Granted Patent
B2
US 12,291,742 · App. 18/588,987 · Granted May 6, 2025
Selective oxidation of 5-methylcytosine by TET-family proteins
Inventors:
Anjana Rao (La Jolla, CA); Mamta Tahiliani (New York, NY); Kian Peng Koh (Jamaica Plain, MA); Suneet Agarwal (Belmont, MA); Aravind Iyer (Bethesda, MD)
Assignees:
The Children's Medical Center Corporation; The United States of America, As Represented by the Secretary, Department of Health & Human Services
C12Q1/6827C12N9/1007C12Q1/26C12Q1/6806C12Q1/6869G01N33/5308C12N2501/70C12N2501/71C12N2501/724C12Q2521/531C12Q2522/10C12Q2537/164C12Q2600/154
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Abstract
The present invention provides for novel methods for regulating and detecting the cytosine methylation status of DNA. The invention is based upon identification of a novel and surprising catalytic activity for the family of TET proteins, namely TET1, TET2, TEM3, and CXXC4. The novel activity is related to the enzymes being capable of converting the cytosine nucleotide 5-methylcytosine into 5-hydroxymethylcytosine by hydroxylation.
Claims (34)
1. A method comprising:
(a) contacting a nucleic acid molecule comprising cytosine and 5-methylcytosine with an isolated enzyme comprising a TET polypeptide, a catalytically active fragment thereof, a variant thereof, or any combination thereof in an amount effective to convert 5-methylcytosine of said nucleic acid molecule to an oxidized derivative thereof;
(b) converting cytosine of said nucleic acid molecule to uracil; and
(c) conducting a sequencing reaction to obtain a sequence of said nucleic acid molecule.
2. The method of claim 1 , wherein said isolated enzyme is present in an amount effective to convert all of said 5-methylcytosine of said nucleic acid molecule to said oxidized derivative thereof.
3. The method of claim 1 , wherein said isolated enzyme comprises an isolated dioxygenase.
4. The method of claim 3 , wherein said isolated dioxygenase comprises a recombinantly expressed dioxygenase.
5. The method of claim 1 , wherein said TET polypeptide comprises a polypeptide having at least 90% sequence identity to any one of SEQ ID NOs: 27, 28, or 29.
6. The method of claim 5 , wherein said TET polypeptide further comprises SEQ ID NO: 1.
7. The method of claim 1 , wherein said TET polypeptide comprises a TET2 polypeptide or a catalytically-active fragment thereof.
8. The method of claim 7 , wherein said TET2 polypeptide comprises a polypeptide having at least 90% sequence identity to SEQ ID NO: 28; or said catalytically active fragment of said TET2 polypeptide comprises a polypeptide having at least 90% sequence identity to a catalytically active fragment of SEQ ID NO: 28.
9. The method of claim 8 , wherein said polypeptide having at least 90% sequence identity to SEQ ID NO: 28 or said polypeptide having at least 90% sequence identity to said catalytically active fragment of SEQ ID NO: 28 comprises SEQ ID NO: 1.
10. The method of claim 9 , wherein said polypeptide having at least 90% sequence identity to SEQ ID NO: 28 comprises a conservatively-substituted variant of SEQ ID NO: 28 or wherein said polypeptide having at least 90% sequence identity to said catalytically active fragment of SEQ ID NO: 28 comprises a conservatively-substituted catalytically active fragment of SEQ ID NO: 28.
11. The method of claim 10 , wherein said TET2 polypeptide comprises a polypeptide comprising SEQ ID NO: 28.
12. The method of claim 1 , wherein said nucleic acid molecule comprises isolated eukaryotic genomic DNA.
13. The method of claim 12 , wherein said isolated eukaryotic genomic DNA is from a somatic cell.
14. The method of claim 1 , further comprising after (a) but before (b) adding a sugar residue to said oxidized derivative of said 5-methylcytosine in said nucleic acid molecule.
15. The method of claim 14 , wherein adding said sugar residue to said oxidized derivative of said 5-methylcytosine in said nucleic acid molecule comprises adding a glucose molecule or a glucose-derivative donor substrate to said oxidized derivative of said 5-methylcytosine in said nucleic acid molecule.
16. The method of claim 15 , wherein said adding said glucose molecule or said glucose-derivative donor substrate to said oxidized derivative of said 5-methylcytosine in said nucleic acid molecule comprises contacting said oxidized derivative of said 5-methylcytosine in said nucleic acid molecule with an a-glucosyltransferase (AGT) polypeptide or a variant thereof.
17. The method of claim 15 , wherein said adding said glucose molecule or said glucose-derivative donor substrate to said oxidized derivative of said 5-methylcytosine in said nucleic acid molecule comprises contacting said oxidized derivative of said 5-methylcytosine in said nucleic acid molecule with a ß-glucosyltransferase (BGT) polypeptide or a conservatively-substituted variant of said BGT polypeptide.
18. The method of claim 17 , wherein said BGT polypeptide comprises the polypeptide sequence of RCSB Accession No. 1J39.
19. The method of claim 17 , wherein said BGT polypeptide comprises residues 100 - 103 , 231 , and 311 relative to RCSB Accession No. 1J39.
20. The method of claim 16 , wherein said AGT polypeptide comprises residues 114 - 116 of AGT relative to RCSB Accession No. 1YA6.
21. A method comprising:
contacting a nucleic acid molecule comprising cytosine and 5-methylcytosine with an isolated enzyme comprising a TET polypeptide, a catalytically active fragment thereof, a variant thereof, or any combination thereof in an amount effective to convert all of said 5-methylcytosine of said nucleic acid molecule to an oxidized derivative thereof.
22. The method of claim 21 , further comprising adding a sugar residue to said oxidized derivative of said 5-methylcytosine in said nucleic acid molecule.
23. The method of claim 22 , wherein adding said sugar residue to said oxidized derivative of said 5-methylcytosine in said nucleic acid molecule comprises adding a glucose molecule or a glucose-derivative donor substrate to said oxidized derivative of said 5-methylcytosine in said nucleic acid molecule.
24. The method of claim 23 , wherein said adding said glucose molecule or said glucose-derivative donor substrate to said oxidized derivative of said 5-methylcytosine in said nucleic acid molecule comprises contacting said oxidized derivative of said 5-methylcytosine in said nucleic acid molecule with a B-glucosyltransferase (BGT) polypeptide or a conservatively-substituted variant of said BGT polypeptide.
25. The method of claim 24 , wherein said BGT polypeptide comprises the polypeptide sequence of RCSB Accession No. 1J39.
26. The method of claim 24 , wherein said BGT polypeptide comprises residues 100 - 103 , 231 , and 311 relative to RCSB Accession No. 1J39.
27. The method of claim 21 , wherein said TET polypeptide comprises a TET2 polypeptide or a catalytically-active fragment thereof.
28. The method of claim 27 , wherein said TET polypeptide or said catalytically-active fragment of said TET polypeptide further comprises SEQ ID NO: 1.
29. The method of claim 21 , wherein said TET polypeptide comprises a polypeptide having at least 90% sequence identity to any one of SEQ ID NOs: 27, 28, or 29.
30. The method of claim 21 , further comprising conducting a sequencing reaction to obtain a sequence of the nucleic acid molecule.
Assignments (5)
ASSIGNMENT OF ASSIGNOR'S INTEREST
Recorded Mar 7, 2024
From: AGARWAL, SUNEET
To: CHILDREN'S MEDICAL CENTER CORPORATION
Reel/Frame 066684/0152 →
ASSIGNMENT OF ASSIGNOR'S INTEREST
Recorded Mar 7, 2024
From: RAO, ANJANA; TAHILIANI, MAMTA; KOH, KIAN PENG
To: IMMUNE DISEASE INSTITUTE, INC.
Reel/Frame 066684/0155 →
MERGER
Recorded Mar 7, 2024
From: IMMUNE DISEASE INSTITUTE, INC.
To: THE CHILDREN'S HOSPITAL CORPORATION
Reel/Frame 066685/0566 →
ASSIGNMENT OF ASSIGNOR'S INTEREST
Recorded Mar 7, 2024
From: THE CHILDREN'S HOSPITAL CORPORATION
To: CHILDREN'S MEDICAL CENTER CORPORATION
Reel/Frame 066685/0581 →
ASSIGNMENT OF ASSIGNOR'S INTEREST
Recorded Mar 7, 2024
From: IYER, ARAVIND
To: THE UNITED STATES OF AMERICA, AS REPRESENTED BY THE SECRETARY, DEPARTMENT OF HEALTH AND HUMAN SERVICES
Reel/Frame 066685/0584 →
Continuity (12)
Continuation
17350181
· Jun 17, 2021
Continuation
13120861
Provisional Application
61121844
· Dec 11, 2008
Provisional Application
61100995
· Sep 29, 2008
Provisional Application
61100503
· Sep 26, 2008
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