Abstract
Many eukaryotic transcription factors (TF) form homodimer or heterodimer complexes to regulate gene expression. Dimerization of BASIC LEUCINE ZIPPER (bZIP) TFs are critical for their functions, but the molecular mechanism underlying the DNA binding and functional specificity of homo- versus heterodimers remains elusive. To address this gap, we present the double DNA Affinity Purification-sequencing (dDAP-seq) technique that maps heterodimer binding sites on endogenous genomic DNA. Using dDAP-seq we profile twenty pairs of C/S1 bZIP heterodimers and S1 homodimers in Arabidopsis and show that heterodimerization significantly expands the DNA binding preferences of these TFs. Analysis of dDAP-seq binding sites reveals the function of bZIP9 in abscisic acid response and the role of bZIP53 heterodimer-specific binding in seed maturation. The C/S1 heterodimers show distinct preferences for the ACGT elements recognized by plant bZIPs and motifs resembling the yeast GCN4 cis-elements. This study demonstrates the potential of dDAP-seq in deciphering the DNA binding specificities of interacting TFs that are key for combinatorial gene regulation.
| Original language | English |
|---|---|
| Article number | 2600 |
| Journal | Nature Communications |
| Volume | 14 |
| Issue number | 1 |
| DOIs | |
| State | Published - Dec 2023 |
Funding
This work was supported by the NIH award R35GM138143 to S.C.H. and NSF Plant Genome Research Project grant IOS-1916804 to S.C.H. and A.G. The work also supported by QBIST NIH T32 Training Program of NYU biology grant 1T32GM132037-01 to W.E.H. We thank Ken Birnbaum and Gloria Coruzzi for comments on the manuscript. The TF expression plasmids were a generous gift from Joseph Ecker. We thank Liang Song and Hong Qiao for suggestions on experimental design. This work was supported in part through the NYU IT High Performance Computing resources, services, and staff expertize. Sequencing was performed by the NYU Genomics Core Facility with generous subsidies from the Zegar Family Foundation. This research was in part supported by the Center for Bioenergy Innovation, a Bioenergy Research Center supported by the Office of Biological and Environmental Research in the U.S. Department of Energy Office of Science. Oak Ridge National Laboratory is managed by UT‐Battelle, LLC for the Office of Science of the U.S. Department of Energy under Contract Number DE‐AC05‐00OR22725. This work was supported by the NIH award R35GM138143 to S.C.H. and NSF Plant Genome Research Project grant IOS-1916804 to S.C.H. and A.G. The work also supported by QBIST NIH T32 Training Program of NYU biology grant 1T32GM132037-01 to W.E.H. We thank Ken Birnbaum and Gloria Coruzzi for comments on the manuscript. The TF expression plasmids were a generous gift from Joseph Ecker. We thank Liang Song and Hong Qiao for suggestions on experimental design. This work was supported in part through the NYU IT High Performance Computing resources, services, and staff expertize. Sequencing was performed by the NYU Genomics Core Facility with generous subsidies from the Zegar Family Foundation. This research was in part supported by the Center for Bioenergy Innovation, a Bioenergy Research Center supported by the Office of Biological and Environmental Research in the U.S. Department of Energy Office of Science. Oak Ridge National Laboratory is managed by UT‐Battelle, LLC for the Office of Science of the U.S. Department of Energy under Contract Number DE‐AC05‐00OR22725.
| Funders | Funder number |
|---|---|
| QBIST NIH | 1T32GM132037-01 |
| National Science Foundation | IOS-1916804 |
| National Institutes of Health | R35GM138143 |
| U.S. Department of Energy | DE‐AC05‐00OR22725 |
| Office of Science | |
| Biological and Environmental Research | |
| Center for Bioenergy Innovation | |
| Zegar Family Foundation |