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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.
Afiliação
  • Li M; Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA.
  • Yao T; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
  • Lin W; Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA.
  • Hinckley WE; Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA.
  • Galli M; Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA.
  • Muchero W; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
  • Gallavotti A; Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA.
  • Chen JG; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
  • Huang SC; Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA. s.c.huang@nyu.edu.
Nat Commun ; 14(1): 2600, 2023 05 05.
Article em En | MEDLINE | ID: mdl-37147307
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.
Assuntos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Arabidopsis / Proteínas de Arabidopsis Idioma: En Revista: Nat Commun Assunto da revista: BIOLOGIA / CIENCIA Ano de publicação: 2023 Tipo de documento: Article País de afiliação: Estados Unidos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Arabidopsis / Proteínas de Arabidopsis Idioma: En Revista: Nat Commun Assunto da revista: BIOLOGIA / CIENCIA Ano de publicação: 2023 Tipo de documento: Article País de afiliação: Estados Unidos