Super-enhancers and methods of use thereof

Abstract

The present invention relates in some aspects to super-enhancers and related compositions, methods, and agents that are useful for modulating expression of cell type-specific genes that are required for maintenance of cell identity (e.g., embryonic stem cell identity) or maintenance of a disease state (e.g., cancer).

1 .- 26 . (canceled) 
     
     
         27 . A cell transfected with a nucleic acid construct comprising a super-enhancer, the super-enhancer comprising:
 a genomic region of deoxyribonucleic acid (DNA) that contains at least two enhancers, wherein the genomic region is occupied when present within a cell by an order of magnitude more transcriptional coactivator or chromatin regulator than the average single enhancer within the cell,   
       wherein upon transfection of the cell with the nucleic acid construct endogenous transcriptional coactivators and chromatin regulators within the cell co-occupy the enhancers and the active transcription start sites of the target gene to stimulate high levels of expression of the target gene within the cell. 
     
     
         28 . The cell of  claim 27 , wherein the cell is a mammalian cell. 
     
     
         29 . The cell of  claim 27 , wherein the cell is a human cell. 
     
     
         30 . The cell of  claim 27 , wherein the cell is an embryonic stem cell or embryonic stem cell-like cell. 
     
     
         31 . The cell of  claim 27 , wherein the cell is a muscle cell. 
     
     
         32 . The cell of  claim 31 , wherein the muscle cell is a myotube. 
     
     
         33 . The cell of  claim 27 , wherein the cell is a B cell. 
     
     
         34 . The cell of  claim 33 , wherein the B cell is a Pro-B cell. 
     
     
         35 . A method of increasing the level of expression of a target gene in a cell, comprising transfecting a cell under conditions suitable for expression of the target gene with a nucleic acid expression construct comprising a nucleic acid sequence encoding the target gene operatively linked to a super-enhancer, wherein upon transfection of the cell endogenous transcriptional coactivators and chromatin regulators within the cell co-occupy enhancers clustered within the super-enhancer by an order of magnitude more than the average single enhancer within the cell and active transcription start sites of the target gene to increase the level of expression of the target gene within the cell. 
     
     
         36 . The method of  claim 35 , wherein the level of expression of the target gene is increased 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, or more within the cell. 
     
     
         37 . A kit for increasing the expression of a target gene in a cell, comprising: (a) a nucleic acid construct comprising an artificial super-enhancer operatively linked to the target gene; (b) a population of cells suitable for expression of said target gene; and (c) a reagent for transfecting said population of cells with said nucleic acid construct. 
     
     
         38 . A method of identifying a super-enhancer in a cell, comprising: (a) identifying a genomic region of DNA within said cell characterized by a cluster of enhancers each of which bind a cognate transcription factor capable of interacting with Mediator to stimulate transcription of the target gene within said cell; (b) measuring in the identified genomic region a level of Mediator; and (c) identifying the genomic region as a super-enhancer if the level of Mediator identified in the genomic region is an order of magnitude greater than the level of Mediator occupying the average single enhancer. 
     
     
         39 .- 40 . (canceled) 
     
     
         41 . The method of  claim 38 , wherein the super-enhancer is identified by performing chromatin immunoprecipitation high-throughput sequencing (ChIP-Seq). 
     
     
         42 .- 50 . (canceled) 
     
     
         51 . A method of treating a proliferative disorder in a patient in need of such treatment, said proliferative disorder characterized by an oncogene-associated super-enhancer occupied by more Mediator or BRD4 than an average single enhancer, comprising administering to the patient an effective amount of an agent that disrupts the function of the oncogene-associated super-enhancer, thereby selectively inhibiting proliferation of the oncogene in the patient. 
     
     
         52 . The method of  claim 51 , wherein the proliferative disorder is a hematological malignancy. 
     
     
         53 . The method of  claim 51 , wherein the proliferative disorder is selected from the group consisting of acute lymphoblastic leukemia (ALL), acute myelogenous leukemia (AML), chronic myelogenous leukemia (CML), chronic lymphocytic leukemia (CLL), hairy cell leukemia, Hodgkin's lymphoma, non-Hodgkin's lymphoma, cutaneous T-cell lymphoma (CTCL), peripheral T-cell lymphoma (PTCL), Mantle cell lymphoma, B-cell lymphoma, acute lymphoblastic T cell leukemia (T-ALL), acute promyelocytic leukemia, and multiple myeloma. 
     
     
         54 . The method of  claim 51 , wherein the agent is a BRD4 inhibitor. 
     
     
         55 . The method of  claim 51 , wherein the agent is JQ1. 
     
     
         56 . (canceled) 
     
     
         57 . A method of treating multiple myeloma involving an IGH-MYC locus that results in aberrant expression of oncogene c-Myc, comprising administering to a patient in need of such treatment an effective amount of an agent that decreases occupancy levels of BRD4 and MED1 at a super-enhancer region associated with the IGH-MYC locus, wherein decreased occupancy levels of BRD4 and MED1 at the super-enhancer disrupt function of the super-enhancer thereby decreasing aberrant expression of oncogene c-Myc such that the multiple myeloma is treated. 
     
     
         58 . The method of  claim 57 , wherein the agent is JQ1 or iBET. 
     
     
         59 . (canceled) 
     
     
         60 . A method of identifying an agent that disrupts a super-enhancer comprising: (a) transfecting a cell with a super-enhancer operably linked to a reporter construct comprising a reporter gene under conditions suitable for the super-enhancer to drive high levels of expression of the reporter gene; (b) contacting the cell with a test agent; (c) and measuring the level of expression of the reporter gene, wherein decreased expression of the reporter gene in the presence of the test agent indicates that the test agent is as an agent that disrupts the super-enhancer. 
     
     
         61 . The method of  claim 60 , wherein the super-enhancer is naturally associated with a gene of interest, wherein the gene of interest is optionally a disease-associated gene, optionally an oncogene. 
     
     
         62 . The method of  claim 60  wherein expression is measured at least in part by measuring the level of a gene product encoded by the gene or by measuring activity of a gene product encoded by the gene. 
     
     
         63 . The method of  claim 62  wherein a gene product is mRNA or polypeptide encoded by the gene. 
     
     
         64 . The method of  claim 61  wherein expression is measured at least in part by measuring the level of a gene product encoded by the gene or by measuring activity of a gene product encoded by the gene.