The transcription factor affinity prediction (TRAP) method calculates the affinity of transcription factors for DNA sequences on the basis of a biophysical model. This method has proven to be useful for several
BMO transcription factor binding prediction BMO (“Bee” MOdel of TF binding) builds on previous reports that the degree of chromatin accessibility around a motif15,16,17 and the presence of co-occurring motifs18 positively correlate with TF occupancy, corresponding to the analogy of TFs behaving ...
Low-affinity transcription factor binding sites shape morphogen responses and enhancer evolution. Philos. Trans. R. Soc. B 368, 20130018 (2013). Article Google Scholar Chong, S. et al. Imaging dynamic and selective low-complexity domain interactions that control gene transcription. Science https:...
Transcription Factor IIIA (TFIIIA) is specifically required for transcription of 5S ribosomal RNA, an essential component of the ribosome. The TFIIIA protein, found in every organism, has been characterized in several species. It shows remarkably poor conservation of primary protein sequence, but ...
Initiation of transcription by RNAPIII begins with the binding to specific core element promoter of the Transcription Factor III A (TFIIIA), Transcription Factor III C (TFIIIC), or snRNA Activating Protein complex (SNAPc) to 5S rRNA, tRNA, and U6 snRNA promoter type respectively. While SNAPc...
Beyer A, Workman C, Hollunder J, Radke D, Moller U, Wilhelm T, Ideker T: Integrated assessment and prediction of transcription factor binding. PLoS Comput Biol. 2006, 2 (6): e70-10.1371/journal.pcbi.0020070. Article PubMed PubMed Central Google Scholar Harbison CT, Gordon DB, Lee TI...
Disclosures Acknowledgements Materials References English Automatically Generated Tags Transcription FactorDNA Binding AffinitiesDissociation ConstantsCompetitive TitrationFluorescence MicroscopyBinding Affinity LandscapeAutomated MeasurementsTitration CurvesProtein-protein InteractionsProtein-drug InteractionsDNA OligomersPCR Pla...
Hu, Z., Hu, B., Collins, J.F.: Prediction of synergistic transcription factors by function conservation. Genome Biol. 8, R257 (2007)View Article About this Chapter Title Transcription Factor Binding Probabilities in Orthologous Promoters: An Alignment-Free Approach to the Inference of ...
code in which canonical sequence features such as TATA-box, Initiator, and GC content do play a significant role, but many additional TFs show distinct spatial biases with respect to TSS location and are important contributors to the accurate prediction of single-peak transcription initiation sites....
Structural insight from transcription factor-DNA (TF-DNA) complexes is of paramount importance to our understanding of the affinity and specificity of TF-DNA interaction, and to the development of structure-based prediction of TF binding sites. Yet the majority of the TF-DNA complexes remain unsolv...