Macy Vollbrecht

All Publications

• Multi-scale dynamics influence the division potential of stomatal lineage ground cells in Arabidopsis. Nature communications Fung, H. F., Amador, G. O., Dale, R., Gong, Y., Vollbrecht, M., Erberich, J. M., Mair, A., Bergmann, D. C. 2025; 16 (1): 2612

  Abstract

  During development, many precursor lineages are flexible, producing variable numbers and types of progeny cells. What determines whether precursors differentiate or continue dividing? Here we take a quantitative approach that combines long-term live imaging, statistical modeling and computational simulations to probe the developmental flexibility of stomatal lineage ground cells (SLGC) in Arabidopsis leaves. We discover that cell size is a strong predictor of SLGC behaviour and that cell size is linked to division behaviour at multiple spatial scales. At the neighbourhood scale, cell size correlates with the strength of cell-cell signaling, which affects the rate at which SPEECHLESS (SPCH), a division-promoting transcription factor, is degraded. At the subcellular scale, cell size correlates with nuclear size, which modulates the concentration of SPCH in the nucleus. Our work shows how initial differences in SPCH levels are canalized by nuclear size and cell-cell signaling to inform the behaviour of a flexible cell type.

  View details for DOI 10.1038/s41467-025-57730-9

  View details for PubMedID 40097420

• bHLH transcription factors cooperate with chromatin remodelers to regulate cell fate decisions during Arabidopsis stomatal development. PLoS biology Liu, A., Mair, A., Matos, J. L., Vollbrecht, M., Xu, S. L., Bergmann, D. C. 2024; 22 (8): e3002770

  Abstract

  The development of multicellular organisms requires coordinated changes in gene expression that are often mediated by the interaction between transcription factors (TFs) and their corresponding cis-regulatory elements (CREs). During development and differentiation, the accessibility of CREs is dynamically modulated by the epigenome. How the epigenome, CREs, and TFs together exert control over cell fate commitment remains to be fully understood. In the Arabidopsis leaf epidermis, meristemoids undergo a series of stereotyped cell divisions, then switch fate to commit to stomatal differentiation. Newly created or reanalyzed scRNA-seq and ChIP-seq data confirm that stomatal development involves distinctive phases of transcriptional regulation and that differentially regulated genes are bound by the stomatal basic helix-loop-helix (bHLH) TFs. Targets of the bHLHs often reside in repressive chromatin before activation. MNase-seq evidence further suggests that the repressive state can be overcome and remodeled upon activation by specific stomatal bHLHs. We propose that chromatin remodeling is mediated through the recruitment of a set of physical interactors that we identified through proximity labeling-the ATPase-dependent chromatin remodeling SWI/SNF complex and the histone acetyltransferase HAC1. The bHLHs and chromatin remodelers localize to overlapping genomic regions in a hierarchical order. Furthermore, plants with stage-specific knockdown of the SWI/SNF components or HAC1 fail to activate specific bHLH targets and display stomatal development defects. Together, these data converge on a model for how stomatal TFs and epigenetic machinery cooperatively regulate transcription and chromatin remodeling during progressive fate specification.

  View details for DOI 10.1371/journal.pbio.3002770

  View details for PubMedID 39150946

• Cell Fate Programming by Transcription Factors and Epigenetic Machinery in Stomatal Development. bioRxiv : the preprint server for biology Liu, A., Mair, A., Matos, J. L., Vollbrecht, M., Xu, S., Bergmann, D. C. 2023

  Abstract

  The development of multi-cellular organisms requires coordinated changes in gene expression that are often mediated by the interaction between transcription factors (TFs) and their corresponding cis-regulatory elements (CREs). During development and differentiation, the accessibility of CREs is dynamically modulated by the epigenome. How the epigenome, CREs and TFs together exert control over cell fate commitment remains to be fully understood. In the Arabidopsis leaf epidermis, meristemoids undergo a series of stereotyped cell divisions, then switch fate to commit to stomatal differentiation. Newly created or reanalyzed scRNA-seq and ChIP-seq data confirm that stomatal development involves distinctive phases of transcriptional regulation and that differentially regulated genes are bound by the stomatal basic-helix-loop-helix (bHLH) TFs. Targets of the bHLHs often reside in repressive chromatin before activation. MNase-seq evidence further suggests that the repressive state can be overcome and remodeled upon activation by specific stomatal bHLHs. We propose that chromatin remodeling is mediated through the recruitment of a set of physical interactors that we identified through proximity labeling - the ATPase-dependent chromatin remodeling SWI/SNF complex and the histone acetyltransferase HAC1. The bHLHs and chromatin remodelers localize to overlapping genomic regions in a hierarchical order. Furthermore, plants with stage-specific knock-down of the SWI/SNF components or HAC1 fail to activate specific bHLH targets and display stomatal development defects. Together these data converge on a model for how stomatal TFs and epigenetic machinery cooperatively regulate transcription and chromatin remodeling during progressive fate specification.

  View details for DOI 10.1101/2023.08.23.554515

  View details for PubMedID 37662219

• Parity-induced changes to mammary epithelial cells control NKT cell expansion and mammary oncogenesis. Cell reports Hanasoge Somasundara, A. V., Moss, M. A., Feigman, M. J., Chen, C., Cyrill, S. L., Ciccone, M. F., Trousdell, M. C., Vollbrecht, M., Li, S., Kendall, J., Beyaz, S., Wilkinson, J. E., Dos Santos, C. O. 2021; 37 (10): 110099

  Abstract

  Pregnancy reprograms mammary epithelial cells (MECs) to control their responses to pregnancy hormone re-exposure and carcinoma progression. However, the influence of pregnancy on the mammary microenvironment is less clear. Here, we used single-cell RNA sequencing to profile the composition of epithelial and non-epithelial cells in mammary tissue from nulliparous and parous female mice. Our analysis indicates an expansion of gammadelta natural killer T-like immune cells (NKTs) following pregnancy and upregulation of immune signaling molecules in post-pregnancy MECs. We show that expansion of NKTs following pregnancy is due to elevated expression of the antigen-presenting molecule CD1d on MECs. Loss of CD1d expression on post-pregnancy MECs, or overall lack of activated NKTs, results in mammary oncogenesis. Collectively, our findings illustrate how pregnancy-induced changes modulate the communication between MECs and the immune microenvironment and establish a causal link between pregnancy, the immune microenvironment, and mammary oncogenesis.

  View details for DOI 10.1016/j.celrep.2021.110099

  View details for PubMedID 34879282

• Fast-TrACC: A Rapid Method for Delivering and Testing Gene Editing Reagents in Somatic Plant Cells. Frontiers in genome editing Nasti, R. A., Zinselmeier, M. H., Vollbrecht, M., Maher, M. F., Voytas, D. F. 2021; 2

  Abstract

  The production of transgenic or gene edited plants requires considerable time and effort. It is of value to know at the onset of a project whether the transgenes or gene editing reagents are functioning as predicted. To test molecular reagents transiently, we implemented an improved, Agrobacterium tumefaciens-based co-culture method called Fast-TrACC (Fast Treated Agrobacterium Co-Culture). Fast-TrACC delivers reagents to seedlings, allowing high throughput, and uses a luciferase reporter to monitor and calibrate the efficiency of reagent delivery. We demonstrate the use of Fast-TrACC in multiple solanaceous species and apply the method to test promoter activity and the effectiveness of gene editing reagents.

  View details for DOI 10.3389/fgeed.2020.621710

  View details for PubMedID 34368798

  View details for PubMedCentralID PMC8344638

• Plant gene editing through de novo induction of meristems. Nature biotechnology Maher, M. F., Nasti, R. A., Vollbrecht, M., Starker, C. G., Clark, M. D., Voytas, D. F. 2020; 38 (1): 84-89

  Abstract

  Plant gene editing is typically performed by delivering reagents such as Cas9 and single guide RNAs to explants in culture. Edited cells are then induced to differentiate into whole plants by exposure to various hormones. The creation of edited plants through tissue culture is often inefficient, time-consuming, works for only limited species and genotypes, and causes unintended changes to the genome and epigenome. Here we report two methods to generate gene-edited dicotyledonous plants through de novo meristem induction. Developmental regulators and gene-editing reagents are delivered to somatic cells of whole plants. This induces meristems that produce shoots with targeted DNA modifications, and gene edits are transmitted to the next generation. The de novo induction of gene-edited meristems sidesteps the need for tissue culture and promises to overcome a bottleneck in plant gene editing.

  View details for DOI 10.1038/s41587-019-0337-2

  View details for PubMedID 31844292

  View details for PubMedCentralID PMC6954279