The genes that encode regulatory RNAs - known as short RNAs (sRNAs) or noncoding sRNAs (ncRNAs) - modulate physiological responses through different mechanisms, such as RNA-RNA interaction or RNA-protein interaction. These molecules are transcribed in trans and in cis relative to the targeted RNA. They are located within the protein coding regions, in the intergenic regions of the genome and show signs of promoter and terminator sequences that are generally Rhoindependent. The size of the ncRNA genes ranges from ~ 50 to ~ 500 nucleotides and several transcripts are processed by RNase with smaller end-products. These modulate the physiological responses through different mechanisms, either by RNA-RNA or RNA-protein interactions, and some of the interactions can be stabilized by the Hfq chaperone. The Riboswitches constitute another class of ncRNAs that are located in the 5’UTR region of an mRNA and induce transcriptional regulation through their molecular interactions with linkers. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) regions have been recently described in prokaryotes, which are based on repeated palindromic sequences. Each replicate consists of small segments of "spacer DNA" taken from exposures prior to the isolation of a bacteriophage virus or exogenous plasmid. CRISPR can be defined as an immune system of resistance to exogenous molecules.
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