Modulation of enhancer rna mediated gene expression

Abstract

Disclosed herein are methods and compounds for inhibiting gene expression by inhibiting enhancer RNAs (eRNAs). Such methods and compounds are useful for reducing expression of certain genes, many of which are associated with a variety of diseases and disorders.

1 . A method of inhibiting gene expression in a cell comprising contacting the cell with an antisense oligonucleotide inhibitor of an enhancer RNA (eRNA) that enhances transcription of matrix metalloproteinase 9 (MMP9), thereby inhibiting expression of one or more genes in the cell,
 wherein the antisense compound comprises:
 a gap segment consisting of linked deoxynucleosides; 
 a 5′ wing segment consisting of linked nucleosides; and 
 a 3′ wing segment consisting of linked nucleosides; 
   wherein the gap segment is positioned between the 5′ wing segment and the 3′ wing segment and wherein each nucleoside of each wing segment comprises a modified sugar.   
     
     
         2 . The method of  claim 1 , wherein the eRNA is transcribed from a genomic enhancer sequence or region. 
     
     
         3 . The method of  claim 2 , wherein the cell is mammalian. 
     
     
         4 . The method of  claim 1 , wherein the eRNA transcription is initiated from a RNA polymerase II (PolII) binding site and is capable of elongating bidirectionally. 
     
     
         5 . The method of  claim 1 , wherein the eRNA is capable of enhancing transcription of the one or more genes MMP9 gene. 
     
     
         6 . The method of  claim 2 , wherein the genomic enhancer sequence or region has a higher level of monomethylated lysine 4 of histone 3 (H3K4me1) than trimethylated lysine 4 of histone 3 (H3K4me3). 
     
     
         7 . The method of  claim 2 , wherein the genomic enhancer sequence or region is enriched for bound RNA polymerase II (PolII). 
     
     
         8 . The method of  claim 2 , wherein the genomic enhancer sequence or region is enriched for bound transcriptional co-activator p300/CBP. 
     
     
         9 . The method of  claim 2 , wherein the genomic enhancer sequence or region is enriched for bound Rev-Erbα or Rev-Erbβ. 
     
     
         10 . The method of  claim 2 , wherein the genomic enhancer sequence or region is enriched for bound estrogen receptor. 
     
     
         11 . The method of  claim 10 , wherein the estrogen receptor is bound to estradiol. 
     
     
         12 . The method of  claim 1 , wherein the eRNA has a relatively short half-life compared to mRNA. 
     
     
         13 . The method of  claim 12 , wherein the eRNA has a half-life of less than about 10-30 minutes. 
     
     
         14 . (canceled) 
     
     
         15 . (canceled) 
     
     
         16 . The method of  claim 2 , wherein the transcriptional start site of the one or more genes is located on a chromosome at least about 1 kilobase (kb) from the genomic enhancer sequence or region. 
     
     
         17 . The method of  claim 1 , wherein the eRNA is not polyadenylated. 
     
     
         18 . The method of  claim 1 , wherein the cell is a hematopoietic cell. 
     
     
         19 . The method of  claim 18 , wherein the hematopoietic cell is a monocyte. 
     
     
         20 . The method of  claim 18 , wherein the hematopoietic cell is a macrophage. 
     
     
         21 . The method of  claim 1 , wherein the cell is a neuron. 
     
     
         22 . The method of  claim 1 , wherein the cell is a breast cell. 
     
     
         23 . The method of  claim 1 , wherein the cell is a cancer cell. 
     
     
         24 . The method of  claim 1 , wherein the cell contacted with a antisense oligonucleotide of an enhancer RNA (eRNA) is in a subject. 
     
     
         25 . (canceled) 
     
     
         26 . The method of  claim 1 , wherein the antisense compound is single-stranded. 
     
     
         27 . The method of  claim 26 , wherein the antisense compound is double-stranded. 
     
     
         28 . The method of  claim 1 , wherein the antisense compound is modified. 
     
     
         29 .- 40 . (canceled) 
     
     
         41 . The method of  claim 1 , wherein the antisense compound comprises:
 a gap segment consisting of ten linked deoxynucleosides;   a 5′ wing segment consisting of 3 linked nucleosides; and   a 3′ wing segment consisting of 3 linked nucleosides;   wherein the gap segment is positioned between the 5′ wing segment and the 3′ wing segment, wherein each nucleoside of each wing segment comprises a 2′-O-methoxyethyl sugar or a constrained ethyl sugar; and wherein each internucleoside linkage is a phosphorothioate linkage.   
     
     
         42 . The method of  claim 41 , wherein the 3 linked nucleosides of the 5′ wing segment comprise a 2′-O-methoxyethyl sugar, a constrained ethyl sugar, and a constrained ethyl sugar in the 5′ to 3′ direction, and the 3 linked nucleosides of the 3′ wing segment comprise a constrained ethyl sugar, a constrained ethyl sugar, and a 2′-O-methoxyethyl sugar in the 5′ to 3′ direction. 
     
     
         43 . The method of  claim 1 , wherein the antisense oligonucleotide comprises a gap segment of ten 2′-deoxynucleotides positioned between wing segments of five 2′-MOE nucleotides. 
     
     
         44 .- 54 . (canceled) 
     
     
         55 . A compound comprising an antisense oligonucleotide inhibitor of a MMP9 enhancer RNA (eRNA), wherein said MMP9 eRNA comprises the nucleic acid sequence of SEQ ID NO:1, wherein the antisense compound comprises:
 a gap segment consisting of linked deoxynucleosides;   a 5′ wing segment consisting of linked nucleosides; and   a 3′ wing segment consisting of linked nucleosides;   wherein the gap segment is positioned between the 5′ wing segment and the  3 ′ wing segment and wherein each nucleoside of each wing segment comprises a modified sugar.   
     
     
         56 .- 87 . (canceled)