AUTHOR=Laganà Alessandro , Shasha Dennis , Croce Carlo Maria TITLE=Synthetic RNAs for Gene Regulation: Design Principles and Computational Tools JOURNAL=Frontiers in Bioengineering and Biotechnology VOLUME=2 YEAR=2014 URL=https://www.frontiersin.org/journals/bioengineering-and-biotechnology/articles/10.3389/fbioe.2014.00065 DOI=10.3389/fbioe.2014.00065 ISSN=2296-4185 ABSTRACT=

The use of synthetic non-coding RNAs for post-transcriptional regulation of gene expression has not only become a standard laboratory tool for gene functional studies but it has also opened up new perspectives in the design of new and potentially promising therapeutic strategies. Bioinformatics has provided researchers with a variety of tools for the design, the analysis, and the evaluation of RNAi agents such as small-interfering RNA (siRNA), short-hairpin RNA (shRNA), artificial microRNA (a-miR), and microRNA sponges. More recently, a new system for genome engineering based on the bacterial CRISPR-Cas9 system (Clustered Regularly Interspaced Short Palindromic Repeats), was shown to have the potential to also regulate gene expression at both transcriptional and post-transcriptional level in a more specific way. In this mini review, we present RNAi and CRISPRi design principles and discuss the advantages and limitations of the current design approaches.