# US 11,306,307 B2 · Targeted transposition for use in epigenetic studies

> Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt

- Number: US 11,306,307 B2
- Document ID: US11306307B2
- Status: Granted
- Kind: B2
- Application number: 16/946,073
- Filed: 2020-06-04
- Published: 2020-09-24
- Granted: 2022-04-19
- Earliest claimed: 2011-11-22
- Assignees: Active Motif, Inc.
- Applicants: Active Motif, Inc.
- Inventors: Mary Anne Jelinek; Brian Stanley Egan; Joseph Fernandez
- Web page: https://patentgrep.com/patent/US11306307B2

## CPC

- C12N 15/1068: {Template (nucleic acid) mediated chemical library synthesis, e.g. chemical and enzymatical DNA-templated organic molecule synthesis, libraries prepared by non ribosomal polypeptide synthesis [NRPS], DNA/RNA-polymerase mediated polypeptide synthesis}
- C07H 21/00: Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
- C12N 15/1006: {by means of a solid support carrier, e.g. particles, polymers}
- C12N 15/1034: {Isolating an individual clone by screening libraries}
- C12N 15/1065: {Preparation or screening of tagged libraries, e.g. tagged microorganisms by STM-mutagenesis, tagged polynucleotides, gene tags}
- C12N 15/1093: {General methods of preparing gene libraries, not provided for in other subgroups}
- C12Q 1/6804: Nucleic acid analysis using immunogens (immunoassay G01N33/53)
- C12Q 1/6806: Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay (C12Q1/6804 takes precedence)
- C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00)
- C07H: SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS (derivatives of aldonic or saccharic acids C07C, C07D; aldonic acids, saccharic acids C07C59/105, C07C59/285; cyanohydrins C07C255/16; glycals C07D; compounds of unknown constitution C07G; polysaccharides, derivatives thereof C08B; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification C12N15/00; sugar industry C13)
- C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES

## Abstract

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.

## Claims

### Claim 1

A binding protein-transposome complex, comprising a binding protein that binds a target, wherein the binding protein comprises Protein A, Protein G, a Protein A fusion protein or a Protein G fusion protein, said binding protein stably attached to a stable transposase:transposon complex (“transposome”), wherein the target is a protein that binds a nucleic acid-associated protein or protein domain, a DNA-binding site, or a protein that binds either of these.

### Claim 2 (depends on 1)

The complex of claim 1, further comprising one or more oligonucleotide bar code sequences to uniquely identify the binding protein.

### Claim 3 (depends on 1)

The complex of claim 1, further comprising an extraction moiety.

### Claim 4 (depends on 3)

The complex of claim 3, where the extraction moiety comprises a sequencing adaptor or PCR primer(s).

### Claim 5

A binding protein-transposome complex, comprising a non- antibody protein, wherein the non-antibody protein comprises Protein A, Protein G, a Protein A fusion protein or a Protein G fusion protein, said protein stably attached to a stable transposase:transposon complex (“transposome”), wherein the non-antibody protein is further bound to a second protein, wherein the second protein binds a nucleic acid-associated protein or protein domain, or a DNA-binding site.

### Claim 6 (depends on 5)

The complex of claim 5, wherein the second protein comprises an antibody.

### Claim 7 (depends on 1)

The composition of claim 1, wherein the binding protein-transposome complex is bound, indirectly, to chromatin.

### Claim 8 (depends on 1)

The composition of claim 1, wherein the binding protein binds a molecule that binds to a nucleic acid-associated protein or protein domain, and wherein the molecule comprises an antibody, biotin or streptavidin.

### Claim 9

A composition comprising:
(a) a primary antibody, wherein the primary antibody binds a nucleic acid-associated protein or protein domain, or a DNA-binding site;
(b) a secondary antibody bound to the primary antibody; and
(c) a binding protein-transposome complex, comprising a non-antibody protein bound to the secondary antibody, wherein the non-antibody protein comprises Protein A, Protein G, a Protein A fusion protein or a Protein G fusion protein, said non-antibody protein stably attached to a stable transposase:transposon complex (“transposome”).

### Claim 10 (depends on 9)

The composition of claim 9, wherein the primary antibody is directly bound to chromatin.

### Claim 11 (depends on 1)

The complex of claim 1, wherein the transposome is biotinylated, the binding protein is biotinylated, and the transposon and binding protein are conjugated through streptavidin.

### Claim 12 (depends on 1)

The complex of claim 1, wherein the transposome is biotinylated, and the binding protein bound to the transposon through a streptavidin-Protein A fusion protein or a streptavidin-Protein G fusion protein.

### Claim 13 (depends on 1)

The complex of claim 1, wherein the binding protein is conjugated to the transposome directly via a chemical crosslinker.

### Claim 14 (depends on 5)

The complex of claim 5, wherein the transposome is biotinylated, the non-antibody protein is biotinylated, and the transposon and binding protein are conjugated through streptavidin.

### Claim 15 (depends on 5)

The complex of claim 5, wherein the transposome is biotinylated, and the non-antibody protein comprises a streptavidin-Protein A fusion protein or a streptavidin-Protein G fusion protein.

### Claim 16 (depends on 5)

The complex of claim 5, wherein the binding protein is conjugated to the transposome directly via a chemical crosslinker.

### Claim 17 (depends on 9)

The composition of claim 9, wherein the transposome is biotinylated, the non-antibody protein is biotinylated, and the transposon and binding protein are conjugated through streptavidin.

### Claim 18 (depends on 9)

The composition of claim 9, wherein the transposome is biotinylated, and the non-antibody protein comprises a streptavidin-Protein A fusion protein or a streptavidin-Protein G fusion protein.

### Claim 19 (depends on 9)

The composition of claim 9, wherein the binding protein is conjugated to the transposome directly via a chemical crosslinker.

### Claim 20 (depends on 5)

The complex of claim 5, wherein the transposon further comprises one or more oligonucleotide bar code sequences to uniquely identify the second protein.

### Claim 21 (depends on 9)

The complex of claim 9, wherein the transposon further comprises one or more oligonucleotide bar code sequences to uniquely identify the primary antibody.

### Claim 22 (depends on 5)

The complex of claim 5, wherein the composition further comprises an extraction moiety.

### Claim 23 (depends on 9)

The complex of claim 9, wherein the composition further comprises an extraction moiety.

### Claim 24 (depends on 6)

The complex of claim 6, wherein the antibody is bound to chromatin.

### Claim 25 (depends on 1)

The complex of claim 1, wherein the target comprises an antibody that binds a nucleic acid-associated protein or protein domain, or a DNA-binding site.

### Claim 26 (depends on 1)

The complex of claim 1, wherein the target comprises a second antibody that binds a first antibody that binds a nucleic acid-associated protein or protein domain, or a DNA-binding site.