The discovery of small RNAs, including miRNAs and siRNAs, has added new layers of complexity to the numerous pathways that direct plant development. These molecules play a fundamental role as negative regulators of gene expression in a variety of developmental processes, including meristem initiation and differentiation, light responses, and proper formation of leaves, roots and inflorescences. My work provides deeper understanding into the function of miR172, and characterizes a novel interfering RNA, encoded by the first intron of the meristem-specific gene CAULIFLOWER. 

The first part of my thesis focuses on the transcriptional regulation of two miR172 genes by the LUG, SEUSS and AP2 co-repressor complex, which binds to the microRNA promoter to negatively and directly regulate its expression. My study provides evidence that a negative regulatory feedback loop exists between miR172 and AP2, where miR172 restricts AP2 function to the outer two floral whorls, while AP2 limits miR172 expression to the inner two floral whorls. Additionally, lug loss-of-function mutation causes a dramatic decrease in the transcript level of AGO1, an essential component of the RISC complex, suggesting that LUG acts as a regulator of AGO1 as well. My thesis work highlights the importance of LUG as a major regulator of the miRNA pathway and further elucidates the molecular mechanisms underlying the antagonistic interactions between class A and class C genes during flower development. 

The second part of my thesis addresses the mechanisms of intron-mediated gene silencing. My project provides data that the intron of the MADS-box transcription factor CAULIFLOWER can silence the expression of its host gene. Specifically, I identified a novel siRNA encoded by the first intron of the CAULIFLOWER gene, which transcriptionally inhibits CAL and restricts its expression domain. Moreover, my results indicate that the intron-derived siRNA leads to heterochromatin repression of the whole CAL gene locus. This silenced epigenetic pattern is stable across generations and can be inherited without the presence of the transgene. Conceivably, my thesis work on the novel intronic small RNA can be used as an effective tool to generate transgenic plants for research and agricultural purposes.