RNA Interactome of Polycomb Repressive Complex 1 (PRC1)

Abstract

This invention relates to polycomb-associated RNAs, libraries and fragments of those RNAs, inhibitory nucleic acids and methods and compositions for targeting RNAs, and methods of use thereof.

1 .- 36 . (canceled) 
     
     
         37 . A method of reducing expression of a target interleukin 1 receptor-associated kinase 1 (IRAK1) gene in a cell, the method comprising delivering to the cell a single stranded oligonucleotide of 15 to 40 nucleotides in length having a region of complementarity that is complementary with at least 15 contiguous nucleotides of an IRAK1 RNA, wherein the oligonucleotide binds to or within 500 nt of SEQ ID NOs: 5874, 5875, 17389, 17390, or 17391, wherein PRC1 binding to the IRAK1 RNA is disrupted. 
     
     
         38 .- 41 . (canceled) 
     
     
         42 . The method of  claim 37 , wherein the cell is in vitro. 
     
     
         43 . The method of  claim 37 , wherein the cell is in vivo. 
     
     
         44 . The method of  claim 37 , wherein at least one nucleotide of the oligonucleotide is a modified nucleotide. 
     
     
         45 .- 48 . (canceled) 
     
     
         49 . The method of  claim 37 , wherein the oligonucleotide has complementarity to the IRAK1 RNA in a region of the IRAK1 RNA that forms a stem-loop structure. 
     
     
         50 . (canceled) 
     
     
         51 . The method of  claim 37 , 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. 
     
     
         52 . The method of  claim 51 , wherein the ribonucleic acid analogue comprises a methylene bridge between the 2′-oxygen and the 4′-carbon. 
     
     
         53 . The method of  claim 37 , wherein at least one nucleotide of the oligonucleotide comprises a modified sugar moiety. 
     
     
         54 . The method of  claim 53 , 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. 
     
     
         55 . The method of  claim 37 , wherein the oligonucleotide comprises at least one modified internucleoside linkage. 
     
     
         56 . The method of  claim 55 , 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. 
     
     
         57 . The method of  claim 37 , wherein the oligonucleotide is configured such that hybridization of the single stranded oligonucleotide to the PRC1-binding RNA does not activate an RNAse H pathway in the cell. 
     
     
         58 .- 61 . (canceled) 
     
     
         62 . The method of  claim 37 , wherein the cell is a cell of a male subject. 
     
     
         63 .- 67 . (canceled) 
     
     
         68 . A method of isolating RNA sequences that interact with a selected protein, e.g., with chromatin complexes, in a cell, the method comprising:
 providing a cell expressing (i) a biotin ligase, e.g., BirA, and (ii) the protein of interest comprising a biotinylation sequence;   exposing the cells to UV-crosslinking;   lysing the cells,   isolating protein-RNA complexes from the lysed cells, e.g., using avidin purification, e.g., streptavidin beads;   washing the complexes in protein-denaturing conditions, e.g., high salt and detergent, e.g., using 8 M urea+0.1% SDS; and   isolating the protein-RNA complexes.   
     
     
         69 .- 75 . (canceled) 
     
     
         76 . A method for treating a subject with systemic lupus erythematosis, the method comprising administering a therapeutically effective amount of an inhibitory nucleic acid targeting a PRC1-binding region on IRAK1 RNA, preferably wherein the PRC1 binding region comprises SEQ ID NO:5874, 5875, or 17389-17391. 
     
     
         77 . The method of  claim 76 , comprising administering an inhibitory nucleic acid targeting a sequence within the 3′UTR of IRAK1. 
     
     
         78 . (canceled) 
     
     
         79 . The method of  claim 76 , wherein the inhibitory nucleic acid comprises at least one locked nucleotide (LNA). 
     
     
         80 .- 83 . (canceled) 
     
     
         84 . The method of  claim 37 , wherein the oligonucleotide binds to or within 100 nt of SEQ ID NOs:5874, 5875, 17389, 17390, or 17391. 
     
     
         85 . The method of  claim 37 , wherein the oligonucleotide binds to or within SEQ ID NOs: 5874, 5875, 17389, 17390, or 17391.