Granted Patent
B2
US 12,338,489 · App. 18/739,955 · Granted Jun 24, 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)
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, TET3, 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 (30)
1. A method of converting a methylated cytosine residue in an isolated eukaryotic nucleic acid molecule to a modified cytosine residue, said method comprising:
(a) contacting said isolated eukaryotic nucleic acid molecule with a polypeptide that converts said methylated cytosine residue to said modified cytosine residue,
wherein said polypeptide comprises a TET1 polypeptide, a TET2 polypeptide, a TET3 polypeptide, or a CXXC4 polypeptide, or a catalytically active fragment thereof, and
(b) contacting said isolated eukaryotic nucleic acid molecule with a glucosyltransferase polypeptide to derivatize said modified cytosine residue, wherein said glucosyltransferase polypeptide comprises β-glucosyltransferase (BGT) or α-glucosyltransferase (AGT).
2. The method of claim 1 , wherein said polypeptide comprises said TET1 polypeptide or said catalytically active fragment of said TET1 polypeptide.
3. The method of claim 2 , wherein: said TET1 polypeptide comprises a polypeptide having at least 90% sequence identity to: SEQ ID NO:27; or said catalytically active fragment is a catalytically active fragment of said TET1 polypeptide comprising a polypeptide having at least 90% sequence identity to SEQ ID NO:27.
4. The method of claim 1 , further comprising detecting a methylation status of said isolated eukaryotic nucleic acid molecule based on a presence or an absence of said modified cytosine residue.
5. The method of claim 4 , wherein said detecting comprises contacting said isolated eukaryotic nucleic acid molecule with bisulfite.
6. The method of claim 1 , wherein (b) further comprises contacting said isolated eukaryotic nucleic acid molecule with a glucose molecule or a glucose-derivative donor substrate.
7. The method of claim 1 , wherein said glucosyltransferase polypeptide comprises said BGT.
8. The method of claim 1 , wherein said glucosyltransferase polypeptide comprises said AGT.
9. The method of claim 1 , wherein said isolated eukaryotic nucleic acid molecule is obtained from a cell sample or a tissue sample of a subject.
10. The method of claim 1 , wherein said isolated eukaryotic nucleic acid molecule is obtained from an extracellular fluid sample.
11. The method of claim 1 , wherein said isolated eukaryotic nucleic acid molecule is obtained from a subject having cancer or suspected of having cancer.
12. The method of claim 1 , wherein said polypeptide comprises said TET2 polypeptide or said catalytically active fragment of said TET2 polypeptide.
13. The method of claim 12 , wherein: said TET2 polypeptide comprises a polypeptide having at least 90% sequence identity to: SEQ ID NO:28; or said catalytically active fragment is a catalytically active fragment of said TET2 polypeptide comprising a polypeptide having at least 90% sequence identity to a catalytically active fragment of SEQ ID NO:28.
14. The method of claim 13 , 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 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 variant of SEQ ID NO: 28 .
15. The method of claim 12 , wherein said polypeptide comprises said TET2 polypeptide, wherein said TET2 polypeptide comprises SEQ ID NO: 28.
16. The method of claim 1 , wherein said polypeptide comprises said TET3 polypeptide or said catalytically active fragment of said TET3 polypeptide.
17. The method of claim 1 , wherein said polypeptide comprises said CXXC4 polypeptide or said catalytically active fragment of said CXXC4 polypeptide.
18. The method of claim 1 , further comprising indirectly labeling said modified cytosine residue with a fluorophore or a biotinyl group.
19. The method of claim 18 , wherein said modified cytosine residue is indirectly labeled with said fluorophore.
20. The method of claim 18 , wherein said modified cytosine residue is indirectly labeled with said biotinyl group.
21. The method of claim 1 , wherein said polypeptide comprises said CXXC4 polypeptide or said catalytically active fragment of said CXXC4 polypeptide, wherein:
said CXXC4 polypeptide comprises a polypeptide having at least 90% sequence identity to SEQ ID NO: 29; or said catalytically active fragment is a catalytically active fragment of said CXXC4 polypeptide comprising a polypeptide having at least 90% sequence identity to a catalytically active fragment of SEQ ID NO: 29.
22. The method of claim 1 , wherein said polypeptide comprises SEQ ID NO: 1 or a variant thereof.
23. The method of claim 1 , wherein said glucosyltransferase polypeptide comprises a conservatively-substituted variant of BGT.
24. The method of claim 1 , wherein said glucosyltransferase polypeptide comprises said BGT, wherein said BGT comprises the polypeptide sequence of RCSB Accession No. 1J39, or a conservatively substituted variant thereof.
25. The method of claim 24 , wherein said BGT comprises residues 100-103, 231, and 311 relative to RCSB Accession No. 1J39.
26. The method of claim 1 , wherein said modified cytosine residue is a hydroxymethylated cytosine residue.
Assignments (5)
ASSIGNMENT OF ASSIGNOR'S INTEREST
Recorded Jul 26, 2024
From: AGARWAL, SUNEET
To: CHILDREN'S MEDICAL CENTER CORPORATION
Reel/Frame 068091/0511 →
ASSIGNMENT OF ASSIGNOR'S INTEREST
Recorded Jul 26, 2024
From: IYER, ARAVIND
To: THE UNITED STATES OF AMERICA, AS REPRESENTED BY THE SECRETARY, DEPARTMENT OF HEALTH AND HUMAN SERVICES
Reel/Frame 068091/0518 →
ASSIGNMENT OF ASSIGNOR'S INTEREST
Recorded Jul 26, 2024
From: RAO, ANJANA; TAHILIANI, MAMTA; KOH, KIAN PENG
To: IMMUNE DISEASE INSTITUTE, INC.
Reel/Frame 068091/0521 →
MERGER
Recorded Jul 26, 2024
From: IMMUNE DISEASE INSTITUTE, INC.
To: THE CHILDREN'S HOSPITAL CORPORATION
Reel/Frame 068091/0569 →
ASSIGNMENT OF ASSIGNOR'S INTEREST
Recorded Jul 26, 2024
From: THE CHILDREN'S HOSPITAL CORPORATION
To: CHILDREN'S MEDICAL CENTER CORPORATION
Reel/Frame 068091/0584 →
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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