Photoperiodic patterns in miRNA-mRNA pairs and tRNA fragments revealed by time-course co-sequencing in Arabidopsis

In plants, the response to photoperiod is marked by global reprogramming of gene expression that drives extensive developmental changes. Small RNAs (sRNAs) play important roles in this process, but a comprehensive characterization of micro RNAs (miRNAs) and the more recently recognized transfer RNA fragments (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 messenger RNA (mRNA) sequencing time-courses, we identified positively- or inversely-correlated miRNA-mRNA pairs between the two co-sequenced datasets that suggest photoperiodic sRNA regulations. Furthermore, we revealed 20 patterns of photoperiodic tRFs. These patterns are linked to the transfer RNA (tRNA) isotypes and positions they derive from, suggesting that tRFs are subjected to photoperiodic regulation. Finally, we present a major update to our web-app "Photo-Graph," (http://gendron-lab.shinyapps.io/PhotoGraph) featuring new visualizations of this mRNA-sRNA co-sequencing dataset. In summary, our findings indicate that plants regulate sRNAs within a diel cycle in a photoperiodic manner and form highly-correlated pairs with mRNAs.