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 is complementary to and binds to or within 500 nt of SEO 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, 17389, 17390, or 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.