Targeted transposition for use in epigenetic studies
Disclosed herein are compositions, methods and kits useful for epigenetic analysis based on the use of transposons that are targeted to specific regions of chromatin based on DNA-DNA interactions, protein-protein interactions, RNA-RNA interactions, and nucleic acid-protein interactions.
1. A method of making a nucleic acid sequence library comprising:
a. extracting chromatin from cells to provide a sample containing chromatin;
b. adding to said sample containing chromatin at least one assembled conjugate comprising a targeting protein covalently conjugated to a stable transposase:transposon complex containing a transposase complexed with a transposon cassette, wherein:
(i) the targeting protein binds a target protein or a target DNA-binding site; and
(ii) the transposon cassette comprises:
(1) transposase recognition sequences required for catalysis of a DNA integration reaction;
(2) one or more oligonucleotide bar code sequences to uniquely identify the conjugated protein; and
(3) primer sites for DNA amplification;
c. allowing said at least one conjugate to locate at its/their target proteins and/or target DNA-binding sites in said chromatin;
d. tagging nucleic acid in said chromatin with said conjugate by inducing an intermolecular reaction between said transposase recognition sequences and said nucleic acid; and
e. performing PCR amplification of the tagged nucleic acid using the primer sites.
2. The method of claim 1 , wherein (a) comprises cross-linking said chromatin.
3. The method of claim 2 further comprising removing the cross-links after said tagging.
4. The method of claim 1 , wherein the chromatin in said provided sample is fragmented.
5. The method of claim 1 , wherein (a) comprises cross-linking and fragmenting said chromatin.
6. The method of claim 1 , wherein the targeting protein binds a target protein.
7. The method of claim 1 , wherein the targeting protein binds a target DNA-binding site.
8. The method of claim 1 , wherein the targeting protein comprises a domain selected from bZIP domain, DNA-binding domain, helix-loop-helix, helix-turn-helix, MG-box, leucine zipper, lexitropsin, nucleic acid simulations, zinc finger, histone methylases, recruitment proteins, Swi6, chromodomain, chromoshadow domain, bromodomain, a methyl binding domain and PHD-finger.
9. The method of claim 1 , wherein the targeting protein comprises an antibody.
10. The method of claim 9 , wherein the targeting protein is an antibody and the target protein is a histone or a polymerase.
11. The method of claim 1 , wherein the transposon recognition sequences comprise Tn5 transposase DNA recognition sequences.
12. The method of claim 1 , wherein the oligonucleotide bar code sequences are fewer than 20 bases.
13. The method of claim 1 , wherein the transposon cassette further comprises platform-specific tags required for next generation sequencing (NGS).
14. The method of claim 1 , wherein the transposon cassette comprises an Epicentre™ EZ-Tn5 Transposome™.
15. The method of claim 1 , wherein the transposase:transposon complex further comprises an extraction moiety.
16. The method of claim 15 wherein the extraction moiety is biotin, avidin or streptavidin.
17. The method of claim 1 , wherein the intermolecular reaction is activated by the addition of a cofactor.
18. The method of claim 17 , wherein the cofactor is Mg2+.
19. The method of claim 1 , further comprising:
f. sequencing said amplified DNA.
20. The method of claim 1 , comprising adding to said provided sample containing chromatin a plurality of the complexes, wherein each complex comprises a targeting protein that targets a different target protein or target DNA binding site and each complex comprises a different bar code sequence to uniquely identify the targeting protein of the complex.
21. The method of claim 20 , further comprising:
f. sequencing said amplified DNA; and
g. using the bar code sequences for the identification of the covalently conjugated targeting protein.