Genome‐wide binding analysis of AtGNC and AtCGA1 demonstrates their cross‐regulation and common and specific functions

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. variance from what has been described in animals, plant GATA transcription factors preferentially recognize and bind GATC rather than the GATA motif, and the two bases in the middle (AT) are more conserved than the flanking sequence of the binding core across the GATA family (Weirauch et al., 2014).--

Coordination of Chloroplast Development through the Action of the GNC and GLK Transcription Factor Families

“…Similar results 351 were observed when examining for the enrichment of the GATC-binding motif in the same 352 dataset. Prior studies suggest an autoregulatory role with members of the GNC family serving to 353 inhibit their own expression (Richter et al, 2010;Ranftl et al, 2016;Xu et al, 2017). We 354 identified GNC binding sites by ChIP-Seq in the promoters of GNC and CGA1, consistent with 355 direct inhibitory regulation, and confirmed that expression of both CGA1 and the native GNC 356 gene is inhibited in the 35S:GNC lines (Fig 5J, K).…”

“…9A). Prior studies have generally assumed that GNC will serve as 484 an activator, this informing the search for target genes (Hudson et al, 2011;Klermund et al, 485 2016;Xu et al, 2017), although a repressive function in the control of SOC1 for flowering time 486 was uncovered (Richter et al, 2013a). Even though the evidence suggests that GNC primarily 487 functions as a repressor, this does not preclude its functioning in some instances as a 488 transcriptional activator as we confirm that induction of GNC stimulates expression of the target 489 gene SPCH, consistent with a prior study .…”

GATA and Phytochrome Interacting Factor Transcription Factors Regulate Light-Induced Vindoline Biosynthesis in Catharanthus roseus

“…GNC and GNL bind the GATA motif in the GLU1 promoter (Hudson et al, 2011), whereas the tobacco GATA TF, AGP1, activates NtMYC2 by binding to the GATC motif in the NtMYC2 promoter (Sugimoto et al, 2003). Moreover, genome-wide binding analysis of GNC and GNL reveals that both GATA and GATC ciselements are enriched in the targets (Xu et al, 2017). We identified multiple GATA and GATC cis-elements in the promoters of DAT, D4H, T3R, T3O, and T16H2.…”

“…Previous studies have demonstrated that GATA TFs bind to both GATA and GATC motifs (Newton et al, 2001;Sugimoto et al, 2003;Xu et al, 2017). The D4H promoter, highly activated by CrGATA1 (Fig.…”

“…Class B GATAs (B-GATAs) are further subdivided into two families based on the presence of a conserved LLM (Leu-Leu-Met) domain or HAN (HANABA TARANU) domain (Behringer and Schwechheimer, 2015). In Arabidopsis, the expression of two homologous LLM B-GATAs, GNC (GATA-nitrate-induciblecarbon metabolism-involved) and GNL (GNC-like/ cytokinin-responsive GATA factor1), is induced by light known to regulate chlorophyll biosynthesis, chloroplast development, nitrate metabolism, seed germination, flowering time, hypocotyl elongation, and stomata development (Richter et al, 2010(Richter et al, , 2013a(Richter et al, , 2013bHudson et al, 2013;Klermund et al, 2016;Ranftl et al, 2016;Xu et al, 2017;Bastakis et al, 2018). In addition to GATA TFs, a small group of bHLH TFs, the Phytochrome Interacting Factors (PIFs), play crucial roles in light-responsive gene expression and downstream biological processes through interacting with phytochromes in plants (Leivar and Monte, 2014).…”