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MicroRNA function transitions from regulating developmental genes to transposable elements during the maturation of pollen

ABSTRACT: Small non-coding RNAs play important roles during the development of eukaryotic organisms. Both animal and plant miRNAs are essential for the spatio-temporal regulation of development but together with this role, plant miRNAs, also control transposable elements and stimulate the production of epigenetically-active small interfering RNAs. This last role is evident in the plant male gamete containing structure, the male gametophyte or pollen grain but how the dual role of plant miRNAs is integrated during its development is unknown. Here, we provide a detailed analysis of miRNA dynamics during pollen development and their genic and transposable element targets using small RNA and PARE high-throughput sequencing. Furthermore we uncover the miRNAs loaded in the two main AGOs in the mature pollen grain, AGO1 and AGO5. Our results indicate that the progression from microspore to mature pollen grain is characterized by a reprogramming from miRNAs focused on the control of development to miRNAs focused in transposable element control.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE132485 | GEO | 2021/11/12

REPOSITORIES: GEO

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Project description:Background: Partial pollen and embryo sac sterilities are the two main reasons for low fertility in autotetraploid rice. Our previous study revealed that small RNAs changes may associate with pollen fertility in autotetraploid rice. However, knowledge on comparative analysis between the development of pollen and embryo sac by small RNAs in autotetraploid rice is still unknown. In the present study, WE-CLSM (whole-mount eosin B-staining confocal laser scanning microscopy) and high-throughput sequencing technology was employed to examine the cytological variations and to analyze small RNAs changes during pollen and embryo sac development in autotetraploid rice compared with its diploid counterpart. Results: A total of 321 and 368 differentially expressed miRNAs (DEM) were detected during development of pollen and embryo sac in autotetraploid rice, respectively. Gene Ontology enrichment analysis on the targets of miRNAs-enriched during the development of pollen and embryo sac in autotetraploid rice revealed 30 prominent functional gene classes, such as cell differentiation and signal transduction during embryo sac development. However, only 7 prominent functional gene classes, such as flower development and transcription factor activity, were detected during pollen development. The expression levels of 39 DEM, which revealed interaction with meiosis-related genes, showed opposite expression levels in pollen and embryo sac development. Of these DEM, osa-miR1436_L+3_1ss5CT and osa-miR167h-3p were associated with the female meiosis, while osa-miR159a.1 and osa-MIR159a-p5 were related with the male meiosis. 21nt-phasiRNAs were detected both during pollen and embryo sac development, while 24nt-phasiRNAs were found only in pollen development, which displayed down-regulation in autotetraploid compared to diploid rice and their spatial-temporal expression patterns were similar to osa-miR2275d. 24nt TEs-siRNAs were found to be up-regulated in embryo sac but down-regulated in pollen development. Conclusion: The above results not only provide the small RNAs changes during four landmark stages of pollen and embryo sac development in autotetraploid rice but also have identified specifically expressed miRNAs, especially meiosis-related miRNAs, pollen-24nt-phasiRNAs and TEs-siRNAs in autotetraploid rice. Together, these findings provide a foundation for understanding the effect of polyploidy on small RNAs expression patterns during pollen and embryo sac development that may lead to different abnormalities in autotetraploid rice.