Ovule siRNAs methylate protein-coding genes in <i>trans</i>

Burgess, Diane; Chow, Hiu Tung; Grover, Jeffrey W.; Freeling, Michael; Mosher, Rebecca A.

doi:10.1101/2021.06.10.447945

Cited by 6 publications

(4 citation statements)

References 73 publications

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“…Siren loci generate 24‐nt siRNAs, first identified for their abundance in rice endosperm (Grover et al., 2020; Rodrigues et al., 2013). These loci map predominantly to genic and intergenic regions rather than transposable elements (Burgess et al., 2022). The siren correspond to approximately 200 loci in Brassica rapa and are present in diverse other angiosperms (Grover et al., 2020; Rodrigues et al., 2013).…”

Section: Discussionmentioning

confidence: 99%

The floral development of the allotetraploid Coffea arabica L. correlates with a small RNA dynamic reprogramming

Cherubino Ribeiro,

Baldrich,

de Oliveira

et al. 2024

The Plant Journal

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SUMMARYNoncoding and coding RNAs are key regulators of plant growth, development, and stress responses. To investigate the types of transcripts accumulated during the vegetative to reproductive transition and floral development in the Coffea arabica L., we sequenced small RNA libraries from eight developmental stages, up to anthesis. We combined these data with messenger RNA and PARE sequencing of two important development stages that marks the transition of an apparent latent to a rapid growth stage. In addition, we took advantage of multiple in silico tools to characterize genomic loci producing small RNAs such as phasiRNAs, miRNAs, and tRFs. Our differential and co‐expression analysis showed that some types of small RNAs such as tRNAs, snoRNAs, snRNAs, and phasiRNAs preferentially accumulate in a stage‐specific manner. Members of the miR482/miR2118 superfamily and their 21‐nucleotide phasiRNAs originating from resistance genes show a robust co‐expression pattern that is maintained across all the evaluated developmental stages. Finally, the majority of miRNAs accumulate in a family stage‐specific manner, related to modulated hormonal responses and transcription factor expression.

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Section: Discussionmentioning

confidence: 99%

The floral development of the allotetraploid Coffea arabica L. correlates with a small RNA dynamic reprogramming

Cherubino Ribeiro,

Baldrich,

de Oliveira

et al. 2024

The Plant Journal

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“…S11, 12 ). A recent preprint reported that, in B. rapa ovules, a fraction of siren siRNAs can silence genes with sequence homology in trans via DNA methylation ( Burgess et al 2021 ). We cannot exclude that the same process might also occur in rice egg cells and zygotes, regardless of the cell type of origin of siren siRNAs.…”

Section: Discussionmentioning

confidence: 99%

Resetting of the 24-nt siRNA landscape in rice zygotes

Gent

et al. 2021

Genome Res.

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The zygote, a totipotent stem cell, is crucial to the life cycle of sexually reproducing organisms. It is produced by the fusion of two differentiated cells - the egg and sperm, which in plants have radically different siRNA transcriptomes from each other, and from multicellular embryos. Due to technical challenges, the epigenetic changes that accompany the transition from differentiated gametes to totipotent zygote are poorly understood. Since siRNAs serve as both regulators and outputs of the epigenome, we performed here the successful characterization of small RNA transcriptomes of zygotes from rice. Zygote small RNAs exhibited extensive maternal carryover and an apparent lack of paternal contribution, indicated by absence of sperm signature siRNAs. Zygote formation was accompanied by widespread redistribution of 24-nt siRNAs relative to gametes, such that ~70% of the zygote siRNA loci did not overlap any egg cell siRNA loci. Newly-detected siRNA loci in zygote are gene proximal and not associated with centromeric heterochromatin, similar to canonical siRNAs, in sharp contrast to gametic siRNA loci which are gene-distal and heterochromatic. In addition, zygote but not egg siRNA loci were associated with high DNA methylation in the mature embryo. Thus, the zygote begins transitioning before the first embryonic division to an siRNA profile that is associated with future RdDM in embryogenesis. These findings indicate that in addition to changes in gene expression, the transition to totipotency in the plant zygote is accompanied by resetting of the epigenetic reprogramming that occurred during gamete formation.

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“…Siren loci generate 24-nt siRNAs, first identified for their abundance in rice endosperm (Rodrigues et al, 2013;Grover et al, 2020). These loci map predominantly to genic and intergenic regions rather than transposable elements (Burgess et al, 2022).…”

Section: Hundreds Of Loci Demonstrate a 24-nt Phasing Pattern But Exc...mentioning

confidence: 99%

The floral development of the allotetraploidCoffea arabicaL. correlates with a small RNA dynamic reprogramming

Ribeiro,

Baldrich,

de Oliveira

et al. 2023

Preprint

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Non-coding and coding RNAs are key regulators of plant growth, development, and stress responses. To investigate the types of transcripts accumulated during the vegetative to reproductive transition and floral development in the Coffea arabica L., we sequenced small RNA libraries from eight developmental stages, up to anthesis. We combined this data with messenger RNA and PARE sequencing of two important development stages that marks the transition of an apparent latent to a rapid growth stage. In addition, we took advantage of multiple in silico tools to characterize genomic loci producing small RNAs such as phasiRNAs, miRNAs and tRFs. Our differential and co-expression analysis showed that some types of small RNAs such as tRNAs, snoRNAs, snRNAs and phasiRNAs preferentially accumulate in a stage- specific manner. Members of the miR482/miR2118 superfamily and their 21-nucleotide phasiRNAs originating from resistance genes show a robust co-expression pattern that is maintained across all the evaluated developmental stages. Finally, the majority of miRNAs accumulate in a family-stage specific manner, related to modulated hormonal responses and transcription factors expression.

show abstract

Ovule siRNAs methylate protein-coding genes in trans

Cited by 6 publications

References 73 publications

The floral development of the allotetraploid Coffea arabica L. correlates with a small RNA dynamic reprogramming

The floral development of the allotetraploid Coffea arabica L. correlates with a small RNA dynamic reprogramming

Resetting of the 24-nt siRNA landscape in rice zygotes

The floral development of the allotetraploidCoffea arabicaL. correlates with a small RNA dynamic reprogramming

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