Abstract
GATA transcription factors are involved in multiple processes in plant growth and development. Two GATA factors, NITRATE‐INDUCIBLE,CARBON METABOLISM‐INVOLVED (GNC) and CYTOKININ‐RESPONSIVE GATA FACTOR 1 (CGA1, also named GNL), are important regulators in greening, flowering, senescence, and hormone signaling. However, their direct target genes related to these biological processes are poorly characterized. Here, GNC and CGA1 are shown to be transcription activators and by using chromatin immunoprecipitation sequencing (ChIP‐seq), 1475 and 638 genes are identified to be associated with GNC and CGA1 binding, respectively. Enrichment of diverse motifs in the peak binding regions for GNC and CGA1 suggests the possibility that these two transcription factors also interact with other transcription factors and in addition genes coding for DNA‐binding proteins are highly enriched among GNC‐ and CGA1‐associated genes. Despite the fact that these two GATA factors are known to share a large portion of co‐expressed genes, our analysis revealed a low percentage of overlapping binding‐associated genes for these two homologues. This suggests a possible cross‐regulation between these, which is verified using ChIP‐qPCR. The common and specific biological processes regulated by GNC and CGA1 also support this notion. Functional analysis of the binding‐associated genes revealed that those encoding transcription factors, E3 ligase, as well as genes with roles in plant development are highly enriched, indicating that GNC and CGA1 mediate complex genetic networks in regulating different aspects of plant growth and development.
Highlights
GATA transcription factors are present across eukaryotic species and are characterized by a distinctive and conserved type IV zinc finger DNA-binding domain, CX2CX17–20CX2C, which recognizes the consensus DNA sequence WGATAR (W = T or A; R = G or A)(Lowry & Atchley, 2000)
Our findings suggest that GNC and CGA1 are associated with complex genetic networks involved in the regulation of developmental processes
Due to the fact that these two transcription factors share a high percentage (~70%) of co-expressed genes according to the ATTED-II database (Aoki, Okamura, Tadaka, Kinoshita, & Obayashi, 2016) (Data S6), we propose that GNC and CGA1 could be cross-regulated
Summary
GNC and CGA1 showed similar expression patterns and loss of function mutants displayed a similar phenotype with additive phenotypes observed in the gnc cga double mutant (Manfield et al, 2007; Mara & Irish, 2008) These two GATA factors were reported to be involved in multiple processes and signaling pathways in Arabidopsis. Other recent studies of the Arabidopsis LLM-domain-containing class B-GATA factors (B-GATAs), including GNC and CGA1, revealed their further and partially redundant functions in greening, hypocotyl elongation, and cytokinin-regulated development (Behringer, Bastakis, Ranftl, Mayer, & Schwechheimer, 2014; Ranftl, Bastakis, Klermund, & Schwechheimer, 2016) They have been suggested to act downstream of light signaling pathways to promote stomatal development in hypocotyls (Klermund et al, 2016). We present evidence that GNC and CGA1 cross-regulate each other which accounts for their overlapping and diverse physiological roles
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