Granted Patent
B2
US 12,331,346 · App. 18/588,930 · Granted Jun 17, 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 (29)
1. A method for detecting a methylated cytosine residue in a mammalian nucleic acid, comprising:
(a) contacting said mammalian nucleic acid comprising said methylated cytosine residue with a polypeptide having at least 90% sequence identity to: (i) a TET1 polypeptide; (ii) a TET2 polypeptide; (iii) a TET3 polypeptide; (iv) a CXXC4 polypeptide; (v) a catalytically active fragment of: (1) said TET1 polypeptide, (2) said TET2 polypeptide, (3) said TET3 polypeptide, or (4) said CXXC4 polypeptide; (vi) a variant thereof; or any combination thereof to generate a product nucleic acid comprising a modified methylated cytosine residue;
(b) derivatizing said modified methylated cytosine residue in said product nucleic acid with a glucose molecule or a glucose-derivative donor substrate; and
(c) performing a reaction on said product nucleic acid or a derivative thereof, to identify a presence of said methylated cytosine residue in said mammalian nucleic acid.
2. The method of claim 1 , wherein (a) comprises contacting said mammalian nucleic acid with a polypeptide having at least 90% sequence identity to any one of SEQ ID NOs: 27 or 29; a catalytically active fragment of a polypeptide having at least 90% sequence identity to any one SEQ ID NOs: 27 or 29; a variant thereof; or any combination thereof.
3. The method of claim 2 , wherein said polypeptide further comprises SEQ ID NO: 1.
4. The method of claim 1 , wherein (a) comprises contacting said mammalian nucleic acid with said TET2 polypeptide or said catalytically-active fragment of said TET2 polypeptide.
5. The method of claim 4 , 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.
6. The method of claim 5 , 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 further comprises SEQ ID NO: 1.
7. The method of claim 6 , 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 of SEQ ID NO: 28.
8. The method of claim 4 , wherein said TET2 polypeptide comprises a polypeptide comprising SEQ ID NO: 28.
9. The method of claim 1 , wherein said reaction is a hybridization reaction.
10. The method of claim 1 , wherein said reaction is an extension reaction.
11. The method of claim 1 , wherein said reaction is a sequencing reaction.
12. The method of claim 11 , wherein said sequencing reaction comprises whole genome sequencing.
13. The method of claim 11 , wherein said sequencing reaction comprises array hybridization.
14. The method of claim 1 , wherein said mammalian nucleic acid is a DNA molecule.
15. The method of claim 14 , wherein said DNA molecule comprises isolated genomic DNA.
16. The method of claim 1 , wherein said mammalian nucleic acid is an RNA molecule.
17. The method of claim 1 , further comprising identifying a location of said methylated cytosine residue in said mammalian nucleic acid.
18. The method of claim 1 , wherein said derivatizing comprises contacting said product nucleic acid with α-glucosyltransferase (AGT) or a conservatively-substituted variant thereof.
19. The method of claim 1 , wherein said derivatizing comprises contacting said product nucleic acid with β-glucosyltransferase (BGT) or a conservatively-substituted variant thereof.
20. The method of claim 19 , wherein said BGT comprises a polypeptide sequence of RCSB Accession No. 1J39, or a conservatively substituted variant thereof.
21. The method of claim 19 , wherein said BGT comprises residues 100-103, 231, and 311 relative to RCSB Accession No. 1J39.
22. The method of claim 18 , wherein said AGT comprises the polypeptide sequence of RCSB Accession No. 1YA6.
23. The method of claim 18 , wherein said AGT comprises residues 114-116 of AGT relative to RCSB Accession No. 1YA6.
24. The method of claim 19 , wherein said derivatizing comprises contacting said product nucleic acid with said BGT in a presence of uridine diphosphate glucose (UDPG) or an analog thereof.
25. The method of claim 1 , further comprising amplifying said product nucleic acid prior to (c).
26. The method of claim 25 , wherein said amplifying comprises a polymerase chain reaction (PCR).
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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