Trafficked rnas for assessment of cell-cell connectivity and neuroanatomy

A method for delivering a barcode nucleic acid to a subcellular compartment or organelle of a mammalian cell, the method comprising contacting the mammalian cell with:

• a) a first plasmid capable of being expressed in the cell, wherein the first plasmid encodes for a fusion protein, wherein the fusion protein comprises a first domain comprising a subcellular compartment and/or organelle-associated protein or a polypeptide sequence that binds a subcellular compartment and/or organelle-associated protein and a second domain comprising a selective nucleic acid binding protein;
• and b) i) a second plasmid capable of being expressed in the cell, wherein the second plasmid encodes for an oligoribonucleotide comprising a selective protein binding nucleic acid domain, and a barcode nucleic acid, wherein the selective protein binding nucleic acid domain is capable of binding the selective nucleic acid binding protein of the first plasmid;
• or ii) an oligonucleotide comprising a selective protein binding nucleic acid domain, and a barcode nucleic acid, wherein the selective protein binding nucleic acid domain is capable of binding the selective nucleic acid binding protein of the first plasmid;
• under suitable conditions for intracellular trafficking and localization to occur,
• thereby delivering the barcode nucleic acid to a subcellular compartment or organelle of the mammalian cell.

A system for determining the localization of a fusion protein in a cell of a subject, the system comprising:

• a first plasmid and a second plasmid, wherein the first plasmid encodes for the fusion protein, wherein the fusion protein comprises a first domain comprising a trafficking protein and a second domain comprising a selective RNA binding protein, and wherein the second plasmid encodes for an oligoribonucleotide comprising a selective protein binding RNA domain and a barcode nucleic acid, wherein the selective protein binding RNA domain is capable of binding the selective RNA binding protein of the first plasmid;
• packaging the first plasmid and the second plasmid in a virus;
• introducing the virus to the subject, wherein upon cellular expression of the fusion protein of the first plasmid and cellular expression of the oligoribonucleotide of the second plasmid, the selective RNA binding protein binds the selective protein binding RNA domain and is thereby trafficked within the cell;
• and
• detecting the barcode nucleic acid;
• thereby determining the localization of the fusion protein in the cell of the subject.