Micro RNA profiling analysis throughout tomato fruit development and ripening reveals potential regulatory role of RIN on micro RNA s accumulation

Summary The development and ripening of tomato fruit are complex processes involving many gene regulatory pathways at the transcriptional and post‐transcriptional level. Ripening inhibitor ( RIN ) is a vital transcription factor, which targets numerous ripening‐related genes at the transcriptional level during tomato fruit ripening. Micro RNA s (mi RNA s) are a class of short noncoding RNA s that play important roles in post‐transcriptional gene regulation. To elucidate the potential regulatory relationship between rin and mi RNA s during fruit development and ripening, we identified known mi RNA s and profiled their expression in wild‐type tomato and rin mutant using a deep sequencing approach combined with quantitative RT ‐ PCR . A total of 33 known mi RNA families were identified, of which 14 mi RNA families were differently accumulated. Subsequent promoter analysis showed that possible RIN ‐binding motifs ( CA r G ‐box) tended to occur frequently in the promoter regions of partial differently expressed mi RNA s. In addition, ethylene may participate in the regulation of mi RNA s accumulation during tomato fruit ripening. Chromatin immunoprecipitation ( C h IP ) and electrophoretic mobility shift assay confirmed the direct binding of RIN to the promoter of MIR 172a . Collectively, these results showed a close correlation between mi RNA expression and RIN as well as ethylene, which further elucidated the regulatory roles of mi RNA s during fruit development and ripening and enriched the regulatory network of RIN in tomato fruit.