Polycomb-associated non-coding RNAs

• US 10,358,644 B2
• Filed: 11/22/2017
• Issued: 07/23/2019
• Est. Priority Date: 11/12/2010
• Status: Active Grant

• Current Assignee: The General Hospital Corporation (Mass General Brigham, Inc.)
• Original Assignee: The General Hospital Corporation (Mass General Brigham, Inc.)
• Inventors: Lee, Jeannie T., Zhao, Jing, Sarma, Kavitha, Borowsky, Mark, Ohsumi, Toshiro Kendrick
• Primary Examiner(s): Bowman, Amy H
• Application Number:
  US15/821,039
• Publication Number:
  US 20180245081A1
• Time in Patent Office: 608 Days
• CPC Class Codes: C12N 15/113 Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing when used in plants C12N15/8218
• CPC Class Codes: C12N 2310/11 Antisense
• CPC Class Codes: C12N 2310/113 targeting other non-coding nucleic acids, e.g. antagomirs
• CPC Class Codes: C12N 2310/20 involving clustered regularly interspaced short palindromic repeats [CRISPRs]
• CPC Class Codes: C12N 2310/3231 having an additional ring, e.g. LNA, ENA

Abstract

This invention relates to polycomb-associated long non-coding RNAs (lncRNAs), libraries and fragments of those ncRNAs, inhibitory nucleic acids and methods and compositions for targeting lncRNAs.

Claims

1. A single stranded oligonucleotide of 5 to 40 nucleotides in length having a region of complementarity that is complementary with at least 5 contiguous nucleotides of a PRC2-binding RNA that regulates expression of a target gene, wherein the oligonucleotide is complementary to and binds specifically within a PRC2-binding region of the PRC2-binding RNA and interferes with binding of PRC2 to the PRC2-binding region without inducing degradation of the PRC2-binding RNA, wherein the PRC2-binding region has a nucleotide sequence protected from nucleases during an RNA immunoprecipitation procedure using an antibody directed against PRC2, wherein the PRC2-binding RNA is transcribed from a sequence of the chromosomal locus of the target gene, wherein the target gene is G6PC or OTC, and wherein the single stranded oligonucleotide comprises at least one nucleotide having a 2′

-fluoro and/or at least one nucleotide having a 2′

-O-methoxyethyl modified sugar moiety and/or at least one ribonucleic acid analogue having a ribose ring having a bridge between its 2′

-oxygen and 4′

-carbon.

2. The single stranded oligonucleotide of claim 1, wherein at least one nucleotide of the oligonucleotide has a 2′

-O-methoxyethyl modified sugar moiety.

3. The single stranded oligonucleotide of claim 1, wherein at least one nucleotide of the oligonucleotide is a ribonucleic acid analogue comprising a ribose ring having a bridge between its 2′

-oxygen and 4′

-carbon.

4. The single stranded oligonucleotide of claim 3, wherein the ribonucleic acid analogue comprises a methylene bridge between the 2′

-oxygen and the 4′

-carbon.

5. The single stranded oligonucleotide of claim 1, wherein at least one nucleotide of the oligonucleotide has a 2′

-O-methoxyethyl modified sugar moiety and at least one nucleotide of the oligonucleotide is a ribonucleic acid analogue comprising a ribose ring having a bridge between its 2′

-oxygen and 4′

-carbon.

6. The single stranded oligonucleotide of claim 1, comprising at least one modified internucleoside linkage.

7. The single stranded oligonucleotide of claim 6, wherein the at least one modified internucleoside linkage is selected from phosphorothioate, phosphorodithioate, alkylphosphonothioate, phosphoramidate, carbamate, carbonate, phosphate triester, acetamidate, carboxymethyl ester, and combinations thereof.

8. The single stranded oligonucleotide of claim 2, wherein the oligonucleotide comprises at least one modified internucleoside linkage.

9. The single stranded oligonucleotide of claim 8, wherein the at least one modified internucleoside linkage is a phosphorothioate.

10. The single stranded oligonucleotide of claim 3, wherein the oligonucleotide comprises at least one modified internucleoside linkage.

11. The single stranded oligonucleotide of claim 10, wherein the at least one modified internucleoside linkage is a phosphorothioate.

12. The single stranded oligonucleotide of claim 5, wherein the oligonucleotide comprises at least one modified internucleoside linkage.

13. The single stranded oligonucleotide of claim 12, wherein the at least one modified internucleoside linkage is a phosphorothioate.

14. The single stranded oligonucleotide of claim 1, wherein at least one nucleotide of the oligonucleotide has a 2′

-O-methoxyethyl modified sugar moiety and at least one nucleotide of the oligonucleotide is a ribonucleic acid analogue comprising a ribose ring having a bridge between its 2′

-oxygen and 4′

-carbon, and wherein each internucleoside linkage of the oligonucleotide is a modified internucleoside linkage.

15. The single stranded oligonucleotide of claim 14, wherein the modified internucleoside linkage is a phosphorothioate.

16. The single stranded oligonucleotide of claim 1, wherein at least one nucleotide of the oligonucleotide is an RNA or DNA nucleotide.

17. The single stranded oligonucleotide of claim 1, wherein the RNA is a long non-coding RNA (lncRNA).