Time-course small RNA sequencing across photoperiods in Arabidopsis thaliana

Small RNAs play important roles in photoperiodism, but a comprehensive characterization of miRNAs and the more recently recognized tRFs within this context is lacking. Herein, we characterize the patterns of miRNAs and tRFs in Arabidopsis by performing time-course sRNA-sequencing across three photoperiods. By comparing with our previous mRNA-sequencing time-courses (GSE221846), we identified 14 negatively-correlated miRNA-mRNA pairs between the two co-sequenced datasets that suggest photoperiodic sRNA regulations. Furthermore, we identified 20 patterns of photoperiodic tRFs. These patterns are linked to the tRNA isotypes and positions they derive from, suggesting that tRFs are subjected to photoperiodic regulations. Seeds were sterilized before being sown onto 1/2 Murashige and Skoog medium plates lined with autoclaved filter papers. For germination, seeds were stratified in the dark for 48 hours before being transferred to a growth chamber under a 12L:12D photoperiod . After germination, seedlings were kept in the same condition for 10 days. On day 11, the seedlings were transferred to 16L:8D, 12L:12D, or 8L:16D photoperiod. On day 13, whole seedlings including shoots and roots were harvested and snap-frozen in liquid nitrogen.