Biology subjects

Myers, Z. A.

Publications and source records attributed to Myers, Z. A..

7 recordsLinked to original sources

bioRxiv2026

Paralog diversification masks conserved diel regulatory programs during cold acclimation in Brassica rapa

Plant stress responses occur within daily cycles of physiology, metabolism, and growth, making timing a critical dimension of acclimation. In Arabidopsis, circadian and diel regulation influence responses to abiotic stress, including cold, but how this temporal regulation is conserved, diversified, or expanded in crop genomes remains unclear. This question is especially challenging in Brassica rapa, which underwent a genome triplication after diverging from Arabidopsis, resulting in multiple retained paralogs that can be grouped by Arabidopsis orthology and ancient homeologous relationships. Here, we generated a B. rapa pangenome spanning six morphotypes and used it to profile diel (24 h) cold acclimation responses across diverse accessions differing in freeze tolerances. Cold altered peak expression time for thousands of genes, which we grouped into distinct phase-change groups. Circadian leaf movement assays revealed accession-specific differences in clock period and temperature compensation under cold, suggesting that altered clock behavior may contribute in part to the diel transcriptome retiming. At the individual gene level, inferred gene regulatory networks (GRNs) were highly accession-specific and lost shared connectivity under cold stress. However, grouping these paralogs by their Arabidopsis orthologs revealed a highly conserved regulatory architecture that was otherwise masked by paralog diversification. Integrating these networks with functional pathways identified key candidate regulators of retimed processes, including modules linked to nighttime phosphorylation and daytime photosynthesis. Finally, analyzing conserved noncoding sequences across the pangenome prioritized specific regulatory targets within cold-retimed groups. Together, these results demonstrate that cold acclimation in B. rapa is shaped by a combination of diel retiming, paralog-specific regulation, and deeply conserved programs.

plant biology↗

bioRxiv2025

Single-Nucleus Transcriptomics Reveals How Tissue Context Shapes the Circadian Transcriptome of the Arabidopsis Leaf

Circadian regulation enables plants to coordinate cellular processes with daily environmental cycles, yet how clocks operate across cell and tissue types remains poorly understood. To resolve circadian regulation in the mature Arabidopsis thaliana leaf, we generated a 24-hour single nucleus RNA-sequencing (snRNA-seq) circadian time course spanning seven circadian time points and ~30,000 nuclei. We recovered all major leaf cell types and identified >7,400 genes with cluster-resolved rhythmic expression. Coexpression analyses defined five major temporal expression clades, revealing cell-type-specific phase shifts, while cluster-specific gene regulatory networks identified shared and unique transcription factor targets. These analyses suggest that core clock components broadly coordinate processes such as photosynthesis and light signaling while fine-tuning hormone, redox, and stress pathways in cell-type-specific manners. To restore the spatial information lost during nuclei isolation, we designed a 100-gene Xenium spatial transcriptomics panel and profiled intact mature leaves at relative dawn and dusk. Spatial transcriptomics validated cell-type-associated expression patterns from the single-nucleus time course and further revealed spatially restricted domains that were not apparent from cluster averages alone, including vascular subdomains and guard cell-associated differences in clock transcript accumulation. Several core clock components had unequal spatial distribution across similar cell types, suggesting potential fine-tuning of the clock in discrete spatial regions. Together, these findings show that the circadian transcriptional programs in the mature leaf are not simply cell-type-specific but spatially organized within the architecture of the organ.

plant biology↗

bioRxiv2024

Transcriptome profiling of maize transcription factor mutants to probe gene regulatory network predictions

Transcription factors (TFs) play important roles in regulation of gene expression and phenotype. A variety of approaches have been utilized to develop gene-regulatory networks (GRNs) to predict the regulatory targets for each TF, such as yeast-one-hybrid (Y1H) screens and gene co-expression network (GCN) analysis. Here we identified potential TF targets and used a reverse genetics approach to test the predictions of several GRNs in maize. Loss-of-function mutant alleles were isolated for 22 maize TFs. These mutants did not exhibit obvious morphological phenotypes. However, transcriptomic profiling identified differentially expressed genes in each of the mutant genotypes, and targeted metabolic profiling indicated variable phenolic accumulation in some mutants. An analysis of expression levels for predicted target genes based on Y1H screens identified a small subset of predicted targets that exhibit altered expression levels. The analysis of predicted targets from GCN-based methods found significant enrichments for prediction sets of some TFs, but most predicted targets did not exhibit altered expression. This could result from false-positive GCN predictions, a TF with a secondary regulatory role resulting in minor effects on gene regulation, or redundant gene regulation by other TFs. Collectively, these findings suggest that loss-of-function for single uncharacterized TFs might have limited phenotypic impacts but can reveal subsets of GRN predicted targets with altered expression.

plant biology↗

bioRxiv2022

Mapping Responsive Genomic Elements to Heat Stress in a Maize Diversity Panel

Many plant species exhibit genetic variation for tolerating environmental stress. A transcriptome investigation of over 100 maize inbreds revealed many cis- and trans-acting eQTLs that influence the expression response to heat stress. The cis-acting eQTL in response to heat stress are identified in genes with differential responses to heat stress between genotypes as well as genes that are only expressed under heat stress. The cis-acting variants for heat stress responsive expression likely result from distinct promoter activities and the differential heat responses of the alleles were confirmed for selected genes using transient expression assays. Global foot-printing of transcription factor binding was performed in control and heat stress conditions to document regions with heat-enriched transcription factor binding occupancies. Footprints enriched near proximal regions of characterized heat-responsive genes in a large association panel can be utilized for prioritizing functional genomic regions that regulate genotype-specific responses under heat stress.

plant biology↗

bioRxiv2022

Conserved and variable responses of the HEAT SHOCK FACTOR transcription factor family in maize and Setaria viridis

Responding to the environment is a core aspect of plant growth and development. Mounting an effective response is important for plants to balance growth and survival. The HEAT SHOCK FACTOR (HSF) transcription factor family is a central and required component of plant heat stress responses and acquired thermotolerance. The HSF family has dramatically expanded in plant lineages, often including a repertoire of 20 or more genes. Here we assess the composition and heat responsiveness of the HSF family in Setaria viridis (Setaria), a model C4 panicoid grass, and make targeted comparisons between the HSF families of Setaria and maize. Examples of both conserved and variable expression responses to a heat stress event were observed when comparing the two species. Novel and existing data on chromatin accessibility, histone modifications, and genome-wide DNA binding profiles were utilized to assess the chromatin of HSF family members with distinct responses to heat stress. We observed significant variability for both expression and chromatin state within syntenic and orthologous sets of HSFs between Setaria and maize, as well as between syntenic pairs of maize HSFs retained following its most recent genome duplication event. These observations collectively support a complex scenario of expansion and sub-functionalization within this transcription factor family that has significant untapped potential for better understanding the evolution of large gene families. Significance StatementA comparison of the Heat Shock Factor transcription factors in maize and Setaria reveals examples of consistent and variable expression responses to heat stress and provides insights into the role of chromatin in predicting expression responses.

plant biology↗

bioRxiv2021

Applying cis-regulatory codes to predict conserved and variable heat and cold stress response in maize

Changes in gene expression are important for response to abiotic stress. Transcriptome profiling performed on maize inbred and hybrid genotypes subjected to heat or cold stress identifies many transcript abundance changes in response to these environmental conditions. Motifs that are enriched near differentially expressed genes were used to develop machine learning models to predict gene expression responses to heat or cold. The best performing models utilize the sequences both upstream and downstream of the transcription start site. Prediction accuracies could be improved using models developed for specific co-expression clusters compared to using all up- or down-regulated genes or by only using motifs within unmethylated regions. Comparisons of expression responses in multiple genotypes were used to identify genes with variable response and to identify cis- or trans-regulatory variation. Models trained on B73 data have lower performance when applied to Mo17 or W22, this could be improved by using models trained on data from all genotypes. However, the models have low accuracy for correctly predicting genes with variable responses to abiotic stress. This study provides insights into cis-regulatory motifs for heat- and cold-responsive gene expression and provides a framework for developing models to predict expression response to abiotic stress across multiple genotypes. One sentence summaryTranscriptome profiling of maize inbred and hybrid seedlings subjected to heat or cold stress was used to identify key cis-regulatory elements and develop models to predict gene expression responses.

plant biology↗

bioRxiv2019

DIMR, a Yeast-Based Synthetic Reporter System for Probing Oligomeric Transcription Factor DNA Binding

Transcription factors (TFs) are fundamental components of biological regulation, facilitating the basal and differential gene expression necessary for life. TFs exert transcriptional regulation through interactions with both DNA and other TFs, ultimately influencing the action of RNA polymerase at a genomic locus. Current approaches are proficient at identification of binding site requirements for individual TFs, but few methods have been adapted to study oligomeric TF complexes. Further, many approaches that have been turned toward understanding DNA binding of TF complexes, such as electrophoretic mobility shift assays, require protein purification steps that can be burdensome or scope-limiting when considering more exhaustive experimental design. In order to address these shortfalls and to facilitate a more streamlined approach to understanding DNA binding by TF complexes, we developed the DIMR (Dynamic, Interdependent TF binding Molecular Reporter) system, a modular, yeast-based synthetic transcriptional activity reporter. As a proof of concept, we focused on the NUCLEAR FACTOR-Y (NF-Y) family of obligate heterotrimeric TFs in Arabidopsis thaliana. The DIMR system was able to reproduce the strict DNA-binding requirements of an experimentally validated NF-YA2/B2/C3 complex with high fidelity, including recapitulation of previously characterized mutations in subunits that either break NF-Y complex interactions or are directly involved in DNA binding. The DIMR system is a novel, powerful, and easy-to-use approach to address questions regarding the binding of oligomeric TFs to DNA.\n\nOne sentence summaryThe DIMR system provides an accessible and easy-to-use platform to elucidate DNA binding and transcriptional regulatory capacity of oligomeric transcription factor complexes

synthetic biology↗