Comprehensive in vitro reporting of cleavage events by sequencing (Circle-seq)

1. A method of preparing a library of covalently closed circular double-stranded DNA (dsDNA) fragments, the method comprising:

providing a sample comprising dsDNA;

randomly shearing the dsDNA to a defined average length to provide a population of dsDNA fragments;

preparing the fragments for end-ligation;

ligating to the ends of the fragments a stem-loop adapter comprising a single deoxyuridine adjacent to or within a single-stranded loop sequence comprising a palindromic sequence for intramolecular ligation, to prepare a population of ligated linear dsDNA fragments;

contacting the population of ligated linear dsDNA fragments with an exonuclease to degrade any remaining linear fragments with unligated ends, to produce a purified population of ligated linear dsDNA fragments,

contacting the purified population of ligated linear dsDNA fragments with enzymes that nick the ligated dsDNA fragments at the deoxyuridine and remove a 3′ terminal phosphate;

incubating the nicked linear dsDNA fragments under conditions sufficient to promote intramolecular ligation and formation of circular dsDNA molecules;

purifying the ligated circular dsDNA fragments by using an exonuclease to degrade any unligated non-circular fragments, thereby preparing a library of covalently closed fully circular dsDNA fragments.

2. The method of claim 1 , further comprising contacting the library of covalently closed fully circular dsDNA fragments with an engineered nuclease to induce site-specific cleavage;

preparing the cleaved fragments for end-ligation;

ligating a sequencing adapter comprising at least a single deoxyuridine and a primer site compatible for use in PCR priming or sequencing, at the cleavage site;

contacting the library with enzymes that nick at the deoxyuridine; and

sequencing resulting fragments using primers that bind to the sequencing adapter.

3. The method of claim 2 , wherein the engineered nuclease cleaves at on- and/or off-target sites.

4. The method of claim 2 , wherein the engineered nuclease induces blunt or staggered/overhanging ends.

5. The method of claim 2 , wherein the engineered nuclease is selected from the group consisting of meganucleases, MegaTALs, zinc-finger nucleases, transcription activator effector-like nucleases (TALEN), Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas RNA-guided nucleases (CRISPR/Cas RGNs), and FokI-dCas9 fusion proteins.

6. The method of claim 5 , wherein the CRISPR/Cas RGN is Cas9 or Cpf1.

7. The method of claim 2 , wherein treating the sample with an engineered nuclease to induce site-specific cleavage, comprises contacting the sample with a Cas9 nuclease complexed with a specific guide RNA (gRNA).

8. The method of claim 7 , wherein the engineered nuclease is a Cas9 nuclease, and the method also includes utilizing a guide RNA that directs the Cas9 nuclease to a target sequence in the genome.

9. The method of claim 2 , wherein the primer site comprises a next generation sequencing primer binding sequence, a randomized DNA barcode or unique molecular identifier (UMI).

10. The method of claim 2 , wherein the sequencing adapter comprises:

a first region;

a second region that forms one or more hairpin loops and comprises a primer site compatible for use in PCR priming and/or sequencing;

a third region that is complementary to the first region with one additional nucleotide; and

wherein the single deoxyuridine is between the second and third regions.

11. The method of claim 10 , further comprising:

contacting the library with enzymes to nick at the deoxyuridine in the sequencing adapter;

using PCR amplification to enrich for adapter-ligated fragments and to add a full sequencing adapter, and

sequencing those fragments bearing a sequencing adapter.

12. The method of claim 11 , wherein the enzymes to nick at the deoxyuridine comprise uracil DNA glycosylase (UDG) and/or endonuclease VIII.

13. The method of claim 1 , wherein the stem-loop adapter comprises:

a first region;

a second region that forms one or more loops and comprises a single deoxyuridine nucleotide adjacent to a palindromic sequence for intramolecular ligation; and

a third region that is complementary to the first region with one additional nucleotide.

14. The method of claim 13 , wherein preparing the fragments for end-ligation comprises and then A-tailing the resulting ends.

15. The method of claim 1 , wherein randomly shearing the dsDNA comprises randomly shearing the dsDNA to an average length of 200-500 bps.

16. The method of claim 1 , wherein the exonuclease used to degrade any remaining linear fragments with unligated ends is a cocktail of nucleases comprising one or more of bacteriophage Lambda exonuclease, E. coli Exonuclease I, and an ATP-dependent exonuclease.

17. The method of claim 1 , wherein preparing the fragments for end-ligation comprises one or both of end-repairing and A-tailing the sheared DNA.

18. The method of claim 1 , wherein the enzyme that nicks at the deoxyuridine comprises one or both of uracil DNA glycosylase (UDG) and endonuclease VIII, and the enzyme that removes the terminal 3′ phosphate comprises T4 Polynucleotide Kinase.

19. The method of claim 1 , wherein the DNA is genomic DNA (gDNA) or synthetic DNA.