Double DAP-seq uncovered synergistic DNA binding of interacting bZIP transcription factors

Li, Miaomiao; Yao, Tao; Lin, Wanru; Hinckley, Will E.; Galli, Mary; Muchero, Wellington; Gallavotti, Andrea; Chen, Jin-Gui; Huang, Shao-shan Carol

doi:10.1038/s41467-023-38096-2

Double DAP-seq uncovered synergistic DNA binding of interacting bZIP transcription factors

Journal Article · Fri May 05 00:00:00 EDT 2023 · Nature Communications

DOI:https://doi.org/10.1038/s41467-023-38096-2· OSTI ID:1994639

^[1]; ^[2]; ^[1]; Hinckley, Will E. ^[1]; ^[3]; ^[2]; ^[3]; ^[2]; ^[1]

New York Univ. (NYU), NY (United States)
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Rutgers Univ., Piscataway, NJ (United States)

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.

View Accepted Manuscript (DOE)

Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH); National Science Foundation (NSF)

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1994639

Journal Information:: Nature Communications, Journal Name: Nature Communications Journal Issue: 1 Vol. 14; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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