Differential expression of miRNAs and their target genes in senescing leaves and siliques: insights from deep sequencing of small RNAs and cleaved target RNAs

MicroRNAs (miRNAs) are a class of small RNAs, which typically function by guiding cleavage of target mRNAs. They are known to play roles in a variety of plant processes including development, responses to environmental stresses and senescence. To identify senescence regulation of miRNAs in Arabidopsis thaliana, eight small RNA libraries were constructed and sequenced at four different stages of development and senescence from both leaves and siliques, resulting in more than 200 million genome-matched sequences. Parallel analysis of RNA ends libraries, which enable the large-scale examination of miRNA-guided cleavage products, were constructed and sequenced, resulting in over 750 million genome-matched sequences. These large datasets led to the identification a new senescence-inducible small RNA locus, as well as new regulation of known miRNAs and their target genes during senescence, many of which have established roles in nutrient responsiveness and cell structural integrity. In keeping with remobilization of nutrients thought to occur during senescence, many miRNAs and targets had opposite expression pattern changes between leaf and silique tissues during the progression of senescence. Taken together, these findings highlight the integral role that miRNAs may play in the remobilization of resources and alteration of cellular structure that is known to occur in senescence. To address the limited knowledge of small RNAs from senescing Arabidopsis on a global scale, we deeply sequenced these molecules from senescing leaves and siliques. Several nutrient-responsive miRNAs and their targets were found to be regulated in opposite directions in leaves and siliques as senescence progressed, which is consistent with these miRNAs playing a role in nutrient remobilization. Additionally, a new senescence-inducible small RNA locus was discovered and shown to target some mRNAs of the alpha tubulin family, which were reduced as senescence progressed. Overall this work implicates small RNAs in the both nutrient remobilization and cellular structure changes that take place during senescence.