Reconstruction of Arabidopsis thaliana fully integrated small RNA pathway

Small non-protein-coding RNAs (ncRNAs) have acquired diverse functions in plant and animals development. These riboregulators have been confirmed to cooperate in plant growth and development in the processes of moderating the levels of specific mRNAs and their translation products through to chromatin remodeling and silencing. According to the specific needs for interpreting and annotating small-RNA-based regulatory networks, it is evident that many additional components remain to be discovered and functionally characterized. Shedding light on the remaining components and uncovering the relation of the small-RNA-generating pathways with the synthesis of other components such as hormones and transcription factors define future challenges as more complicated mechanisms are expected to be characterized. In this review, we summarize our current understanding of the molecular and biological roles of ncRNAs in gene regulation/expression, describe in detail the specific and shared components for each pathway and highlight the advances in currently identified relationships and interactions between small ncRNAs. We present a fully integrated pathway connecting ncRNA entities such as miRNAs, siRNAs, ta-siRNAs, and nat-siRNAs, to each other within Arabidopsis thaliana.