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

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. Overall design: Analysis of sRNA accumulation during pollen grain development and PARE sequencing on mature pollen grains