TF Profiler: a transcription factor inference method that broadly measures transcription factor activity and identifies mechanistically distinct networks
Abstract TF Profiler is a method of inferring transcription factor (TF) regulatory activity, i.e., when a TF is present and actively participating in the regulation of transcription, directly from nascent sequencing assays such as PRO-seq and GRO-seq. While ChIP assays have measured DNA localization...
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| Format: | Article |
| Language: | English |
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BMC
2025-04-01
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| Series: | Genome Biology |
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| Online Access: | https://doi.org/10.1186/s13059-025-03545-2 |
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| author | Taylor Jones Rutendo F. Sigauke Lynn Sanford Dylan J. Taatjes Mary A. Allen Robin D. Dowell |
| author_facet | Taylor Jones Rutendo F. Sigauke Lynn Sanford Dylan J. Taatjes Mary A. Allen Robin D. Dowell |
| author_sort | Taylor Jones |
| collection | DOAJ |
| description | Abstract TF Profiler is a method of inferring transcription factor (TF) regulatory activity, i.e., when a TF is present and actively participating in the regulation of transcription, directly from nascent sequencing assays such as PRO-seq and GRO-seq. While ChIP assays have measured DNA localization, they fall short of identifying when and where the effector domain of a transcription factor is active. Our method uses RNA polymerase activity to infer TF effector domain activity across hundreds of data sets and transcription factors. TF Profiler is broadly applicable, providing regulatory insights on any PRO-seq sample for any transcription factor with a known binding motif. |
| format | Article |
| id | doaj-art-88d0a165608e4e9b97baf38fa419ee19 |
| institution | OA Journals |
| issn | 1474-760X |
| language | English |
| publishDate | 2025-04-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj-art-88d0a165608e4e9b97baf38fa419ee192025-08-20T02:17:09ZengBMCGenome Biology1474-760X2025-04-0126112510.1186/s13059-025-03545-2TF Profiler: a transcription factor inference method that broadly measures transcription factor activity and identifies mechanistically distinct networksTaylor Jones0Rutendo F. Sigauke1Lynn Sanford2Dylan J. Taatjes3Mary A. Allen4Robin D. Dowell5BioFrontiers Institute, University of Colorado BoulderBioFrontiers Institute, University of Colorado BoulderBioFrontiers Institute, University of Colorado BoulderBiochemistry, University of Colorado BoulderBioFrontiers Institute, University of Colorado BoulderBioFrontiers Institute, University of Colorado BoulderAbstract TF Profiler is a method of inferring transcription factor (TF) regulatory activity, i.e., when a TF is present and actively participating in the regulation of transcription, directly from nascent sequencing assays such as PRO-seq and GRO-seq. While ChIP assays have measured DNA localization, they fall short of identifying when and where the effector domain of a transcription factor is active. Our method uses RNA polymerase activity to infer TF effector domain activity across hundreds of data sets and transcription factors. TF Profiler is broadly applicable, providing regulatory insights on any PRO-seq sample for any transcription factor with a known binding motif.https://doi.org/10.1186/s13059-025-03545-2Transcription factorCellular regulationTissue specificity |
| spellingShingle | Taylor Jones Rutendo F. Sigauke Lynn Sanford Dylan J. Taatjes Mary A. Allen Robin D. Dowell TF Profiler: a transcription factor inference method that broadly measures transcription factor activity and identifies mechanistically distinct networks Genome Biology Transcription factor Cellular regulation Tissue specificity |
| title | TF Profiler: a transcription factor inference method that broadly measures transcription factor activity and identifies mechanistically distinct networks |
| title_full | TF Profiler: a transcription factor inference method that broadly measures transcription factor activity and identifies mechanistically distinct networks |
| title_fullStr | TF Profiler: a transcription factor inference method that broadly measures transcription factor activity and identifies mechanistically distinct networks |
| title_full_unstemmed | TF Profiler: a transcription factor inference method that broadly measures transcription factor activity and identifies mechanistically distinct networks |
| title_short | TF Profiler: a transcription factor inference method that broadly measures transcription factor activity and identifies mechanistically distinct networks |
| title_sort | tf profiler a transcription factor inference method that broadly measures transcription factor activity and identifies mechanistically distinct networks |
| topic | Transcription factor Cellular regulation Tissue specificity |
| url | https://doi.org/10.1186/s13059-025-03545-2 |
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