Biology subjects

Maranas, C. J.

Publications and source records attributed to Maranas, C. J..

5 recordsLinked to original sources

bioRxiv2026

Auxin coordinates cell states during Arabidopsis root development

Cell-to-cell variation in gene expression can be highly detrimental and, in some contexts, is actively buffered out; however, in other contexts, it is crucial and actively amplified. For example, variation must be minimized to build organs with consistent size and shape, yet the initiation of organogenesis requires a subset of cells to take on a new fate, a process that often relies on small differences between cells. In plants, much of development is controlled by the hormone auxin, which has been hypothesized to coordinate cell responses by inducing degradation of transcriptional repressors. To quantify the level of cell-to-cell variation and directly test its connection to auxin signaling, we assessed variation in expression of a lateral root founder cell marker GATA23 when auxin levels or responsiveness was modulated. We found that auxin acted as both an amplifier and a constrainer of transcriptional variation during the initiation of a new root. We then extended this work to analysis of root regeneration, where auxin was also found to play a critical role in coordinating cells during fate transitions. ARTICLE SUMMARYDuring organogenesis, cell-to-cell variation is induced, enabling some cells to adopt a new identity and differentiate. Despite this dependence on variation, organogenesis is robust in developmental stages and outcomes. In plants, organogenesis is usually controlled by the hormone auxin, and we hypothesized that auxin ensures coordination among differentiating cells to enable robust development. Using Arabidopsis lateral root development as a model, our results showed that cells receiving the highest auxin dosage both amplify their own auxin response and repress the auxin response in neighboring cells receiving lower auxin dosage, establishing separation between differentiating and non-differentiating cells and ensuring coordinated organogenesis.

developmental biology↗

bioRxiv2024

A Hot-Swappable Genetic Switch: Building an inducible and trackable functional assay for the essential gene MEDIATOR 21

Essential genes, estimated at approximately 20% of the Arabidopsis genome, are broadly expressed and required for reproductive success. They are difficult to study, as interfering with their function leads to premature death. Transcription is one of the essential functions of life, and the multi-protein Mediator complex coordinates the regulation of gene expression at nearly every eukaryotic promoter. In this study, we focused on a core Mediator component called MEDIATOR21 (MED21), which is required for activation of transcription. Our previous work has also shown a role for MED21 in repression of gene expression through its interaction with a corepressor protein. Here, we sought to differentiate the role MED21 plays in activation versus repression using the model plant Arabidopsis. As mutations in MED21 lead to embryo lethal phenotypes, we constructed a set of synthetic switches using PhiC31 serine integrases to create an "on-to-off" inducible loss of function MED21 in a non-essential tissue. Our technology, which we call Integrase Erasers, made it possible for med21 mutant plants to survive into adulthood by ablating protein expression selectively in lateral root primordia, allowing quantification and characterization of med21 mutant phenotypes in a post-embryonic context. In addition, we engineered chemical induction of the Integrase Eraser to ablate MED21 expression in whole seedlings at a user-specified timepoint. Finally, we extended this technology to build a hot swappable Integrase Isoform Switch where expression of the integrase toggled cells from expressing wildtype MED21 to expressing MED21 sequence variants. Our analysis of the entire set of new integrase-based tools demonstrates that this is a highly efficient and robust approach to the study of essential genes.

synthetic biology↗

bioRxiv2024

A history-dependent integrase recorder of plant gene expression with single cell resolution

During development, most cells experience a progressive restriction of fate that ultimately results in a fully differentiated mature state. Understanding more about the gene expression patterns that underlie developmental programs can inform engineering efforts for new or optimized forms. Here, we present a four-state integrase-based recorder of gene expression history and demonstrate its use in tracking gene expression events in Arabidopsis thaliana in two developmental contexts: lateral root initiation and stomatal differentiation. The recorder uses two serine integrases to mediate sequential DNA recombination events, resulting in step-wise, history-dependent switching between expression of fluorescent reporters. By using promoters that express at different times along each of the two differentiation pathways to drive integrase expression, we successfully tied fluorescent status to an ordered progression of gene expression along the developmental trajectory. In one snapshot of a mature tissue, our recorder was able to reveal past gene expression with single cell resolution. In this way, we were able to capture heterogeneity in stomatal development, confirming the existence of two alternate paths of differentiation.

synthetic biology↗

bioRxiv2023

A comparative analysis of stably expressed genes across diverse angiosperms exposes flexibility in underlying promoter architecture

Promoters regulate both the amplitude and pattern of gene expression--key factors needed for optimization of many synthetic biology applications. Previous work in Arabidopsis found that promoters that contain a TATA-box element tend to be expressed only under specific conditions or in particular tissues, while promoters which lack any known promoter elements, thus designated as Coreless, tend to be expressed more ubiquitously. To test whether this trend represents a conserved promoter design rule, we identified stably expressed genes across multiple angiosperm species using publicly available RNA-seq data. Comparisons between core promoter architectures and gene expression stability revealed differences in core promoter usage in monocots and eudicots. Furthermore, when tracing the evolution of a given promoter across species, we found that core promoter type was not a strong predictor of expression stability. Our analysis suggests that core promoter types are correlative rather than causative in promoter expression patterns and highlights the challenges in finding or building constitutive promoters that will work across diverse plant species.

plant biology↗

bioRxiv2022

An integrase toolbox to record gene-expression during plant development.

There are many open questions about the mechanisms that coordinate the dynamic, multicellular behaviors required for organogenesis. Synthetic circuits that can record in vivo signaling networks have been critical in elucidating animal development. Here, we report on the transfer of this technology to plants using orthogonal serine integrases to mediate site-specific and irreversible DNA recombination visualized by switching between fluorescent reporters. When combined with promoters expressed during lateral root initiation, integrases amplified reporter signal and permanently marked all descendants. In addition, we have developed a suite of methods to tune the threshold for integrase switching, including: RNA/protein degradation tags, a nuclear localization signal, and a split-intein system. These tools improved the robustness of integrase-mediated switching with different promoters and the stability of switching behavior over multiple generations. This integrase toolbox can be used to build history-dependent circuits to decode the order of expression during organogenesis in many contexts.

synthetic biology↗