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Abstract The precise onset of flowering is crucial to ensure successful plant reproduction. The geneFLOWERING LOCUS T(FT) encodes florigen, a mobile signal produced in leaves that initiates flowering at the shoot apical meristem. In response to seasonal changes,FTis induced in phloem companion cells located in distal leaf regions. Thus far, a detailed molecular characterization of theFT-expressing cells has been lacking. Here, we used bulk nuclei RNA-seq and single nuclei RNA (snRNA)-seq to investigate gene expression inFT-expressing cells and other phloem companion cells. Our bulk nuclei RNA-seq demonstrated thatFT-expressing cells in cotyledons and in true leaves differed transcriptionally. Within the true leaves, our snRNA-seq analysis revealed that companion cells with highFTexpression form a unique cluster in which many genes involved in ATP biosynthesis are highly upregulated. The cluster also expresses other genes encoding small proteins, including the flowering and stem growth inducer FPF1-LIKE PROTEIN 1 (FLP1) and the anti-florigen BROTHER OF FT AND TFL1 (BFT). In addition, we found that the promoters ofFTand the genes co-expressed withFTin the cluster were enriched for the consensus binding motifs of NITRATE-INDUCIBLE GARP-TYPE TRANSCRIPTIONAL REPRESSOR 1 (NIGT1). Overexpression of the paralogousNIGT1.2andNIGT1.4repressedFTexpression and significantly delayed flowering under nitrogen-rich conditions, consistent with NIGT1s acting as nitrogen-dependentFTrepressors. Taken together, our results demonstrate that majorFT-expressing cells show a distinct expression profile that suggests that these cells may produce multiple systemic signals to regulate plant growth and development. 

Abstract Proper cell-type identity relies on highly coordinated regulation of gene expression. Regulatory elements such as enhancers can produce cell type-specific expression patterns, but the mechanisms underlying specificity are not well understood. We previously identified an enhancer region capable of driving specific expression in giant cells, which are large, highly endoreduplicated cells in the Arabidopsis thaliana sepal epidermis. In this study, we use the giant cell enhancer as a model to understand the regulatory logic that promotes cell type-specific expression. Our dissection of the enhancer revealed that giant cell specificity is mediated primarily through the combination of two activators and one repressor. HD-ZIP and TCP transcription factors are involved in the activation of expression throughout the epidermis. High expression of HD-ZIP transcription factor genes in giant cells promoted higher expression driven by the enhancer in giant cells. Dof transcription factors repressed the activity of the enhancer such that only giant cells maintained enhancer activity. Thus, our data are consistent with a conceptual model whereby cell type-specific expression emerges from the combined activities of three transcription factor families activating and repressing expression in epidermal cells. 

Abstract ARGONAUTES are the central effector proteins ofRNAsilencing which bind target transcripts in a smallRNA‐guided manner.Arabidopsis thalianahas 10ARGONAUTE(AGO) genes, with specialized roles inRNA‐directedDNAmethylation, post‐transcriptional gene silencing, and antiviral defense. To better understand specialization amongAGOgenes at the level of transcriptional regulation we tested a library of 1497 transcription factors for binding to the promoters ofAGO1,AGO10, andAGO7using yeast 1‐hybrid assays. A ranked list of candidateDNA‐bindingTFs revealed binding of theAGO7promoter by a number of proteins in two families: the miR156‐regulatedSPLfamily and the miR319‐regulatedTCPfamily, both of which have roles in developmental timing and leaf morphology. Possible functions forSPLandTCPbinding are unclear: we showed that these binding sites are not required for the polar expression pattern ofAGO7, nor for the function ofAGO7in leaf shape. NormalAGO7transcription levels and function appear to depend instead on an adjacent 124‐bp region. Progress in understanding the structure of this promoter may aid efforts to understand how the conservedAGO7‐triggeredTAS3pathway functions in timing and polarity.