Abstract: The present invention provides a method of identifying mRNA transcripts in the transcriptome of a cell comprising i) delivering into the cell a donor expression vector comprising nucleotides in a sequence encoding a trans-splicing barcode cassette, ii) exposing the cell to conditions such that the cell produces multiple copies of the trans-splicing barcode cassette encoded by the donor expression vector, which multiple copies of the trans-splicing barcode cassette each splice the barcode polynucleotide onto a mRNA transcript of the cell, thereby forming multiple mRNA transcripts of the cell, each spliced to the barcode polynucleotide; and iii) identifying the multiple mRNA transcripts that are spliced to the barcode polynucleotides, thereby identifying mRNA transcripts in the transcriptome of the cell.

Abstract: The present invention provides a method of identifying mRNA transcripts in the transcriptome of a cell comprising i) delivering into the cell a donor expression vector comprising nucleotides in a sequence encoding a trans-splicing barcode cassette, wherein the trans-splicing barcode cassette comprises a) a first portion, the nucleotide sequence of which encodes an intron comprising as part of its 3? end, or followed at its 3? end by a splice-site nucleotide sequence; followed at its 3? end by, b) a second portion, the nucleotide sequence of which encodes a barcode polynucleotide; followed at its 3? end by c) a third portion, which encodes a nucleotide identification element sequence, ii) exposing the cell to conditions such that the cell produces multiple copies of the trans-splicing barcode cassette encoded by the donor expression vector, which multiple copies of the trans-splicing barcode cassette each splice the barcode polynucleotide onto a mRNA transcript of the cell, thereby forming multiple mRNA transc

Abstract: The present invention provides a trans-splicing ribozyme comprising i) a targeting nucleotide sequence that is complementary to a target nucleotide sequence within a mRNA that is expressed in a cell; contiguous with ii) a catalytic RNA sequence; contiguous with iii) a donor transcript, which donor transcript comprises at least a nucleotide sequence that encodes a trans-activator, wherein when the trans-splicing ribozyme is expressed in a cell, the catalytic RNA sequence cleaves the mRNA and ligates the donor transcript to the mRNA to generate a spliced mRNA which comprises the donor transcript, such that the donor transcript is translated as part of the spliced mRNA in the cell, as well as methods of using the trans-splicing ribozyme. The present invention also provides variants of Cre and other recombinases, as well as method of using the variants.