For many years, gene expression manipulations were only possible with a handful of characterized promoters and transcription factors. However, recently, we have seen increasingly more RNA-based regulation inspired by natural RNA-based systems. Our genome is extensively transcribed into many species of long noncoding RNA (lncRNA), performing a variety of defined functions, tightly related to the structural versatility of RNA. And while this versatility makes RNA an appealing target for genomic regulation, it holds the biggest challenge of RNA engineering: design of functional synthetic lncRNA (slncRNA). Therefore, we need to further explore the relationship between sequence, structure and function of lncRNA molecules in a more systematically manner. In this work, I studied RNA regulation from two different perspectives: understanding translation regulation of mRNA from a structural perspective and engineering synthetic lncRNA (slncRNA) for transcriptional activation. In the first part of my research I employed Selective 2′Hydroxyl acylation Analyzed by Primer Extension followed by sequencing (SHAPE-Seq) to reveal the underlying structural changes lead to post-transcription down- or up-regulation phenomena previously observed in bacterial mRNA encoding for binding sites of RNA -binding proteins (RBP). I developed an extension to the SHAPE protocol by using a purified recombinant RBP added to in vitro RNA sample, to accomplish a complementary observation to the in vivo settings. By using the different SHAPE-Seq protocols, we established that the down-regulation effect is due to a transition from nonstrcutured translationally active state to repressed state exhibiting structured signature, which in turn inhibits translation. Additionally, the up-regulation effect apparently stems from highly closed structure that blocks translation, which is stabilized upon binding of the corresponding protein to facilitate translation. In the second part, I describe the design of a slncRNA library and a screening system for functional variants. I successfully established a stable reporter cell-line based on an inducible mCherry gene, characterized by low basal levels and strong expression activation only in the presence of a transcription activator. Additionally, I took an innovative approach for oligo-pool study in mammalian cells by integrating it into an artificial chromosome of CHO cells. Although the overall goal of the second part of my research was not completed, I believe the work presented in this thesis may open the door to future work in the field of regulatory synthetic RNA.