Location: Plant Gene Expression Center
2022 Annual Report
Objectives
The long-term goal of this program is to define the molecular mechanisms by which the phy family of sensory photoreceptors perceive and transduce informational light signals from the environment to photoresponsive genes in regulating plant adaptational growth and development. The central goal of this proposal is to define the mechanisms by which the phys induce and modulate the Shade-Avoidance Response (SAR) in the constantly fluctuating light environment encountered in dense crop vegetational canopies. Toward this goal, the specific objectives for this funding period are:
Objective 1: Define the biological functions of the multiple Phy-Interacting transcription Factor (PIF)-family members in controlling the shade-avoidance response, including dissection of the relative contributions of the individual PIFs to this process.
Objective 2: Define the direct gene-targets of shade-active-PIF transcriptional regulation, and determine whether, and to what extent, this regulation involves differential direct targeting of rapidly shade-responsive genes by the individual PIF-family members.
Objective 3: Define the mechanism by which genes that lack apparent PIF regulation during skotomorphogenesis, but acquire PIF-dependent shade responsiveness in green seedlings (‘shade-specific’ genes), acquire this capacity.
Approach
Objective 1: To define the biological functions of the multiple Phy-Interacting transcription Factor (PIF)-family members in controlling the Shade-Avoidance Response (SAR), including dissection of the relative contributions of the individual PIFs to this process, we will perform phenotypic analyses of our array of higher order, pentuple and sextuple combinations of the pif mutants. This will enable us to define the relative quantitative contributions of the individual PIFs to the various facets of the SAR.
Objective 2: To define the direct gene-targets of shade-active-PIF transcriptional regulation, and determine whether, and to what extent, this regulation involves differential direct targeting of rapidly shade-responsive genes by the individual PIF-family members, we will analyze the global expression profiles of this set of higher-order pif-mutant combinations in response to shade, using RNA-seq, and identify the PIF-bound subset of these genes by ChIP-seq analysis. Direct targets of transcriptional regulation by the individual PIFs will be identified by integrating the RNA-seq and ChIP-seq data for each PIF as we have done for the PIF quartet in dark-grown seedlings.
Objective 3: To define the mechanism by which genes that lack apparent PIF regulation during skotomorphogenesis, but acquire PIF-dependent shade responsiveness in green seedlings (‘shade-specific’ genes), acquire this capacity, we will use ChIP-seq analysis for altered accessibility of PIF-binding sites and altered histone marks, indicative of nucleosome modifications, in response to shade. This will enable us to interrogate the genomes of light- and dark-grown Arabidopsis seedlings for differential histone-mark signatures correlated with the acquisition of PIF-dependent shade-signal responsiveness.
Progress Report
Three broad categories of light-signal-responsive genes, controlled directly by the phy-PIF module (DTGs), are known: those repressed by light and conversely induced by shade; those repressed by light, but subsequently unresponsive to shade; and those responsive to shade only. By using RNA sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq), time-resolved profiling of transcript and histone 3 lysine 4 trimethylation (H3K4me3) levels, respectively, ARS and University of California, Berkeley, researchers, in Albany, California, have shown that, whereas the initial dark-to-light transition triggers a rapid, temporally-coincident decline of both parameters, the light-to-shade transition, conversely, induces rapid increases in transcript levels, but these precede the increases in H3K4me3 levels. Together with other recent findings, these data indicate that, rather than being causal in the shade-induced expression changes, H3K4me3 may function to buffer the rapidly fluctuating shade/light switching that is intrinsic to plant canopies under natural sunlight conditions.
Accomplishments
1. Contemporary analysis of nucleosome modifications in phy-PIF sensory module under light and shade. ARS researchers in Albany, California, have performed research to help better understand photo and thermal responses in crops. Shade avoidance and other related phenomena have significant consequences for crop productivity and health and are controlled by genetic pathways that are conserved but not yet fully understood. A more complete understanding of the regulatory machinery that controls these responses will enable farmers and breeders of all crops to have better control of crop phenotypes under diverse future climate scenarios, including increased temperatures. To accomplish this, the researchers performed contemporaneous analysis of nucleosome modifications and transcriptional changes, mediated by the phy-PIF sensory module, in response to light and shade. The results revealed contrasting roles of induced chromatin modifications in regulating target-gene transcription, by these two environmental light signals.
Review Publications
Calderon, R.H., Dalton, J., Zhang, Y., Quail, P.H. 2022. Shade triggers posttranscriptional Phytochrome- interacting factor-dependent increases in H3K4 trimethylation. Plant Physiology. Article kiac282. https://doi.org/10.1093/plphys/kiac282.
Gonzalez-Grandio, E., Alamos, S., Zhang, Y., Dalton-Roesler, J., Niyogi, K.K., Garcia, H.G., Quail, P.H. 2022. Chromatin changes in Phytochrome interacting factor-regulated genes parallel their rapid transcriptional response to light. Frontiers in Plant Science. 13. Article 803441. https://doi.org/10.3389/fpls.2022.803441.
