{"search_session":{},"preferences":{"l":"en","queryLanguage":"en"},"patentId":"071-953-056-642-052","frontPageModel":{"patentViewModel":{"ref":{"entityRefId":"071-953-056-642-052","entityRefType":"PATENT"},"entityMetadata":{"linkedIds":{"empty":true},"tags":[],"collections":[{"id":8635,"type":"PATENT","title":"MIT Patent Portfolio","description":"","access":"OPEN_ACCESS","displayAvatar":true,"attested":false,"itemCount":30193,"tags":[],"user":{"id":91044780,"username":"Cambialens","firstName":"","lastName":"","created":"2015-05-04T00:55:26.000Z","displayName":"Cambialens","preferences":"{\"usage\":\"public\",\"beta\":false}","accountType":"PERSONAL","isOauthOnly":false},"notes":[{"id":8198,"type":"COLLECTION","user":{"id":91044780,"username":"Cambialens","firstName":"","lastName":"","created":"2015-05-04T00:55:26.000Z","displayName":"Cambialens","preferences":"{\"usage\":\"public\",\"beta\":false}","accountType":"PERSONAL","isOauthOnly":false},"text":"
Select Applicants and Owners= \"MIT\", \" Massachusetts Institute of Technology \", \"Massachus* Insti* Tech*\", \"Media Lab Massachus* Insti* Tech*\", \"Massachus* Tech* Inst*\".
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Select Applicants and Owners= \"MIT\", \" Massachusetts Institute of Technology \", \"Massachus* Insti* Tech*\", \"Media Lab Massachus* Insti* Tech*\", \"Massachus* Tech* Inst*\".
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determining an amount of ligand bound to each enhancer in the cross-linked complex in the cell; and\n
utilizing the determined amount of ligand bound to each enhancer to identify a super-enhancer,\n
wherein the identified super-enhancer is bound to at least 10-fold more ligand than the median amount of ligand bound to enhancer within the cell."],"number":1,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1, wherein the component is BRD4 and the ligand is an antibody to BRD4."],"number":2,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1, wherein the component is a Mediator component and the ligand is an antibody to a Mediator component."],"number":3,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1, wherein the component is H3K27Ac and the ligand is an antibody to H3K27Ac."],"number":4,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1, comprising fragmenting the chromosomal nucleic acid of the cross-linked complex prior to the step of determining the amount of ligand bound."],"number":5,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 5, comprising fragmenting the chromosomal nucleic acid after forming the complex between the cross-linked complex and the ligand."],"number":6,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1, wherein the cross-linking of the cross-linked complex comprises covalent cross-linking."],"number":7,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1, further comprising identifying a gene associated with said super-enhancer."],"number":8,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 8, wherein said associated gene is identified by proximity to the super-enhancer."],"number":9,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 8, wherein said associated gene is identified using high throughput chromatin conformation capture data."],"number":10,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 8, wherein the gene associated with said super-enhancer is an endogenous gene within the cell."],"number":11,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1, wherein the component is endogenous to the cell."],"number":12,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1, wherein determining an amount of ligand bound to each enhancer in the cell is achieved by ChiP-Seq."],"number":13,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1, wherein at least a portion of the chromosomal nucleic acid is sequenced after contacting the cross-linked complex with the ligand."],"number":14,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1, wherein utilizing the determined amount of ligand bound to each enhancer to identify a super-enhancer comprises:\n
identifying a portion of the chromosomal nucleic acid that is bound to at least 10-fold more ligand than the median amount of ligand bound to enhancers within the cell."],"number":15,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1, wherein utilizing the determined amount of ligand bound to each enhancer to identify a super-enhancer comprises:\n
determining the median amount of ligand bound to enhancers within the cell;\n
identifying a portion of the chromosomal nucleic acid that is bound to at least 10-fold more ligand than the median as a super-enhancer."],"number":16,"annotation":false,"claim":true,"title":false},{"lines":["A method of identifying a super-enhancer in a sample comprising chromatin, comprising:\n
obtaining chromatin from a cell wherein said chromatin has been cross-linked such that chromosomal nucleic acid in the chromatin is cross-linked to a component selected from the group consisting of BRD4, a Mediator component and H3K27Ac with which the chromosomal nucleic acid is associated to form a cross-linked complex;\n
contacting said cross-linked complex with a ligand having affinity for the component, said ligand selected from the group consisting of an antibody to BRD4, an antibody to a Mediator component, and an antibody to H3K27Ac, to form complex between the cross-linked complex and the ligand;\n
determining an amount of ligand bound to each enhancer in the cross-linked complex in the cell; and\n
utilizing the determined amount of ligand to each enhancer to identify a super-enhancer, wherein the identified super-enhancer has an amount of ligand bound that is above the point where the slope of the tangent is 1 in a rank-ordered graph of the amount of ligand bound to each of the enhancers in the cell."],"number":17,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 17, wherein utilizing the determined amount of ligand bound to each enhancer to identify a super-enhancer comprises:\n
rank ordering the enhancers according to the amount of ligand bound;\n
identifying, with respect to the amount of ligand bound, the point where the slope of the tangent is 1 which would occur if said rank order were graphed; and\n
identifying any enhancer that falls above that point as a super-enhancer."],"number":18,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 17, wherein utilizing the determined amount of ligand bound to each enhancer to identify a super-enhancer comprises:\n
graphing, in rank order of the amount of ligand bound, the enhancer and the amount of ligand bound to said enhancer;\n
identifying the point of the graph where the slope of the tangent is 1; and\n
identifying any enhancer that falls above that point as a super-enhancer."],"number":19,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 17, wherein the component is BRD4 and the ligand is an antibody to BRD4."],"number":20,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 17, wherein the component is a Mediator component and the ligand is an antibody to the Mediator component."],"number":21,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 17, wherein the component is H3K27Ac and the ligand is an antibody to H3K27Ac."],"number":22,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 17, comprising fragmenting the chromosomal nucleic acid of the cross-linked complex prior to the step of determining the amount of ligand bound."],"number":23,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 23, comprising fragmenting the chromosomal nucleic acid after forming the complex between the cross-linked complex and the ligand."],"number":24,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 17, wherein the cross-linking of the cross-linked complex comprises covalent cross-linking."],"number":25,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 17, further comprising identifying a gene associated with said super-enhancer."],"number":26,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 26, wherein said associated gene is identified by proximity to the super-enhancer."],"number":27,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 17, wherein the component is endogenous to the cell."],"number":28,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 17, wherein determining an amount of ligand bound to each enhancer in the cell is achieved by ChiP-Seq."],"number":29,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 17, wherein at least a portion of the chromosomal nucleic acid is sequenced after contacting the cross-linked complex with the ligand."],"number":30,"annotation":false,"claim":true,"title":false}]}},"filters":{"npl":[],"notNpl":[],"applicant":[],"notApplicant":[],"inventor":[],"notInventor":[],"owner":[],"notOwner":[],"tags":[],"dates":[],"types":[],"notTypes":[],"j":[],"notJ":[],"fj":[],"notFj":[],"classIpcr":[],"notClassIpcr":[],"classNat":[],"notClassNat":[],"classCpc":[],"notClassCpc":[],"so":[],"notSo":[],"sat":[]},"sequenceFilters":{"s":"SEQIDNO","d":"ASCENDING","p":0,"n":10,"sp":[],"si":[],"len":[],"t":[],"loc":[]}}