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Identification of plant transcriptional activation domains.
Morffy, Nicholas; Van den Broeck, Lisa; Miller, Caelan; Emenecker, Ryan J; Bryant, John A; Lee, Tyler M; Sageman-Furnas, Katelyn; Wilkinson, Edward G; Pathak, Sunita; Kotha, Sanjana R; Lam, Angelica; Mahatma, Saloni; Pande, Vikram; Waoo, Aman; Wright, R Clay; Holehouse, Alex S; Staller, Max V; Sozzani, Rosangela; Strader, Lucia C.
Affiliation
  • Morffy N; Department of Biology, Duke University, Durham, NC, USA.
  • Van den Broeck L; Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA.
  • Miller C; Department of Biology, Duke University, Durham, NC, USA.
  • Emenecker RJ; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA.
  • Bryant JA; Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA.
  • Lee TM; Biological Systems Engineering, Virginia Tech, Blacksburg, VA, USA.
  • Sageman-Furnas K; Department of Biology, Duke University, Durham, NC, USA.
  • Wilkinson EG; Department of Biology, Duke University, Durham, NC, USA.
  • Pathak S; Department of Biology, Duke University, Durham, NC, USA.
  • Kotha SR; Department of Biology, Duke University, Durham, NC, USA.
  • Lam A; Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.
  • Mahatma S; Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.
  • Pande V; Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA.
  • Waoo A; Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA.
  • Wright RC; Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA.
  • Holehouse AS; Biological Systems Engineering, Virginia Tech, Blacksburg, VA, USA.
  • Staller MV; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA.
  • Sozzani R; Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA.
  • Strader LC; Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.
Nature ; 632(8023): 166-173, 2024 Aug.
Article in En | MEDLINE | ID: mdl-39020176
ABSTRACT
Gene expression in Arabidopsis is regulated by more than 1,900 transcription factors (TFs), which have been identified genome-wide by the presence of well-conserved DNA-binding domains. Activator TFs contain activation domains (ADs) that recruit coactivator complexes; however, for nearly all Arabidopsis TFs, we lack knowledge about the presence, location and transcriptional strength of their ADs1. To address this gap, here we use a yeast library approach to experimentally identify Arabidopsis ADs on a proteome-wide scale, and find that more than half of the Arabidopsis TFs contain an AD. We annotate 1,553 ADs, the vast majority of which are, to our knowledge, previously unknown. Using the dataset generated, we develop a neural network to accurately predict ADs and to identify sequence features that are necessary to recruit coactivator complexes. We uncover six distinct combinations of sequence features that result in activation activity, providing a framework to interrogate the subfunctionalization of ADs. Furthermore, we identify ADs in the ancient AUXIN RESPONSE FACTOR family of TFs, revealing that AD positioning is conserved in distinct clades. Our findings provide a deep resource for understanding transcriptional activation, a framework for examining function in intrinsically disordered regions and a predictive model of ADs.
Subject(s)

Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Transcription Factors / Transcriptional Activation / Arabidopsis / Gene Expression Regulation, Plant / Arabidopsis Proteins / Protein Domains Language: En Journal: Nature Year: 2024 Document type: Article Affiliation country: Estados Unidos Country of publication: Reino Unido

Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Transcription Factors / Transcriptional Activation / Arabidopsis / Gene Expression Regulation, Plant / Arabidopsis Proteins / Protein Domains Language: En Journal: Nature Year: 2024 Document type: Article Affiliation country: Estados Unidos Country of publication: Reino Unido