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RNA-seq of Wild type Arabidopisis and two Nup96 mutants

ABSTRACT: Lines of evidence indicate that nuclear pore complex profoundly affects the timing of plant flowering, but the underlying mechanisms remain poorly elucidated. Here, we report that Nucleoporin 96 (Nup96) acts as a negative regulator of long-day photoperiodic flowering in Arabidopsis. Through multiple approaches, we identified and verified an E3 ubiquitin ligase HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE 1 (HOS1) interacting in vivo with Nup96. Nup96 and HOS1 proteins mainly localize and interact on nuclear membrane. Loss-of-function of Nup96 leads to destruction of HOS1 proteins without changing its mRNA abundance, which results in over-accumulation of the key activator of long-dayphotoperiodic flowering, CONSTANS (CO) proteins, as that in hos1 mutants. Unexpectedly, we observed that mutation of HOS1 gene strikingly diminishes Nup96 protein level, suggesting that Nup96 and HOS1 are mutually stabilized and thus they form a novel repressive module to regulate CO protein turnover. Therefore, the nup96 and hos1 single mutants and nup96 hos1 double mutant have very much similar early-flowering phenotypes and overlapping transcriptome changes. Together, this study reveals a new repression mechanism, where the Nup96-HOS1 repressive module gates the level of CO proteins, to prevent precocious flowering of Arabidopsis under long day conditions.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE138706 | GEO | 2019/10/31

REPOSITORIES: GEO

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Project description:The transition to flowering in plants is controlled by a regulatory network that responds to both developmental and environmental signals. The MADS-box genes FLOWERING LOCUS C (FLC) and SHORT VEGETATIVE PHASE (SVP) are major flowering repressors that enhance responses to environmental cues such as winter temperatures, high ambient temperatures and photoperiod. FLC and SVP physically interact in vivo and mutation of each gene causes early flowering while the double mutant is more extreme. The molecular mechanisms underlying these genetic interactions are mostly unknown. We addressed the regulatory input of these two key transcription factors (TFs) both individually and as a complex at the genome-wide level through ChIP-seq and microarray expression analysis in single and double mutants. Analysis of each TF demonstrated that the complex acts predominantly via functional redundancy in the repression of flowering. SVP and FLC bind to the same regions of the flowering genes SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) and FLOWERING LOCUS T (FT) but do not require the presence of the other to bind. However, genome-wide identification of SVP and FLC occupancy events revealed that their binding scenarios are quantitatively and qualitatively affected by the presence of the cognate partner. A subgroup of genes whose regulation by these TFs depends exclusively on combinatorial binding of both proteins was identified, demonstrating a qualitatively essential role of the SVP-FLC complex. Some of these genes are involved in the control of flowering through direct and indirect regulation of Gibberellin-related processes. Cis-regulatory elements enriched only at such complex-bound sites were identified. Thus the regulatory output mediated by SVP and FLC reveals substantial flexibility, leading to dependent and independent DNA binding that enables additive, cooperative and repressive modes of co-regulation. In total 48 samples; 24 leaf samples corresponding to two different growing conditions, 24 apex samples corresponding to two different growing conditions.

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RNA-seq of Wild type Arabidopisis and two Nup96 mutants

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