HISTONE DEACETYLASE 9 stimulates auxin-dependent thermomorphogenesis in Arabidopsis thaliana by mediating H2A.Z depletion

Many plant species respond to unfavorable high ambient temperatures by adjusting their vegetative body plan to facilitate cooling. This process is known as thermomorphogenesis and is induced by the phytohormone auxin. Here, we demonstrate that the chromatin-modifying enzyme HISTONE DEACETYLASE 9 (HDA9) mediates thermomorphogenesis but does not interfere with hypocotyl elongation during shade avoidance. HDA9 is stabilized in response to high temperature and mediates histone deacetylation at the YUCCA8 locus, a rate-limiting enzyme in auxin biosynthesis, at warm temperatures. We show that HDA9 permits net eviction of the H2A.Z histone variant from nucleosomes associated with YUCCA8, allowing binding and transcriptional activation by PHYTOCHROME INTERACTING FACTOR 4, followed by auxin accumulation and thermomorphogenesis

Splicing-related genes are alternatively spliced upon changes in ambient temperatures in plants

Plants adjust their development and architecture to small variations in ambient temperature. In a time in which temperatures are rising world-wide, the mechanism by which plants are able to sense temperature fluctuations and adapt to it, is becoming of special interest. By performing RNA-sequencing on two Arabidopsis accession and one Brassica species exposed to temperature alterations, we showed that alternative splicing is an important mechanism in ambient temperature sensing and adaptation. We found that amongst the differentially alternatively spliced genes, splicing related genes are enriched, suggesting that the splicing machinery itself is targeted for alternative splicing when temperature changes. Moreover, we showed that many different components of the splicing machinery are targeted for ambient temperature regulated alternative splicing. Mutant analysis of a splicing related gene that was differentially spliced in two of the genotypes showed an altered flowering time response to different temperatures. We propose a two-step mechanism where temperature directly influences alternative splicing of the splicing machinery genes, followed by a second step where the altered splicing machinery affects splicing of downstream genes involved in the adaptation to altered temperatures

Splicing-related genes are alternatively spliced upon changes in ambient temperatures in plants

<div><p>Plants adjust their development and architecture to small variations in ambient temperature. In a time in which temperatures are rising world-wide, the mechanism by which plants are able to sense temperature fluctuations and adapt to it, is becoming of special interest. By performing RNA-sequencing on two Arabidopsis accession and one Brassica species exposed to temperature alterations, we showed that alternative splicing is an important mechanism in ambient temperature sensing and adaptation. We found that amongst the differentially alternatively spliced genes, splicing related genes are enriched, suggesting that the splicing machinery itself is targeted for alternative splicing when temperature changes. Moreover, we showed that many different components of the splicing machinery are targeted for ambient temperature regulated alternative splicing. Mutant analysis of a splicing related gene that was differentially spliced in two of the genotypes showed an altered flowering time response to different temperatures. We propose a two-step mechanism where temperature directly influences alternative splicing of the splicing machinery genes, followed by a second step where the altered splicing machinery affects splicing of downstream genes involved in the adaptation to altered temperatures.</p></div

Alternative splicing in <i>FLM</i> and <i>MAF3</i>.

<p><b>(A)</b> Alternative splicing events in <i>FLM</i>. Top: raw reads in Integrative Genomics Viewer (IGV). Bottom: intron/exon structure of <i>FLM</i> with all detected splicing events. <b>(B)</b> Alternative splicing response of <i>MAF3</i> upon low ambient temperature in the IGV browser. Up: raw RNAseq reads of <i>MAF3</i> visualised in the IGV browser and the intron/exon structure of <i>MAF3</i> with all alternative splicing events. In grey the reads of the control temperature of 23°C, in blue the reads of the 16°C temperature treatment. The skipping of exon 2 is differential between the two temperatures, indicated by the asterisk (*). <b>(C)</b> RT-PCR on the same samples with <i>MAF3</i> primers at the start and stop codons and loaded on a 2% agarose gel. On the left the control temperature of 23° C, on the right the 16° C temperature treatment, each temperature with two biological replicates. The four different splicing events result in six different splice forms, as depicted next to the gel and was confirmed by Sanger sequencing (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0172950#pone.0172950.s009" target="_blank">S2 Fig</a>). Note that isoforms 3 and 4 are the only splice forms annotated in TAIR10. (N = 2 (16 plants per sample).</p

<i>atu2af65a</i> mutant has a flowering time phenotype and adapts differently to ambient temperature differences.

<p><b>(A)</b> Gene structure of <i>ATU2AF65A</i> showing the position of the T-DNA insertion in SALK_144790, used for mutant analysis, and the position of the temperature-sensitive splicing events. <b>(B)</b> wild type and <i>atu2af65a</i> plants grown at 16°C. Besides the flowering time phenotype shown in panel A, <i>atu2af65a</i> has a wild type appearance. <b>(C)</b> compared to wild type, <i>atu2af65a</i> showed an increased flowering time response upon higher ambient temperature, as calculated by the Total Leaf Number (TLN, including rosette and cauline leaves) at 22°C divided by the TLN at 27°C (presented as the ratio (R)_22°C:27°C). N = 21 plants (wild type 22°C, 27°C and <i>atu2af65a</i> 22°C) and 22 plant (<i>atu2af65a</i> 27°C). Error bars represent standard deviations.</p

Classes of splicing related Arabidopsis Col-0 genes that show differential splicing of at least one of the class members.

<p>Bars represent percentage of genes that is differentially spliced in each class. Total numbers of differentially spliced genes and all genes in each class (between brackets) are given at the end of each bar.</p

GO-term enrichment of differentially spliced Arabidopsis Col-0 genes upon ambient temperature treatment.

<p>GO terms with a corrected P-value < 0.005.–log10(corrected P-value) is shown for visualisation purposes.</p

Splicing events.

<p><b>(A)</b> Overview of splicing events that can occur. Alternative events are depicted in red, conventional events are depicted in black. Boxes represent exons, lines represent introns. <b>(B)</b> Distribution of the differential splicing events upon shifts to higher or lower ambient temperature, compared to the events in the total dataset. The asterisk * indicates a significant difference of the abundance of the event compared to the overall abundance (Using Pearson’s Chi-square test, for data used for significance test, see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0172950#pone.0172950.s002" target="_blank">S2 Table</a>).</p

HISTONE DEACETYLASE 9 stimulates auxin-dependent thermomorphogenesis in Arabidopsis thaliana by mediating H2A.Z depletion

Many plant species respond to unfavorable high ambient temperatures by adjusting their vegetative body plan to facilitate cooling. This process is known as thermomorphogenesis and is induced by the phytohormone auxin. Here, we demonstrate that the chromatin-modifying enzyme HISTONE DEACETYLASE 9 (HDA9) mediates thermomorphogenesis but does not interfere with hypocotyl elongation during shade avoidance. HDA9 is stabilized in response to high temperature and mediates histone deacetylation at the YUCCA8 locus, a rate-limiting enzyme in auxin biosynthesis, at warm temperatures. We show that HDA9 permits net eviction of the H2A.Z histone variant from nucleosomes associated with YUCCA8, allowing binding and transcriptional activation by PHYTOCHROME INTERACTING FACTOR 4, followed by auxin accumulation and thermomorphogenesis