Gene regulatory networks and methods of interdiction for controlling the differentiation state of a cell

Abstract

The invention provides a method of modulating a regulatory state of a cell. The method consists of: (a) identifying a point of interdiction within a cis regulatory network specifying a genetic regulatory architecture of a cell, and (b) introducing into a progenitor cell two or more network elements within said network to induce a predetermined series of cis regulatory network interactions resulting in a specified regulatory state of said progenitor cell. Also provided is a method of modulating a regulatory state of a cell. The method consists of: (a) identifying a point of interdiction within a cis regulatory network specifying a genetic regulatory architecture of a cellular state, and (b) introducing into a progenitor cell two or more network elements within said network to induce a predetermined series of cis regulatory network interactions resulting in a specified regulatory state of said progenitor cell. A cell having a specified regulatory state consisting of a modified genetic regulatory architecture is further provided. Methods of diagnosing and methods of treating an individual suffering from a cellular defect also are provided. The invention additionally provides a method of identifying a compound having differentiation or cell fate inducing activity.

What is claimed is:  
     
         1 . A method of modulating a regulatory state of a cell, comprising: 
 (a) identifying a point of interdiction within a cis regulatory network specifying a genetic regulatory architecture of a cell, and    (b) introducing into a progenitor cell two or more network elements within said network to induce a predetermined series of cis regulatory network interactions resulting in a specified regulatory state of said progenitor cell.    
     
     
         2 . The method of  claim 1 , wherein said point of interdiction comprises a cis regulatory module.  
     
     
         3 . The method of  claim 2 , wherein said cis regulatory module controls the expression of a transcription activator or repressor.  
     
     
         4 . The method of  claim 3 , wherein said transcription activator or repressor lock down or prevent a regulatory state.  
     
     
         5 . The method of  claim 1 , wherein said network element comprises a transcription factor.  
     
     
         6 . The method of  claim 5 , wherein said transcription factor comprises a transcription activator, a transcription repressor, or combination thereof.  
     
     
         7 . The method of  claim 1 , wherein said cis regulatory network comprises cis regulatory modules and transcription factors interconnected through binding activity.  
     
     
         8 . The method of  claim 7 , wherein said genetic regulatory architecture of said cell comprises transcription factor interactions within two or more regulatory territories.  
     
     
         9 . The method of  claim 8 , wherein said two or more regulatory territories comprise territories selected from the group consisting of a zygote, a primary germ layer, endoderm, mesoderm, ectoderm and a terminally differentiated cell.  
     
     
         10 . The method of  claim 1 , wherein said introduction of two or more network elements further comprises expression of a nucleic acid encoding said network elements.  
     
     
         11 . The method of  claim 10 , wherein at least one of said two or more network elements bind to a cis regulatory module at a point of interdiction.  
     
     
         12 . The method of  claim 10 , wherein said two or more network elements bind to a cis regulatory module at a point downstream from a point of interdiction.  
     
     
         13 . The method of  claim 1 , wherein said regulatory state comprises a differentiation state.  
     
     
         14 . The method of  claim 1 , wherein said progenitor cell is selected from the group consisting of a zygote, a pluripotent stem cell, a pluripotent lineage specific progenitor, a progenitor cell, and a terminally differentiated cell.  
     
     
         15 . A method of modulating a regulatory state of a cell, comprising: 
 (a) identifying a point of interdiction within a cis regulatory network specifying a genetic regulatory architecture of a cellular state, and    (b) introducing into a progenitor cell two or more network elements within said network to induce a predetermined series of cis regulatory network interactions resulting in a specified regulatory state of said progenitor cell.    
     
     
         16 . The method of  claim 15 , wherein said point of interdiction comprises a cis regulatory module.  
     
     
         17 . The method of  claim 16 , wherein said cis regulatory module controls the expression of a transcription activator or repressor.  
     
     
         18 . The method of  claim 17 , wherein said transcription activator or repressor lock down or prevent a regulatory state.  
     
     
         19 . The method of  claim 15 , wherein said network element comprises a transcription factor.  
     
     
         20 . The method of  claim 19 , wherein said transcription factor comprises a transcription activator, a transcription repressor, or combination thereof.  
     
     
         21 . The method of  claim 15 , wherein said cis regulatory network comprises cis regulatory modules and transcription factors interconnected through binding activity.  
     
     
         22 . The method of  claim 21 , wherein said genetic regulatory architecture of said cell comprises transcription factor interactions within two or more regulatory territories.  
     
     
         23 . The method of  claim 22 , wherein said two or more regulatory territories comprise territories selected from the group consisting of a zygote, a primary germ layer, endoderm, mesoderm, ectoderm and a terminally differentiated cell.  
     
     
         24 . The method of  claim 15 , wherein said introduction of two or more network elements further comprises expression of a nucleic acid encoding said network elements.  
     
     
         25 . The method of  claim 24 , wherein at least one of said two or more network elements bind to a cis regulatory module at a point of interdiction.  
     
     
         26 . The method of  claim 24 , wherein said two or more network elements bind to a cis regulatory module at a point downstream from a point of interdiction.  
     
     
         27 . The method of  claim 15 , wherein said regulatory state comprises a differentiation state.  
     
     
         28 . The method of  claim 15 , wherein said progenitor cell is selected from the group consisting of a zygote, a pluripotent stem cell, a pluripotent lineage specific progenitor, a progenitor cell, and a terminally differentiated cell.  
     
     
         29 . A cell having a specified regulatory state, comprising a cis regulatory network having a modified genetic regulatory architecture, said modification comprising two or more exogenous transcription factors activating a predetermined series of cis regulatory network interactions, said series of cis regulatory network interactions resulting in a specified non-naturally occurring regulatory state of said cell.  
     
     
         30 . The cell of  claim 29 , wherein said cis regulatory network comprises cis regulatory modules and transcription factors interconnected through binding activity.  
     
     
         31 . The cell of  claim 30 , wherein said genetic regulatory architecture of said cell comprises transcription factor interactions within two or more regulatory territories.  
     
     
         32 . The cell of  claim 31 , wherein said two or more regulatory territories comprise territories selected from the group consisting of a zygote, a primary germ layer, endoderm, mesoderm, ectoderm, and a terminally differentiated cell.  
     
     
         33 . The cell of  claim 29 , wherein said exogenous transcription factors comprises a transcription activator, a transcription repressor, or combination thereof.  
     
     
         34 . The cell of  claim 33 , wherein said transcription activator or repressor lock down or prevent a regulatory state.  
     
     
         35 . The cell of  claim 29 , wherein said modification further comprises expression of a nucleic acid encoding said two or more exogenous transcription factors.  
     
     
         36 . The cell of  claim 29 , wherein said regulatory state comprises a differentiation state.  
     
     
         37 . The cell of  claim 29 , wherein said cell is selected from the group consisting of a zygote, a pluripotent stem cell, a pluripotent lineage specific progenitor, a progenitor cell, and a terminally differentiated cell.  
     
     
         38 . A method of diagnosing an individual suffering from a cellular defect, comprising: 
 (a) measuring an activity or amount of a plurality of cis regulatory network elements in a sample from an individual suspected of having a cellular defect, and    (b) comparing a genetic regulatory architecture of said plurality of cis regulatory network elements in said sample to a reference genetic regulatory architecture indicative of a cell or cellular state, wherein a change or similarity in pattern of said activity or amount of said plurality of elements compared to said reference genetic regulatory architecture indicates that said individual has a cellular defect.    
     
     
         39 . The method of  claim 38 , wherein said plurality of cis regulatory network elements comprise transcription activators or transcription repressors corresponding to points of interdiction within a cis regulatory network.  
     
     
         40 . The method of  claim 38 , wherein said plurality of cis regulatory network elements comprise transcription activators or transcription repressor controlled by cis regulatory modules at points of interdiction within a cis regulatory network.  
     
     
         41 . The method of  claim 38 , wherein said genetic regulatory architecture of said plurality of cis regulatory network elements specifies a genetic regulatory architecture of a cell.  
     
     
         42 . The method of  claim 38 , wherein said genetic regulatory architecture of said plurality of cis regulatory network elements specifies a genetic regulatory architecture of a cellular state.  
     
     
         43 . The method of  claim 38 , wherein said reference genetic regulatory architecture comprises the genetic regulatory architecture of a cell or cellular state selected from the group consisting of a zygote, a primary germ cell, endoderm, a mesoderm, ectoderm, pluripotent stem cell, pluripotent lineage specific progenitor cell, a progenitor cell and terminally differentiated cell.  
     
     
         44 . The method of  claim 38 , wherein said reference genetic regulatory architecture is obtained from a normal cell or cellular state.  
     
     
         45 . The method of  claim 44 , wherein said comparison comprises a change in pattern indicating a cellular defect.  
     
     
         46 . The method of  claim 38 , wherein said reference genetic regulatory architecture is obtained from a cell having a cellular defect.  
     
     
         47 . The method of  claim 46 , wherein said comparison comprises a similarity in pattern indicating a cellular defect.  
     
     
         48 . A method of treating an individual suffering from a cellular defect, comprising: 
 (a) identifying a point of interdiction within a cis regulatory network specifying a genetic regulatory architecture of a cell or cellular state;    (b) introducing into a progenitor cell two or more network elements within said network to induce a predetermined-series of cis regulatory network interactions resulting in a specified regulatory state of said progenitor cell, and    (c) implanting said progenitor cell having said specified regulatory state into an individual suffering from a cellular defect under conditions sufficient for viability in an effective amount sufficient to renew a deficient cellular component.    
     
     
         49 . The method of  claim 48 , wherein said point of interdiction comprises a cis regulatory module.  
     
     
         50 . The method of  claim 49 , wherein said cis regulatory module controls the expression of a transcription activator or repressor.  
     
     
         51 . The method of  claim 48 , wherein said network element comprises a transcription factor.  
     
     
         52 . The method of  claim 48 , wherein said cis regulatory network comprises cis regulatory modules and transcription factors interconnected through binding activity.  
     
     
         53 . The method of  claim 52 , wherein said genetic regulatory architecture of said cell comprises transcription factor interactions within two or more regulatory territories.  
     
     
         54 . The method of  claim 53 , wherein said two or more regulatory territories comprise territories selected from the group consisting of a zygote, a primary germ layer, endoderm, mesoderm, ectoderm and a terminally differentiated cell.  
     
     
         55 . The method of  claim 48 , wherein said introduction of two or more network elements further comprises expression of a nucleic acid encoding said network elements.  
     
     
         56 . The method of  claim 55 , wherein at least one of said two or more network elements bind to a cis regulatory module at a point of interdiction.  
     
     
         57 . The method of  claim 55 , wherein said two or more network elements bind to a cis regulatory module at a point downstream from a point of interdiction.  
     
     
         58 . The method of  claim 48 , wherein said regulatory state comprises a differentiation state.  
     
     
         59 . The method of  claim 48 , wherein said progenitor cell is selected from the group consisting of a zygote, a pluripotent stem cell, a pluripotent lineage specific progenitor, a progenitor cell, and a terminally differentiated cell.  
     
     
         60 . A method of identifying compounds having differentiation inducing activity, comprising: 
 (a) contacting a progenitor cell with a test compound under conditions sufficient for inducing a cis regulatory network interaction, and    (b) measuring an activity or amount of a plurality of indicators within a cis regulatory network, wherein a specific pattern of said plurality of indicators corresponding to a specified regulatory state indicates that said test compound has differentiation inducing activity.