Selective Reactivation of Genes on the Inactive X Chromosome

Abstract

Methods and compositions for selectively reactivating genes on the inactive X chromosome (Xi) in a locus-specific manner, e.g., genes associated with X-linked diseases, e.g., Rett Syndrome, Factor VIII or IX deficiency, Fragile X Syndrome, Duchenne muscular dystrophy, and PNH, in heterozygous females.

1 . A method of activating an inactive X-linked allele in a cell,
 preferably a cell of a female heterozygous subject, the method comprising administering to the cell   an inhibitory oligonucleotide comprising at least one bridged nucleotide targeting a polycomb-associated RNA (pa-RNA) associated with the X-linked allele, wherein the pa-RNA associated with the X-linked allele intersects an EZH2 or SUZ12 binding site within 100 kB of the transcription start site of the allele.   
     
     
         2 . The method of  claim 1 , wherein the inactive X-linked allele is associated with an X-linked disorder, and the oligonucleotide is administered in a therapeutically effective amount. 
     
     
         3 . The method of  claim 1 , wherein the cell is in a living subject. 
     
     
         4 . The method of  claim 1 , wherein the inhibitory oligonucleotide is complementary to at least 8 consecutive nucleotides of a paRNA as set forth in SEQ ID NOs: 1-226, 867-1363, or 2838-5932, or 10169. 
     
     
         5 . The method of  claim 1 , wherein the oligonucleotide does not comprise three or more consecutive guanosine nucleotides. 
     
     
         6 . The method of  claim 1 , wherein the oligonucleotide does not comprise four or more consecutive guanosine nucleotides. 
     
     
         7 . The method of  claim 1 , wherein the oligonucleotide is 8 to 30 nucleotides in length. 
     
     
         8 . The method of  claim 1 , wherein at least one nucleotide of the oligonucleotide is a nucleotide analogue. 
     
     
         9 . The method of  claim 1 , wherein at least one nucleotide of the oligonucleotide comprises a 2′ O-methyl. 
     
     
         10 . The method of  claim 1 , wherein each nucleotide of the oligonucleotide comprises a 2′ O-methyl. 
     
     
         11 . The method of  claim 1 , wherein the oligonucleotide further comprises at least one ribonucleotide or at least one deoxyribonucleotide. 
     
     
         12 . The method of  claim 1 , wherein the at least one bridged nucleotide is a LNA nucleotide, a cEt nucleotide or a ENA modified nucleotide. 
     
     
         13 . The method of  claim 1 , wherein each nucleotide of the oligonucleotide is a LNA nucleotide. 
     
     
         14 . The method of  claim 1 , wherein one or more of the nucleotides of the oligonucleotide comprise 2′-fluoro-deoxyribonucleotides. 
     
     
         15 . The method of  claim 1 , wherein one or more of the nucleotides of the oligonucleotide comprise 2′-O-methyl nucleotides. 
     
     
         16 . The method of  claim 1 , wherein one or more of the nucleotides of the oligonucleotide comprise ENA nucleotide analogues. 
     
     
         17 . The method of  claim 1 , wherein one or more of the nucleotides of the oligonucleotide comprise LNA nucleotides. 
     
     
         18 . The method of  claim 1 , wherein the nucleotides of the oligonucleotide comprise comprising phosphorothioate internucleotide linkages between at least two nucleotides. 
     
     
         19 . The method of  claim 1 , wherein the nucleotides of the oligonucleotide comprise phosphorothioate internucleotide linkages between all nucleotides. 
     
     
         20 .- 37 . (canceled) 
     
     
         38 . The method of  claim 1 , wherein the inactive X-linked allele is MECP2, and wherein the pa-RNA associated with the X-linked allele comprises SEQ ID NO:10169. 
     
     
         39 . The method of  claim 2 , wherein the inactive X-linked allele is MECP2, and wherein the pa-RNA associated with the X-linked allele comprises SEQ ID NO:10169.