Genome Wide Binding Site Analysis Reveals Transcriptional Coactivation of Cytokinin-Responsive Genes by DELLA Proteins

• DOI: 10.1371/journal.pgen.1005337
• Publication Date: 2015-07-02T18:12:33Z
• Authors: Nora Marín-de la ...; Anne Pfeiffer; Kristine Hill; Antonella Locascio; Rishikesh P. Bhal...; Pal Miskolczi; Anne L. Grønlund; Aakriti Wanchoo-K...; Stephen G. Thomas; Malcolm J. Bennett; Jan U. Lohmann; Miguel A. Blázquez; David Alabadí
• Keywords: Transcriptional Activation; 0301 basic medicine; 570; Chromatin Immunoprecipitation; Signaling pathways; Cytokinins; Gibberellin metabolism; DNA, Plant; Arabidopsis; Plant Development; QH426-470; Plant Roots; Arabidopsis-thaliana; 03 medical and health sciences; Genetics (medical genetics to be 30107 and agricultural genetics to be 40402); Gene Expression Regulation, Plant; Genetics; Molecular-mechanism; Promoter Regions, Genetic; 2. Zero hunger; Binding Sites; Base Sequence; Arabidopsis Proteins; Apical hook development; Root-meristem size; Functional genomics; Sequence Analysis, DNA; Coordinated regulation; DNA-Binding Proteins; Repressor Proteins; De-etiolation; Target genes; Research Article; Signal Transduction; Transcription Factors

The ability of plants to provide a plastic response to environmental cues relies on the connectivity between signaling pathways. DELLA proteins act as hubs that relay environmental information to the multiple transcriptional circuits that control growth and development through physical interaction with transcription factors from different families. We have analyzed the presence of one DELLA protein at the Arabidopsis genome by chromatin immunoprecipitation coupled to large-scale sequencing and we find that it binds at the promoters of multiple genes. Enrichment analysis shows a strong preference for cis elements recognized by specific transcription factor families. In particular, we demonstrate that DELLA proteins are recruited by type-B ARABIDOPSIS RESPONSE REGULATORS (ARR) to the promoters of cytokinin-regulated genes, where they act as transcriptional co-activators. The biological relevance of this mechanism is underpinned by the necessity of simultaneous presence of DELLAs and ARRs to restrict root meristem growth and to promote photomorphogenesis.