Biology subjects

Lee, T. A.

Publications and source records attributed to Lee, T. A..

6 recordsLinked to original sources

bioRxiv2026

Transient cell states encode positional information to direct asymmetric growth

How tissues generate asymmetric growth from spatially and temporally restricted signals remains a fundamental challenge in developmental biology. We show that transient cell states encode positional information that instructs asymmetric growth in plants. Using spatial single-cell transcriptomics and multi-omics, we uncover a surprisingly complex landscape of transient cell states in the apical hook, including a previously unrecognized population in the apical hypocotyl region that integrates developmental and hormonal cues and bifurcates into opposing growth trajectories. Gene regulatory network analysis and functional perturbation establish GATA TRANSCRIPTION FACTOR 2 (GATA2) as a central regulator that promotes cell elongation through gibberellin signaling. These results reveal that diverse, spatially localized transient cell states function as regulatory hubs that convert positional information into divergent growth programs, providing a unifying framework for how dynamic cellular states shape organ morphology.

plant biology↗

bioRxiv2026

Precision-Based Filtering Facilitates Integration of Conventional and Single-Nucleus Transcriptomes to Identify Time- and Temperature-Sensitive Cell Populations

Transcriptome analysis via RNA sequencing (RNAseq) has become a ubiquitous method of molecular characterization from whole organisms, dissected tissues, and single cells. These experiments have provided an extraordinary volume of data describing the molecular states and responses to many conditions. However, standard approaches to RNAseq analysis commonly use expression level filters that eliminate potentially useful data in the service of decreasing noise. Here we describe the implementation of a coefficient of variation-based filter for RNAseq gene expression data. This filter prioritizes consistent data across replicates, allowing lowly-expressed genes with low-variation measurements to be retained for downstream analysis. We show that, in our Arabidopsis RNAseq data set, this filter allows for the inclusion of many more transcription factors than even a low-stringency expression level filter. We find that these lowly-expressed genes mark specific cell clusters in our single-nucleus (sn)RNAseq dataset. We further characterize communities of co-expressed genes, sampled across the day at two growth temperatures, in relation to snRNAseq cell clusters, finding evidence for a highly photosynthetic cell population, and a cell state marked by high cell division and translation. These methods can be expanded to RNAseq analysis in many systems, facilitating the construction of more detailed models of tissue-specific gene regulatory networks.

bioinformatics↗

bioRxiv2024

Cybernetic control of a natural microbial co-culture

A key obstacle in the widespread application of microbial co-cultures in bioprocesses is their compositional instability, as faster-growing species outcompete and dominate the culture. While several synthetic biology approaches have demonstrated control over co-culture composition, there has been an increased interest in computer-based cybernetic control approaches that can offload burdensome genetic control circuitry to computers and enable dynamic control and real-time noise rejection. This work extends that approach, demonstrating a cybernetic control method that is not reliant on any genetic engineering, instead interfacing cells with computers by exploiting their natural characteristics to measure and actuate the composition. We apply this to a Pseudomonas putida (P. putida) and Escherichia coli (E. coli) co-culture grown in Chi.Bio bioreactors, first showing how composition estimates calculated from different bioreactor measurements can be combined with a system model using an extended Kalman filter to generate accurate estimates of a noisy system. We also demonstrate that because the species have different optimal temperature niches, adjusting the temperature of the culture can drive the composition in either direction. By using a proportional-integral control algorithm to calculate the temperature that would bring the measured composition towards the desired composition, we are able to track dynamic references and stabilised the co-culture for 7 days ([~]250 generations), with the experiment ending before the cells could adapt out of the control. This cybernetic framework is broadly applicable, with different microbes unique features and specific growth niches enabling robust control over diverse co-cultures.

systems biology↗

bioRxiv2023

Time-resolved single-cell and spatial gene regulatory atlas of plants under pathogen attack

Plant leaf intercellular space provides a nutrient-rich and heterogeneous niche for microbes that critically impacts plant health. However, how individual plant cells respond to heterogeneous microbial colonization remains largely elusive. Here, by time-resolved simultaneous single-cell transcriptome and epigenome profiling of plants (Arabidopsis thaliana) infected by virulent and avirulent bacterial pathogens (Pseudomonas syringae), we present cell atlases with gene regulatory logic involving transcription factors, putative cis-regulatory elements, and target genes associated with disease and immunity. We also identify previously uncharacterized cell populations with distinct immune gene expression within major developmental cell types. Furthermore, we employ time-resolved spatial transcriptomics to reveal spatial heterogeneity of plant immune responses linked to pathogen distribution. Integrating our single-cell multiomics and spatial omics data enables spatiotemporal mapping of defense gene regulatory logic with pathogen cells. Our study provides a molecularly-defined spatiotemporal map of plant-microbe interaction at the single-cell resolution.

plant biology↗

bioRxiv2023

A Single-Nucleus Atlas of Seed-to-Seed Development in Arabidopsis

Extensive studies of the reference plant Arabidopsis have enabled a deep understanding of tissues throughout development, yet a census of cell types and states throughout development is lacking. Here, we present a single-nucleus transcriptome atlas of seed-to-seed development employing over 800,000 nuclei, encompassing a diverse set of tissues across ten developmental stages, with spatial transcriptomic validation of the dynamic seed and silique. Cross-organ analyses revealed transcriptional conservation of cell types throughout development and heterogeneity within individual cell types influenced by organ-of-origin and developmental timing, including groups of transcription factors, suggesting gatekeeping by transcription factor activation. This atlas provides a resource for the study of cell type specification throughout the development continuum and a reference for stimulus-response and genetic perturbations at the single-cell resolution.

plant biology↗

bioRxiv2018

Integrated multiomic analysis from chromatin to translation of stimulus-regulated gene activity exposes dominant patterns of nuclear-level control

Gene regulation is modulated from chromatin to translation. To better understand the integration of nuclear and cytoplasmic gene regulatory dynamics, we performed a multi-omic survey of the epigenome through the translatome of the response of Arabidopsis seedlings to hypoxia and reoxygenation. This included eight assays of chromatin (histones, accessibility, RNAPII and transcription factor binding) and three assays of RNA (nuclear, polyadenylated, and ribosome-associated). Dynamic patterns of nuclear regulation distinguished stress-induced and growth-associated mRNAs. The rapid upregulation of hypoxia-responsive gene transcripts and their preferential translation was accompanied by increased chromatin accessibility, RNAPII engagement and reduced Histone 2A.Z association. The more progressive upregulation of heat stress gene transcripts was characterized by early engagement of RNAPII and elevation of nuclear over polyadenylated RNA. Promoters of the rapidly versus progressively upregulated gene cohorts were enriched for cis-elements of ethylene-responsive and heat shock factor transcription factor families, respectively. By contrast, genes associated with growth including ribosomal proteins underwent distinct histone modifications, yet retained RNAPII engagement and accumulated nuclear transcripts during the stress. Upon reaeration, many of the progressively upregulated and growth-associated gene transcripts were mobilized to ribosomes. Thus, multi-level nuclear regulation distinguishes transcript synthesis, accumulation and translation in response to a transient stress.

plant biology↗