated rice cells may serve as an ideal system for studying the molecular mechanism underlying the rice zygotic division to initiate seed formation.

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“…Isolation and transfection of rice leaf protoplasts were conducted as previously described (Wang et al, 2013). Isolation of rice egg cells and zygotes was conducted as previously described (Li et al, 2019, 2020 and 2022). Transfection of isolated rice egg cells and zygotes was based on previous reports (Koiso et al, 2017; Toda et al, 2019) with modifications.…”

Section: Methodsmentioning

confidence: 99%

A CDKB/KRP/FB3 cell cycle core complex functions in rice gametes and zygotes

Bartley

Libault

et al. 2022

Preprint

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The cell cycle controls division and proliferation of all eukaryotic cells and is tightly regulated at multiple checkpoints by complexes of core cell cycle proteins. Due to the difficulty in accessing female gametes and zygotes of flowering plants, little is known about the molecular mechanisms underlying initiation embryogenesis despite the crucial importance of this process for seed crops. In this study, we reveal four levels of factors involved in rice zygotic cell cycle control and characterize their functions and regulation. Protein-protein interaction studies, including within zygote cells, and in vitro biochemical analyses delineate a model of the zygotic cell cycle core complex for rice. In this model, CDKB1, a major regulator of plant mitosis, is a cyclin (CYCD5)-dependent kinase; its activity is coordinately inhibited by two cell cycle inhibitors, KRP4 and KRP5; and both KRPs are regulated via F-box protein 3 (FB3)-mediated proteolysis. Supporting their critical role in controlling the rice zygotic cell cycle, mutations in KRP4, KRP5, and FB3 result in the compromised function of sperm cells and abnormal organization of female germ units, embryo and endosperm, thus significantly reducing seed-set rates. This work helps reveal regulatory mechanisms controlling the zygotic cell cycle toward seed formation in angiosperms.

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Resetting of the 24-nt siRNA landscape in rice zygotes

Cited by 4 publications

References 98 publications

Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting

Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting

Isolation and Transfection of Rice Egg Cells and Zygotes for Cellular Localization

A CDKB/KRP/FB3 cell cycle core complex functions in rice gametes and zygotes

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