Recent advances in the chromatin-based mechanism of FLOWERING LOCUS C repression through autonomous pathway genes

Proper timing of flowering, a phase transition from vegetative to reproductive development, is crucial for plant fitness. The floral repressor FLOWERING LOCUS C (FLC) is the major determinant of flowering in Arabidopsis thaliana. In rapid-cycling A. thaliana accessions, which bloom rapidly, FLC is constitutively repressed by autonomous pathway (AP) genes, regardless of photoperiod. Diverse AP genes have been identified over the past two decades, and most of them repress FLC through histone modifications. However, the detailed mechanism underlying such modifications remains unclear. Several recent studies have revealed novel mechanisms to control FLC repression in concert with histone modifications. This review summarizes the latest advances in understanding the novel mechanisms by which AP proteins regulate FLC repression, including changes in chromatin architecture, RNA polymerase pausing, and liquid-liquid phase separation- and ncRNA-mediated gene silencing. Furthermore, we discuss how each mechanism is coupled with histone modifications in FLC chromatin.N

The two clock proteins CCA1 and LHY activate VIN3 transcription during vernalization through the vernalization-responsive cis-element

Vernalization, a long-term cold-mediated acquisition of flowering competence, is critically regulated by VERNALIZATION INSENSITIVE 3 (VIN3), a gene induced by vernalization in Arabidopsis. Although the function of VIN3 has been extensively studied, how VIN3 expression itself is upregulated by long-term cold is not well understood. In this study, we identified a vernalization-responsive cis-element in the VIN3 promoter, VREVIN3, composed of a G-box and an evening element (EE). Mutations in either the G-box or the EE prevented VIN3 expression from being fully induced upon vernalization, leading to defects in the vernalization response. We determined that the core clock proteins CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1) and LATE-ELONGATED HYPOCOTYL (LHY) associate with the EE of VREVIN3, both in vitro and in vivo. In a cca1 lhy double mutant background harboring a functional FRIGIDA allele, long-term cold-mediated VIN3 induction and acceleration of flowering were impaired, especially under mild cold conditions such as at 12°C. During prolonged cold exposure, oscillations of CCA1/LHY transcripts were altered, while CCA1 abundance increased at dusk, coinciding with the diurnal peak of VIN3 transcripts. We propose that modulation of the clock proteins CCA1 and LHY participates in the systems involved in sensing long-term cold for the activation of VIN3 transcription.N

Comparaison des echantillonnages aleatoires et stratifies pour la mesure de la biomasse sur pied d'un parcours herbeux a Oryza longistaminata des plaines d'inondation du Niger

Etude comparative de divers protocoles de mesure de la biomasse aerienne du tapis herbace pour inventorier le potentiel fourrager des parcours a Oryza longistaminata des plaines d'inondation du Niger proche de Moura et de ses abords saheliens a l'aide d'une comparaison de deux modes d'echantillonage aleatoire et stratifie

Heterophyllic leaf developments depending on environments are shown in <i>R</i>. <i>trichophyllus</i> but not in sister species, <i>R</i>. <i>sceleratus</i>.

<p>Seedling morphologies and microscopic images of <i>R</i>. <i>trichophyllus</i> (A) and <i>R</i>. <i>sceleratus</i> (B) grown under aerial vs aquatic environments. Seeds of <i>R</i>. <i>trichophyllus</i> or <i>R</i>. <i>sceleratus</i> were germinated on solid MS media for 1 week, then transferred to aerial or aquatic environments. The true leaves produced at 7 days after transference were used for analysis. (<i>a-d</i>) terrestrial and (<i>e-h</i>) aquatic/submerged plants, (<i>b</i>, <i>c</i>) cell shapes of terrestrial leaves and (<i>f</i>, <i>g</i>) those of aquatic/submerged leaves, (<i>d</i>) vasculature of terrestrial and (<i>h</i>) that of aquatic leaves. (<i>i-k</i>) Statistical analyses of leaf indices (<i>i</i>), stomatal densities (<i>j</i>), and number of vessel elements (<i>k</i>) in terrestrial and aquatic/submerged leaves. Data are collected from 24 individual samples and presented as means ± SD from three biological replicates. Black arrowheads denote stomata and white arrowheads denote individual vessel element.</p

Effects of ethylene and ABA signalings on the promoter activation of leaf polarity genes and genes critical for stomata and vascular developments.

<p>(A and B) Luminescence analysis of <i>proRtKANa</i>::<i>LUC</i> when added with ACC, an ethylene precursor, or ABA in protoplast solution (A), control; without chemical treatment, and when cotransfected with <i>CFP-RtEIN3</i> in protoplasts (B), control; cotransfected with <i>CFP</i> construct. (C) Effects of <i>CFP-RtEIN3</i> transfection on the relative expressions of endogenous <i>KAN</i> genes in protoplasts, control; transfected with <i>CFP</i> construct. (D and E) Luminescence analysis of <i>proHD-ZIPIIIa</i>::<i>LUC</i> when added with ACC or ABA in protoplast solution (D), control; without chemical treatment, and when cotransfected with <i>CFP-RtABI3</i> in protoplasts (E), control; cotransfected with CFP construct. (F) Effects of <i>CFP-RtABI3</i> transfection on the relative expressions of endogenous <i>HD-ZIPIII</i> genes in protoplasts, control; transfected with <i>CFP</i> construct. (G) Relative transcript levels of <i>RtSTO</i> and <i>RtVDN7</i>, encoding critical regulators of stomata and vascular developments, when transfected with <i>Rt-EIN3</i>, <i>Rt-ABI3</i>, and <i>RtHD-ZIPIIIa</i> fused with <i>CFP</i> coding sequence. Control; transfected with <i>CFP</i> construct. (H) Comparison of transcript levels of <i>RtSTO</i> and <i>RtVND7</i> between terrestrial and aquatic leaves of <i>R</i>. <i>trichophyllus</i>. *<i>P</i> < 0.05; **<i>P</i> < 0.01; ***<i>P</i> < 0.001 (unpaired Student’s <i>t</i>-test).</p

Differential expression of ethylene and ABA-related genes under terrestrial and aquatic environments is specific to amphibious <i>R</i>. <i>trichophyllus</i>.

<p>(A and B). Contents of ethylene (A) and ABA (B) in terrestrial vs aquatic leaves. (C and D). Comparison of transcript levels of ethylene- (A) and ABA- (B) biosynthesis and responsive genes following submergence into water. Plants harvested at 7 hours (7h), 1 day (1d), and 2 days (2d) after submergence were compared with terrestrial and aquatic plants for expressions. (E) Effects of submergence on the expression levels of <i>AAO3</i> genes in <i>R</i>. <i>trichophyllus</i>, Arabidopsis, and <i>R</i>. <i>sceleratus</i>. For submergence, two weeks old plants grown on solid MS media were submerged into water for 5 days for RNA extraction. The data represent means ± standard error from three biological and two technical replicates.</p

Cold and hypoxia induce aquatic leaf development in <i>R</i>. <i>trichophyllus</i>.

<p>(A) Heterophylly induced by cold and hypoxia. 1 week-old seedlings after germination on the MS media were transferred to cold chamber (4°C) for 1 month or hypoxia chamber (1% O₂) for 2 weeks. The column Room Temp is a control at 22°C with 20% O₂. (B and C) Gene expression analyses of <i>KAN</i> genes (B), and <i>HD-ZIPIII</i> genes (C) in the leaves after cold for 1 month and hypoxia for 2 weeks treated. *<i>P</i> < 0.05; **<i>P</i> < 0.01 (unpaired Student’s <i>t</i>-test).</p

Transcriptome analysis of aquatic vs terrestrial plants of <i>R</i>. <i>trichophyllus</i>.

<p>(A) Venn diagram of differentially expressed transcripts with two fold changes for three independent experiments. Numbers are up- or down-regulated genes in aquatic plants compared to terrestrial plants. (B) Diagram for large ontology categories showing up-regulation in aquatic plants by BinGo software. Number of genes is represented by relative size of circles that belong to each gene ontology term. (C) Relative expression of genes affiliated to four developmental GO terms for terrestrial vs aquatic plants of <i>R</i>. <i>trichophyllus</i>. Up-regulated genes are painted with red and down-regulated genes are painted with blue. (D) Diagram of up-regulated genes in aquatic plants for ontology categories of plant hormone response genes by the BinGo software. The seedlings, 1 week-old after germination, were transferred to terrestrial or aquatic condition for 10 days. Upper parts of seedlings including leaves and shoot apexes were harvested for RNA sequencing.</p

Expressions of leaf polarity genes, <i>KANs</i> and <i>HD-ZIPIIIs</i> are dependent on the environment.

<p>(A and B) Gene expression analyses of <i>KAN</i> genes (A), and <i>HD-ZIPIII</i> genes in terrestrial and aquatic leaves. (C and D) Transcript levels of leaf polarity genes after chemical treatments. The data are presented as means ± SD from three biological and two technical replicates. ACC, an ethylene precursor, was treated as ethylene. *<i>P</i> < 0.05; **<i>P</i> < 0.01 (unpaired Student’s <i>t</i>-test) (E) Model of heterophyllic developments regulated by ABA and ET activating leaf polarity genes, <i>KANs</i> and <i>HD-ZIPIIIs</i>, respectively. K; <i>KANADIs</i>, H; <i>HD-ZIPIIIs</i>. (F-M) Whole mount <i>in situ</i> hybridization for <i>RtKANa</i> (F-I) and <i>RtHD-ZIPIIIa</i> (J-M). Ab, abaxial side; Ad, adaxial side.</p

Ethylene and ABA control heterophylly of <i>R</i>. <i>trichophyllus</i>.

<p>(A) Images of seedlings, stomata, and vessel elements for terrestrial leaf and the leaf after ethylene treatment. (B) Images of seedling, stomata, and vessel elements for aquatic leaf and the leaf after treatment of ABA and AgNO₃, an ethylene inhibitor. (C-E) Statistical analyses of leaf indices (C), stomatal densities (D), and number of vessel elements (E) after treatment with hormones (ethylene, ABA, and GA) and hormone inhibitors (AgNO₃ and PBZ). Data are collected from 16–24 individual samples and presented as means ± SD from three biological replicates. Black arrowheads denote stomata and white arrowheads denote individual vessel element. *<i>P</i> < 0.05; **<i>P</i> < 0.01 (unpaired Student’s <i>t</i>-test).</p