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In vitro, genomic context identification of transcription factor binding sites for bZIP C/S1 homodimers and heterodimers

ABSTRACT: In eukaryotes, many transcription factors (TF) usually form dimers or oligomers with itself or other TFs to regulate gene expression. To study how homo- and heterodimerization of TFs affect DNA binding specificity, we developed a double DNA Affinity Purification sequencing (double DAP-seq; dDAP-seq) technique that maps heterodimer binding sites in endogenous genome context and applied it to elucidate the binding profiles of homo- and heterodimers of the Group C and S1 basic leucine zipper (bZIP) transcription factors in Arabidopsis. Genome-wide binding profiles of twenty pairs of bZIP C/S1 heterodimers and bZIP S1 homodimers revealed that heterodimerization significantly expands the DNA binding preferences of homodimers, creating unique binding sites and target gene functions. In addition to the classical ACGT elements recognized by plant bZIPs, we found the Group C/S1 dimers bind to sequence motifs that might share an origin with the yeast bZIP GCN4. Further analysis of heterodimer-specific binding sequences uncovered two types of motif recognition patterns that mediate heterodimer specificity. Our study shed light on the functions and mechanisms of TF dimerization and demonstrated the potential of dDAP-seq in deciphering the complexity of these interactions within or across TF families.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE198873 | GEO | 2023/04/06

REPOSITORIES: GEO

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Project description:Boehm2014 - isoform-specific dimerization of pSTAT5A and pSTAT5B To study STAT5 activation, the authors build a dynamic model of pSTAT5 isoform dimerization. Combinatorial binding of pSTAT5A and pSTAT5B is analysed using model hypotheses and concurrent experiments. Model parameters are derived from the experiments on Ba/F3 cells. Results show that pSTAT5 heterodimerization hypothesis for STAT5 activation favours experimental results. This model is described in the article: Identification of isoform-specific dynamics in phosphorylation-dependent STAT5 dimerization by quantitative mass spectrometry and mathematical modeling Boehm ME, Adlung L, Schilling M, Roth S, Klingmüller U, Lehmann WD J Proteome Res. 2014 Dec 5;13(12):5685-94 Abstract: STAT5A and STAT5B are important transcription factors that dimerize and transduce activation signals of cytokine receptors directly to the nucleus. A typical cytokine that mediates STAT5 activation is erythropoietin (Epo). Differential functions of STAT5A and STAT5B have been reported. However, the extent to which phosphorylated STAT5A and STAT5B (pSTAT5A, pSTAT5B) form homo- or heterodimers is not understood, nor is how this might influence the signal transmission to the nucleus. To study this, we designed a concept to investigate the isoform-specific dimerization behavior of pSTAT5A and pSTAT5B that comprises isoform-specific immunoprecipitation (IP), measurement of the degree of phosphorylation, and isoform ratio determination between STAT5A and STAT5B. For the main analytical method, we employed quantitative label-free and -based mass spectrometry. For the cellular model system, we used Epo receptor (EpoR)-expressing BaF3 cells (BaF3-EpoR) stimulated with Epo. Three hypotheses of dimer formation between pSTAT5A and pSTAT5B were used to explain the analytical results by a static mathematical model: formation of (i) homodimers only, (ii) heterodimers only, and (iii) random formation of homo- and heterodimers. The best agreement between experimental data and model simulations was found for the last case. Dynamics of cytoplasmic STAT5 dimerization could be explained by distinct nuclear import rates and individual nuclear retention for homo- and heterodimers of phosphorylated STAT5. This model is hosted on BioModels Database and identified by: BIOMD0000000591. To cite BioModels Database, please use: BioModels: Content, Features, Functionality, and Use.. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

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In vitro, genomic context identification of transcription factor binding sites for bZIP C/S1 homodimers and heterodimers

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