RNA tagging

1. A method for identifying, among a total RNA population, an RNA to which a protein of interest selectively binds in a cellular environment of a cell of interest, the method comprising:

(a) expressing a fusion protein within the cellular environment, the fusion protein comprising at least part of the protein of interest and a tagging domain, the tagging domain introducing a selective tag to an RNA to which the fusion protein selectively binds, the selective tag comprising a selective tag sequence or a selective covalent modification;

(b) allowing the tagging domain to tag the RNA to which the protein of interest selectively binds by waiting for about 1 minute to about 28 days; and

(c) identifying the tagged RNA.

2. The method of claim 1 wherein step (c) includes:

(d) isolating the total RNA population of the cell of interest from other cellular material resulting in isolated total RNA;

(e) reverse transcribing the isolated total RNA using a primer having a sequence that is complementary to at least part of the selective tag sequence or the selective covalent modification resulting in a single-stranded cDNA complementary to RNA including the selective tag;

(f) synthesizing a cDNA strand complementary to the single-stranded cDNA resulting in a dsDNA;

(g) amplifying the dsDNA;

(h) purifying the amplified dsDNA resulting in purified dsDNA; and

(i) sequencing the purified dsDNA.

3. The method of claim 1 , wherein the total RNA population is a total RNA population of a subcellular structure, a total RNA population of a secreted component, a total RNA population of a virus, a total RNA population of cellular origin, or a combination thereof.

4. The method in claim 1 , wherein expressing the fusion protein includes exposing the cell of interest to an extracellular structure containing the fusion protein.

5. The method of claim 4 , wherein the extracellular structure is viral.

6. A method for identifying, among a total RNA population of a cell of interest, any RNA to which any protein of interest selectively binds in a cellular environment of the cell of interest, the method comprising:

(a) expressing a fusion protein within the cellular environment, the fusion protein comprising the protein of interest and a tagging domain, the tagging domain introducing a selective tag to RNA to which the fusion protein selectively binds, the selective tag comprising a selective tag sequence or a selective covalent modification;

(b) isolating RNA from the cell resulting in isolated total RNA;

(c) attaching an in vitro added tail to the 3′ end of the isolated total RNA resulting in tailed total RNA, the in vitro added tail comprising a tail sequence;

(d) selectively reverse transcribing the tailed total RNA using a primer having a sequence that is complementary to at least part of the selective tag sequence or the selective covalent modification and at least part of the tail sequence resulting in a single-stranded cDNA complementary to RNA including the selective tag and the in vitro added tail;

(e) synthesizing a cDNA strand complementary to the single-stranded cDNA resulting in a dsDNA;

(f) amplifying the dsDNA;

(g) purifying the amplified dsDNA resulting in purified dsDNA; and

(h) sequencing the purified dsDNA.

7. The method of claim 6 , the method further comprising:

(i) depleting rRNA and tRNA from the isolated total RNA resulting in rRNA/tRNA-depleted isolated total RNA,

wherein step (c) utilizes the rRNA/tRNA-depleted isolated total RNA in place of the isolated total RNA.

8. The method of claim 7 , the method further comprising:

(j) poly(A) selecting the isolated total RNA resulting in poly(A)-selected isolated total RNA,

wherein step (i) utilizes the poly(A)-selected isolated total RNA in place of the isolated total RNA.

9. The method of claim 6 , the method further comprising:

(k) cleaning the dsDNA.

10. The method of claim 6 , the method further comprising:

(l) analyzing biological function relative to sequences that are shared among the RNA to which the protein of interest selectively bind.

11. A method of selectively sequencing a sub-selection of a total RNA population, the method comprising:

(a) selectively tagging the sub-selection with a selective tag having a selective sequence or a selective covalent modification;

(b) in vitro tailing the total RNA population;

(c) selectively reverse transcribing the sub-selection using a primer having a sequence that is complementary to at least part of the selective tag sequence or the selective covalent modification and at least part of the in vitro-added tail sequence to produce cDNA complementary to the sub-selection;

(d) synthesizing a cDNA strand complementary to the single-stranded cDNA resulting in a dsDNA;

(e) amplifying the dsDNA;

(f) purifying the amplified dsDNA resulting in purified dsDNA; and

(g) sequencing the purified dsDNA.

12. The method of claim 11 , the method further comprising:

(h) analyzing biological function relative to sequences that are shared among the sub-selection.

13. The method of claim 1 , wherein multiple, non-identical fusion proteins are expressed in step (a).

14. The method of claim 13 wherein the non-identical fusion proteins differ in the tagging domain.

15. The method of claim 13 wherein the non-identical fusion proteins differ in the protein of interest.