IP Library › Granted Patent US 12,522,823
Granted Patent B2
US 12,522,823 · App. 17/698,917 · Granted Jan 13, 2026

Methods and compositions for modulating gene expression

Inventors: David Arthur Berry (Chestnut Hill, MA); Rahul Karnik (Cambridge, MA); Laura Gabriela Lande (Chestnut Hill, MA)
Assignee: FLAGSHIP PIONEERING INNOVATIONS V, INC.
C12N15/113A61K35/12C12N9/00C12N9/1007C12N9/22C12N9/80C12N15/63C12N15/85C12N15/87C12N15/90C12N15/907C12Y201/01037C12Y201/01043C12Y305/01098A01K2217/056A01K2227/706A01K2267/0318C07K2319/00C07K2319/85C12N2310/14C12N2310/20
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Quick Facts
Patent No.
US 12,522,823
App. No.
17/698,917
Granted
Jan 13, 2026
Kind
B2
Abstract

The present disclosure provides compositions with a modulating gene expression and methods for modulating transcription.

Claims (20)

1 . A method of decreasing expression of a gene within a cell, the gene being within an anchor sequence-mediated conjunction that comprises a first anchor sequence, a second anchor sequence, and an internal enhancing sequence, the method comprising a step of:

contacting the cell with a composition comprising a targeting element or a nucleic acid encoding the targeting element, wherein the targeting element comprises a zinc finger array which targets the first anchor sequence, the second anchor sequence, or both of the first anchor sequence and the second anchor sequence, wherein the first and second anchor sequences each comprise a CTCF binding site, and wherein the CTCF binding site has the sequence of SEQ ID NO: 1 or SEQ ID NO: 2.

2 . The method of claim 1 , wherein neither the first nor second anchor sequences are located within an enhancer or a promoter.

3 . The method of claim 1 , wherein the gene is FOXJ3, MYC, SHMT2, or CDK6.

4 . The method of claim 1 , wherein the cell is a human cell.

5 . The method of claim 1 , wherein contacting comprises transfecting the cell with the composition.

6 . The method of claim 1 , wherein the composition physically interferes with formation and/or maintenance of the anchor sequence-mediated conjunction.

7 . The method of claim 1 , wherein the gene is an oncogene, a tumor suppressor, or a gene associated with a nucleotide repeat.

8 . The method of claim 1 , wherein the targeting element is linked to an effector domain with an amino acid linker.

9 . The method of claim 8 , wherein the effector domain comprises a DNA methyltransferase, histone methyltransferase, acetyltransferase, or deacetylase.

10 . The method of claim 8 , wherein the effector domain comprises a KRAB domain.

11 . The method of claim 8 , wherein the effector domain promotes DNA methylation.

12 . The method of claim 1 , wherein the CTCF binding site has the sequence of SEQ ID NO: 1.

13 . The method of claim 1 , wherein the CTCF binding site has the sequence of SEQ ID NO: 2.

14 . The method of claim 1 , wherein the gene is separated from the first anchor sequence or the second anchor sequence by about 100 bp to about 500 Mb.

15 . The method of claim 1 , wherein the anchor sequences are between 20-80 nucleotides.

16 . The method of claim 1 , wherein the targeting element binds the sequence of SEQ ID NO: 1 or SEQ ID NO: 2.

17 . The method of claim 1 , wherein the targeting element binds a sequence proximal to SEQ ID NO: 1 or SEQ ID NO: 2.

18 . The method of claim 1 , which comprises contacting the cell with the nucleic acid encoding the targeting element.

19 . The method of claim 1 , wherein the nucleic acid comprises mRNA.

Assignments (6)
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Dec 15, 2025
From: FLAGSHIP PIONEERING, INC.
To: FLAGSHIP PIONEERING INNOVATIONS V, INC.
Reel/Frame 073213/0846 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Mar 26, 2025
From: KARNIK, RAHUL
To: OMEGA THERAPEUTICS, INC.
Reel/Frame 070639/0331 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Mar 26, 2025
From: LANDE-DINER, LAURA GABRIELA; BERRY, DAVID ARTHUR
To: FLAGSHIP PIONEERING, INC.
Reel/Frame 070639/0392 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Mar 26, 2025
From: OMEGA THERAPEUTICS, INC.
To: FLAGSHIP PIONEERING, INC.
Reel/Frame 070639/0514 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Mar 26, 2025
From: FLAGSHIP PIONEERING, INC.
To: FLAGSHIP PIONEERING INNOVATIONS V, INC.
Reel/Frame 070639/0543 →
SECURITY INTEREST Recorded Feb 10, 2025
From: OMEGA THERAPEUTICS, INC.
To: PIONEERING MEDICINES 08- B, INC.
Reel/Frame 070167/0243 →
Continuity (7)
Continuation 15821632 · Nov 22, 2017
Continuation PCTUS2017050553 · Sep 7, 2017
Provisional Application 62542703 · Aug 8, 2017
Provisional Application 62439327 · Dec 27, 2016
Provisional Application 62416501 · Nov 2, 2016
Provisional Application 62384603 · Sep 7, 2016
Related Publication 20230054672A1 · Feb 23, 2023
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