Polycomb-Associated Non-Coding RNAs

Patent metadata

Field	Value
Publication number	US-2017037396-A1
Application number	US-201313921738-A
Country	US
Kind code	A1
Filing date	Jun 19, 2013
Priority date	Nov 12, 2010
Publication date	Feb 9, 2017
Grant date	—

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.

First claim

1 - 46 . (canceled)

47 . 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 at least one nucleotide of the oligonucleotide is a modified nucleotide, wherein the target gene is SMN1, SMN2, PTEN, FOXP3, UTRN, LAMA1, APOA1, ATP2A2, MBNL1, BDNF, or MECP2.

48 . The single stranded oligonucleotide of claim 47 , wherein the RNA is a long non-coding RNA (lncRNA).

49 . The single stranded oligonucleotide of claim 47 , wherein the PRC2-binding RNA regulates expression of the target gene in a cis manner.

50 . The single stranded oligonucleotide of claim 47 , wherein the PRC2-binding RNA is transcribed from the same strand as the target gene in a genomic region containing the target gene.

51 . The single stranded oligonucleotide of claim 47 , wherein the oligonucleotide has complementarity to a region of the PRC2-binding RNA transcribed from a portion of the target gene corresponding to an exon, intron-exon junction, a translation initiation region, a translation termination region, a promoter, an intron, a 5′-UTR, or a 3′-UTR.

52 . The single stranded oligonucleotide of claim 47 , wherein the oligonucleotide has complementarity to the PRC2-binding RNA in a region of the PRC2-binding RNA that forms a stem-loop structure.

53 . The single stranded oligonucleotide of claim 47 , wherein at least one nucleotide of the oligonucleotide is an RNA or DNA nucleotide.

54 . The single stranded oligonucleotide of claim 47 , 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.

55 . The single stranded oligonucleotide of claim 54 , wherein the ribonucleic acid analogue comprises a methylene bridge between the 2′-oxygen and the 4′-carbon.

56 . The single stranded oligonucleotide of claim 47 , wherein at least one nucleotide of the oligonucleotide comprises a modified sugar moiety.

57 . The single stranded oligonucleotide of claim 56 , wherein the modified sugar moiety comprises a 2′-O-methoxyethyl modified sugar moiety, a 2′-methoxy modified sugar moiety, a 2′-O-alkyl modified sugar moiety, or a bicyclic sugar moiety.

58 . The single stranded oligonucleotide of claim 47 comprising at least one modified internucleoside linkage.

59 . The single stranded oligonucleotide of claim 58 , 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.

60 . The single stranded oligonucleotide of claim 47 configured such that hybridization of the single stranded oligonucleotide to the PRC2-binding RNA does not activate an RNAse H pathway in a cell.

61 . The single stranded oligonucleotide of claim 47 configured such that hybridization of the single stranded oligonucleotide to the PRC2-binding RNA does not induce substantial′ cleavage or degradation of the PRC2-binding RNA in a cell.

62 . The single stranded oligonucleotide of claim 47 configured such that hybridization of the single stranded oligonucleotide to the PRC2-binding RNA interferes with interaction of the RNA with PRC2 in a cell.

63 . A compound comprising the single stranded oligonucleotide of claim 47 conjugated to a second 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.

64 . 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 inhibits expression of a target gene in cis, wherein the oligonucleotide has complementarity to the PRC2-binding RNA in a region of the PRC2-binding RNA that is transcribed from the sense strand of the target gene, wherein the target gene is SMN1, SMN2, PTEN, FOXP3, UTRN, LAMA1, APOA1, ATP2A2, MBNL1, BDNF, or MECP2.

65 . The single stranded oligonucleotide of claim 66 , wherein the RNA is a lncRNA.

66 . A method of inducing expression of a target gene in a cell, the method comprising delivering to the cell 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 inhibits expression of the target gene, wherein the oligonucleotide is complementary to and binds specifically to the PRC2-binding RNA, and wherein the target gene is SMN1, SMN2, PTEN, FOXP3, UTRN, LAMA1, APOA1, ATP2A2, MBNL1, BDNF, or MECP2.

67 . The method of claim 66 , wherein the RNA is a lncRNA.

68 . The method of claim 66 further comprising detecting expression of the PRC2-binding RNA in the cell, wherein expression of the PRC2-binding RNA in the cell indicates that the single stranded oligonucleotide is suitable for increasing expression of the target gene in the cell.

69 . The method of claim 66 further comprising detecting a change in expression of the target gene following delivery of the single stranded oligonucleotide to the cell, wherein an increase in expression of the target gene compared with an appropriate control cell indicates effectiveness of the single stranded oligonucleotide.

70 . The method of claim 66 further comprising detecting a change in recruitment of PRC2 to the target gene in the cell following delivery of the single stranded oligonucleotide to the cell, wherein a decrease in recruitment compared with an appropriate control cell indicates effectiveness of the single stranded oligonucleotide.

71 . The method of claim 66 , wherein the cell is in vitro.

72 . The method of claim 66 , wherein the cell is in vivo.

73 . A method of inducing expression of a target gene in a cell, the method comprising delivering to the cell 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 inhibits expression of the target gene, wherein the oligonucleotide is complementary to and binds specifically to the PRC2-binding lncRNA, wherein the delivery results in an increase in expression of the target gene of at least 50% compared with an appropriate control cell, and wherein the target gene is SMN1, SMN2, PTEN, FOXP3, UTRN, LAMA1, APOA1, ATP2A2, MBNL1, BDNF, or MECP2.

74 . The method of claim 73 , wherein the delivery results in an increase in expression of the target gene of at least 100% compared with an appropriate control cell.

75 . The method of claim 73 , wherein the RNA is a lncRNA.

Assignees

• Massachusetts Gen Hospital

Inventors

• Lee Jeannie T
• Zhao Jing
• Sarma Kavitha
• Borowsky Mark
• Ohsumi Toshiro Kendrick

Classifications

• C12N2310/20

  involving clustered regularly interspaced short palindromic repeats [CRISPR] · CPC title

• C12N2310/3231

  having an additional ring, e.g. LNA, ENA · CPC title

• C12N2310/11

  Antisense · CPC title

• C12N15/113 Primary

  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 title

• C12N2310/113

  targeting other non-coding nucleic acids, e.g. antagomirs · CPC title