{"search_session":{},"preferences":{"l":"en","queryLanguage":"en"},"patentId":"164-921-178-050-843","frontPageModel":{"patentViewModel":{"ref":{"entityRefId":"164-921-178-050-843","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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(i) identifying a set of regions of genomic DNA to which the protein of interest is bound in the cell;\n
(ii) identifying candidate DNA-binding sites in the identified regions of genomic DNA, wherein a candidate DNA-binding site comprises a sequence corresponding to a DNA-sequence motif for the protein of interest, and wherein said DNA sequence motif is enriched in said identified regions by a statistically significant amount relative to a set of genomic regions which are bound by a mutant form of the protein of interest in the cell;\n
(iii) determining if the candidate DNA-binding sites are conserved in an equivalent genomic region in one or more species different from the species from which the cell is obtained, wherein a candidate DNA-binding site that is conserved in at least one of the different species is a biologically-active DNA-binding site."],"number":1,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1, wherein the regions of genomic DNA comprise promoter regions."],"number":2,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1, wherein a candidate DNA-binding site is conserved if the equivalent genomic region in at least one different species comprises a nucleic acid sequence that matches the DNA-sequence motif for the protein of interest."],"number":3,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1, wherein the candidate DNA-binding site is less than 20 bp in length."],"number":4,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1, wherein the DNA-sequence motif is degenerate in at least one position."],"number":5,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1, wherein step (iii) comprises determining if the candidate DNA-binding sites are conserved in equivalent genomic regions in two or more different species."],"number":6,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1, wherein the set of biologically-active DNA-binding sites comprises one or more biologically-active DNA-binding sites."],"number":7,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1, wherein two regions of genomic DNA are equivalent if they both comprise a sequence of at least one orthologous gene."],"number":8,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1, wherein the cell is an eukaryotic cell."],"number":9,"annotation":false,"claim":true,"title":false},{"lines":["A method of identifying an agent which alters the set of biologically-active DNA-binding sites for a protein of interest in the genome of a cell, the method comprising\n
(i) contacting an experimental cell with a candidate agent;\n
(ii) identifying a set of biologically-active DNA-binding sites for a protein of interest in the genome of the cell of step (i) by:\n
(a) identifying a set of regions of genomic DNA to which the protein of interest is bound in the cell;\n
(b) identifying candidate DNA-binding sites in the identified regions of genomic DNA, wherein a candidate DNA-binding site comprises a sequence corresponding to a DNA-sequence motif for the protein of interest, wherein the DNA sequence motif is enriched by a statistically significant amount relative to a suitable control;\n
(c) determining if the candidate DNA-binding sites are conserved in an equivalent genomic region in one or more species different from the species from which the cell is obtained, wherein a candidate DNA-binding site that is conserved in at least one of the different species is a biologically-active DNA-binding site;\n
thereby generating an experimental set of biologically-active DNA-binding sites;\n
(iii) comparing\n"],"number":10,"annotation":false,"claim":true,"title":false},{"lines":["A method of identifying a pathway that is transcriptionally regulated by a protein of interest in a cell, the method comprising\n(1) the experimental set of biologically-active DNA-binding sites to\n(2) a control set of biologically-active DNA-binding sites for the protein of interest;\nwherein a candidate agent is identified if the experimental set and the control set differ.\n
(i) identifying a set of biologically-active DNA-binding sites for a protein of interest in the genome of the cell according to the method of claim 1; and\n
(ii) identifying at least two candidate genes likely to be regulated by binding of the protein of interest to the set of biologically-active DNA-binding sites identified in (i); wherein a pathway that is transcriptionally regulated by the protein of interest is identified if at least two candidate genes are members of the same pathway."],"number":11,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 11, wherein the pathway is a gene expression pathway."],"number":12,"annotation":false,"claim":true,"title":false},{"lines":["A method of identifying two sets of conditions in which a protein of interest differentially binds to the genome of a cell, the method comprising:\n
(i) identifying, according to the method of claim 1,\n\n(1) a first set of biologically-active DNA-binding sites for the protein of interest in the genome of a cell, wherein the cell is exposed to a first set of conditions; and\n(2) identifying a second set of biologically-active DNA-binding sites for the protein of interest in the genome of a cell, wherein the cell is exposed to a second set of conditions; and\n
(ii) identifying a difference in the first set of biologically-active DNA-binding sites relative to the second set of biologically-active DNA-binding sites, thereby identifying two sets of conditions in which a protein of interest differentially binds to the genome of a cell."],"number":13,"annotation":false,"claim":true,"title":false},{"lines":["A method of identifying a property of a gene product of a gene of interest that correlates with the binding activity of a polypeptide encoded by the gene of interest to the genome of a cell, the method comprising\n
(i) identifying two sets of conditions in which a protein of interest differentially binds to the genome of the cell according to the method of claim 13;\n
(ii) determining a property of a gene product of the gene of interest in (a) a cell exposed to the first set of conditions; and in (b) a cell exposed to the second set of conditions; and\n
(iii) determining if at least one property of the gene product differs in the two cells of step (ii),\n
thereby identifying a property of said gene product that correlates with the binding activity of a said polypeptide to the genome of a cell."],"number":14,"annotation":false,"claim":true,"title":false},{"lines":["A method of identifying a property of a gene product of a gene of interest that correlates with the binding activity of a polypeptide encoded by the gene of interest to the genome of a cell, the method comprising\n
(i) identifying an agent which alters the set of biologically-active DNA-binding sites for a protein of interest in the genome of a cell according to the method of claim 10;\n
(ii) determining a property of a gene product of the gene of interest in (a) a cell contacted with the agent; and in (b) a cell not contacted with the agent; and\n
(iii) determining if at least one property of the gene product differs in the two cells of step (ii),\n
thereby identifying a property that correlates with the binding activity of a gene of interest to the genome of a cell."],"number":15,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 14, wherein the property is selected from the group consisting of a protein modification, expression level, enzymatic activity and intracellular localization."],"number":16,"annotation":false,"claim":true,"title":false},{"lines":["A method of identifying two cell genotypes in which a protein of interest differentially binds to the genome, the method comprising:\n
(i) identifying a first set of biologically-active DNA-binding sites for the protein of interest in the genome of a cell of a first genotype;\n
(ii) identifying a second set of biologically-active DNA-binding sites for the protein of interest in the genome of a cell of a second genotype;\n
(iii) comparing the first set of biologically-active DNA-binding sites to the second set of biologically-active DNA-binding sites and determining if the two sets differ, thereby identifying two cell genotypes in which said protein of interest differentially binds to the genome."],"number":17,"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":[]}}