The present specification discloses engineered Type II CRISPR-Cas9-associated split-nexus polynucleotide (sn-casPNs) systems, including systems comprising three split- nexus polynucleotides (snl-casPN/sn2-casPN/sn3casPN) and systems comprising two split-nexus polynucleotides (snl-casPN/sn2-casPN). Together with a Cas9 protein, the sn-casPNs facilitate site-specific modifications, including cleavage and mutagenesis, of a target polynucleotide in vitro and in vivo. Furthermore, the engineered Type II CRISPR-Cas9-associated split-nexus polynucleotide systems comprising sn-casPNs are useful in methods of regulating expression of a target nucleic acid. Methods are described herein for the creation of a variety of engineered Type II CRISPR- Cas9-associated split-nexus polynucleotide systems comprising two or more sn-casPNs. Polynucleotide sequences, expression cassettes, vectors, compositions, and kits for carrying out a variety of methods are also described. Furthermore, the present specification provides genetically modified cells, compositions of modified cells, transgenic organisms, pharmaceutical compositions, as well as a variety of compositions and methods involving the engineered Type II CRISPR-Cas9-associated split-nexus polynucleotide systems.