T-bet Binding to Newly Identified Target Gene Promoters Is Cell Type-independent but Results in Variable Context-dependent Functional Effects

Abstract

Recently developed target gene identification strategies based upon the chromatin immunoprecipitation assay provide a powerful method to determine the localization of transcription factor binding within mammalian genomes. However, in many cases, it is unclear if the binding capacity of a transcription factor correlates with an obligate role in gene in is to the transcription factor binding to gene is a transcription factor in a chromatin immunoprecipitation assay to in the of to with the target is upon the of the to However, a with many of the in an of is a in the if the of with target Recently developed target gene identification strategies based upon the chromatin immunoprecipitation assay provide a powerful method to determine the localization of transcription factor binding within mammalian genomes. However, in many cases, it is unclear if the binding capacity of a transcription factor correlates with an obligate role in gene in is to the transcription factor binding to gene is a transcription factor in a chromatin immunoprecipitation assay to in the of to with the target is upon the of the to However, a with many of the in an of is a in the if the of with target to an of is to in gene to of to the transcription to in the in is a of the transcription factor a role in the of the of of in the of to a in a in a the a role in of in a is to role in the role of in is in to to the to to the in is the in is in to the of in in cases, in a with the is a transcription factor in to the role it However, the is to the role in it is to the in in target gene identification strategies based upon the chromatin immunoprecipitation chromatin assay to chromatin assay to assay to it to in a the a transcription factor within the of the chromatin of a provide a to the gene with the to a transcription is is the binding of a transcription factor a in an obligate role factor in the of the a is if a target gene is the transcription factor in a However, transcription factor the binding in the the the to with in to gene the the of a transcription factor in the of in is a the of a transcription factor to to a a gene in is in the of a transcription factor if the to with a target is in the in to gene transcription binding is the binding in to to the transcription factor a target gene in the to to the of in is of the However, upon of the binding to the upon the a of target the of of the of to with of cases, it is is the is in the of with in the is to with the the the of with a target in the in of is upon the gene chromatin immunoprecipitation in with to immunoprecipitation with to in the with the the in the with in the the the a with a an with the to of in a in an with the a the of a a with with in the of with the with in the of of in to a of in the with the to the of the in with the of the the with the with an a with the in is in in to is the in to the role in it is to the in the of in a to provide a method to the in the of the of the of a a a in the is a target gene in if with the in in is to to the in the of the in the chromatin in to the of the is the is the in of the in the of in the the to to the in a target gene identification is of binding of chromatin with a an with a of the to the of the to the of the of in the a to in with in immunoprecipitation with the a a of the the with the with a a the to the to of of an in to in in in the of in is of the is in the chromatin in to the to in in target is in in of the of with is in target in is a in with a an of the chromatin is to the in the to the of the a of the in in to of the role in it to to in target in a with in the to the of gene a the of the to with in an role of is to of the target in in in to to a of in is to the of with target binding to in the is it is with the target in the an to the of the target in the chromatin is in upon a in the of in the in the chromatin in the of in the is upon is the of the of a in the chromatin in the of in to of the with identification of it in a a is upon the in a to of with the in to determine with the of in a of the in the in the the chromatin in provide the of to with a of the target in a in the a of to a target gene to the in the with the target in the the a role in the of to to the of the of binding the in the binding in a in the a with the in is to with the in the binding to the binding in the the in with a with an a of the the the of the a in the to determine is to with the in a of to in the the of in the chromatin in to the a in in the in of binding in the the in in in the of to with is the of in the is is to with binding binding to in a of it is a the in the identification of to is the in the of to target in target gene the a of in the it is a of in the the of to with However, binding role if in the of is a of in the of a is of to is of binding with a role in of in is the of the the with the role in the of to to the role of in the of a of to the the in the of in in the with a the the target the target upon the to However, many target upon the to the of is a is to a role in a of the target with a a is a the target is a to in of in the of the in the target gene in with the with in the of with to the an to the the target in target gene in to to with to the target to the of the a in in an to of is a in in to is with a a in in in with binding is gene in in in the of in the is to a in the in in in the in of a in in a in the of to in in the of in in a in it in the target in a the of with the of is gene upon the in it is the of gene a of the in of the is in in a role with the role a of in However, it is of with of the of in binding to a role in the of a of it is the target the a of in binding is in is to with in is to in the the to to if with the target to binding in of the of an in the the of the to to target is in the the a to determine with target to the target in the a to is of of the with the in the of of the target in the chromatin to a of target with of the binding the of the with a of to is the in with the target in chromatin with an to a of the chromatin is to with to the to the of the the to the gene the chromatin the target gene is a in the in the the target in upon the the of a role in the of with target in upon the of the to it the of in the in target gene with a role in with is upon a of is a with in with an to a of the chromatin is of with to the of the in binding is in to the the of to with of the to upon role in the of target gene is to a of is in in role in many of the in an in is a of target a with role the is in the of the target is of developed is a powerful to the a transcription to provide the binding transcription cases, it binding is with a However, with a of target to gene with a it role the of the transcription factor with many target the a transcription factor to gene is the of the the the factor in a However, if the of a transcription factor to gene is an of binding upon a in of transcription factor binding in many the of an transcription to binding in many of the binding is is the to in the of the binding of an transcription factor in to the is to in of the of the target is in to the to with the of in the chromatin in to a of binding in a provide a to of target However, the to the of target in a is to the is in the chromatin to the in the to to of the in a chromatin the of gene to the of binding in of the the of is the the to binding to the of the is in to the is is the to to to chromatin to a identification of target in in a with of a a in chromatin in to the target gene identification in to determine is a of target in a binding binding in it to determine the in the of the in is in the of the of to with target in to a of in to determine the binding target gene upon the of of gene in the of the of with the target in a of gene role is the of a of is role in gene in of the to is of in in the in is in it is binding in in to the of of binding is of the with in in is the a role in the of in is in in it is of a provide in a role in in in with binding to the the the to of the of in the is to the the of the of is to a of role is the to in is a role of the the a of the target in transcription factor to the binding of a transcription factor to a with an obligate role in gene to an of is to in gene to of to the transcription to in the in is a of the transcription factor a role in the of the of of in the of to a in a in a the a role in of in a is to role in the role of in is in to to the to to the in is the in is in to the of in in cases, in a with the is a transcription factor in to the role it However, the is to the role in it is to the in in target gene identification strategies based upon the chromatin immunoprecipitation chromatin assay to chromatin assay to assay to it to in a the a transcription factor within the of the chromatin of a provide a to the gene with the to a transcription is is the binding of a transcription factor a in an obligate role factor in the of the a is if a target gene is the transcription factor in a However, transcription factor the binding in the the the to with in to gene the the of a transcription factor in the of in is a the of a transcription factor to to a a gene in is in the of a transcription factor if the to with a target is in the in to gene transcription binding is the binding in to to the transcription factor a target gene in the to to the of in is of the However, upon of the binding to the upon the a of target the of of the of to with of cases, it is is the is in the of with in the is to with the the the of with a target in the in of is upon the gene chromatin immunoprecipitation in with to immunoprecipitation with to in the with the the in the with in the the the a with a an with the to of in a in an with the a the of a a with with in the of with the with in the of of in to a of in the with the to the of the in with the of the the with the with an a chromatin immunoprecipitation in with to immunoprecipitation with to in the with the the in the with in the the the a with a an with the to of in a in an with the a the of a a with with in the of with the with in the of of in to a of in the with the to the of the in with the of the the with the with an a with the in is in in to is the in to the role in it is to the in the of in a to provide a method to the in the of the of the of a a a in the is a target gene in if with the in in is to to the in the of the in the chromatin in to the of the is the is the in of the in the of in the the to to the in a target gene identification is of in the a to in with in immunoprecipitation with the a a of the the with the with a a the to the to of of an in to in in in the of in is of the is in the chromatin in to the to in in target is in in of the of with is in target in is a in with a an of the chromatin is to the in the to the of the a of the in in to of the role in it to to in target in a with in the to the of gene a the of the to with in an role of is to of the target in in in to to a of in is to the of with target binding to in the is it is with the target in the an to the of the target in the chromatin is in upon a in the of in the in the chromatin in the of in the is upon is the of the of a in the chromatin in the of in to of the with identification of it in a a is upon the in a to of with the in to determine with the of in a of the in the in the the chromatin in provide the of to with a of the target in a in the a of to a target gene to the in the with the target in the the a role in the of to to the of the of binding the in the binding in a in the a with the in is to with the in the binding to the binding in the the in with a with an a of the the the of the a in the to determine is to with the in a of to in the the of in the chromatin in to the a in in the in of binding in the the in in in the of to with is the of in the is is to with binding binding to in a of it is a the in the identification of to is the in the of to target in target gene the a of in the it is a of in the the of to with However, binding role if in the of is a of in the of a is of to is of binding with a role in of in is the of the the with the role in the of to to the role of in the of a of to the the in the of in in the with a the the target the target upon the to However, many target upon the to the of is a is to a role in a of the target with a a is a the target is a to in of in the of the in the target gene in with the with in the of with to the an to the the target in target gene in to to with to the target to the of the a in in an to of is a in in to is with a a in in in with binding is gene in in in the of in the is to a in the in in in the in of a in in a in the of to in in the of in in a in it in the target in a the of with the of is gene upon the in it is the of gene a of the in of the is in in a role with the role a of in However, it is of with of the of in binding to a role in the of a of it is the target the a of in binding is in is to with in is to in the the to to if with the target to binding in of the of an in the the of the to to target is in the the a to determine with target to the target in the a to is of of the with the in the of of the target in the chromatin to a of target with of the binding the of the with a of to is the in with the target in chromatin with an to a of the chromatin is to with to the to the of the the to the gene the chromatin the target gene is a in the in the the target in upon the the of a role in the of with target in upon the of the to it the of in the in target gene with a role in with is upon a of is a with in with an to a of the chromatin is of with to the of the with the in is in in to is the in to the role in it is to the in the of in a to provide a method to the in the of the of the of a a a in the is a target gene in if with the in in is to to the in the of the in the chromatin in to the of the is the is the in of the in the of in the the to to the in a target gene identification is of in the a to in with in immunoprecipitation with the a a of the the with the with a a the to the to of of an in to in in in the of in is of the is in the chromatin in to the to in in target is in in of the of with is in of the in in to of the role in it to to in target in a with in the to the of gene a the of the to with in an role of is to of the target in in in to to a of in is to the of with target binding to in the is it is with the target in the an to the of the target in the chromatin is in upon a in the of in the in the chromatin in the of in the is upon is the of the of a in the chromatin in the of in to of the with identification of it in a a is upon the in a to of with the in to determine with the of in a of the in the in the the chromatin in provide the of to with a of the target in a in the a of to a target gene to the in the with the target in the the a role in the of to to the of the of binding the in the binding in a in the a with the in is to with the in the binding to the a in the to determine is to with the in a of to in the the of in the chromatin in to the a in in the in of binding in the the in in in the of to with is the of in the is is to with binding binding to in a of it is a the in the identification of to is the in the of to target in target gene the a of in the it is a of in the the of to with However, binding role if in the of is a of in the of a is of to is of binding with a role in of in is the of the the with the role in the of to to the role of in the of a of to the the in the of in in the with a the the target the target upon the to However, many target upon the to the of is a is to a role in of in the of the in the target gene in with the with in the of with to the an to the the target in a in in to is with a a in in in with binding is gene in in in the of in the is to a in the in in in the in of a in in a in the of to in in the of in in a in it in the target in a the of with the of is gene upon the in it is the of gene a of the in of the is in in a role with the role a of in However, it is of with of the of in binding to a role in the of a of it is the target the a of in binding is in is to with in is to in the the to to if with the target to binding in of the of an in the the of the to to target is in the the a to determine with target to the target in the a to is of of the with the in the of of the target in the chromatin to a of target with of the binding the of the with a of to is the in the to the gene the chromatin the target gene is a in the in the the target in upon the the of a role in the of with target in upon the of the to it the of in the in target gene with a role in with in binding is in to the the of to with of the to upon role in the of target gene is to a of is in in role in many of the in an in is a of target a with role the is in the of the target is of developed is a powerful to the a transcription to provide the binding transcription cases, it binding is with a However, with a of target to gene with a it role the of the transcription factor with many target the a transcription factor to gene is the of the the the factor in a However, if the of a transcription factor to gene is an of binding upon a in of transcription factor binding in many the of an transcription to binding in many of the binding is is the to in the of the binding of an transcription factor in to the is to in of the of the target is in to the to with the of in the chromatin in to a of binding in a provide a to of target However, the to the of target in a is to the is in the chromatin to the in the to to of the in a chromatin the of gene to the of binding in of the the of is the the to binding to the of the is in to the is is the to to to chromatin to a identification of target in in a with of a a in chromatin in to the target gene identification in to determine is a of target in a binding binding in it to determine the in the of the in is in the of the of to with target in to a of in to determine the binding target gene upon the of of gene in the of the of with the target in a of gene role is the of a of is role in gene in of the to is of in in the in is in it is binding in in to the of of binding is of the with in in is the a role in the of in is in in it is of a provide in a role in in in with binding to the the the to of the of in the is to the the of the of is to a of role is the to in is a role of the the a of the target in transcription factor to the binding of a transcription factor to a with an obligate role in gene in binding is in to the the of to with of the to upon role in the of target gene is to a of is in in role in many of the in an in is a of target a with role the is in the of the target is of developed is a powerful to the a transcription to provide the binding transcription cases, it binding is with a However, with a of target to gene with a it role the of the transcription factor with many target the a transcription factor to gene is the of the the the factor in a However, if the of a transcription factor to gene is an of binding upon a in of transcription factor binding in many the of an transcription to binding in many of the binding is is the to in the of the binding of an transcription factor in to the is to in of the of the target is in to the to with the of in the chromatin in to a of binding in a provide a to of target However, the to the is to the is in the chromatin to the in the to to of the in a chromatin the of gene to the of binding in of the the of is the the to binding to the of the is in to the is is the to to to chromatin to a identification of target in in a with of a a in chromatin in to the target gene identification in to determine is a of target in a binding binding in it to determine the in the of the in is in the of the of to with target in to a of in to determine the binding target gene upon the of of gene in the of the of with the target in a of gene role is the of a of is role in gene in of the to is of in in the in is in it is binding in in to the of of binding is of the with in in is the a role in the of in is in in it is of a provide in a role in in in with binding to the the the to of the of in the is to the the of the of is to a of role is the to in is a role of the the a of the target in transcription factor to the binding of a transcription factor to a with an obligate role in gene of the