Small regulatory RNAs (micro RNAs and small interfering RNAs) regulate gene expression during growth and development and initiate epigenetic changes to DNA and chromatin (Bartel 2009; Carthew and Sontheimer 2009). The main objective of this project is to identify the full complement of miRNAs and siRNAs in animals and plants by using bioinformatics, genomics, biochemistry, cell biology and genetics. Further to provide a perspective for the future our main aim will be to address and understand how these RNAs are produced and processed, how they are transported and how they target specific genes and RNAs for silencing. Expression of different short RNA and mRNA can reveal complex dynamic interplay between these molecules. The overall goal is to develop methods that would allow analysis of sRNA expression and linking of that to mRNA expression data analyses.