Marina Oliva (@moliva.bsky.social)

Marina Oliva

@moliva.bsky.social

Biologist at The University of Western Australia

@moliva.bsky.social

Are plant roots really made up of concentric layers of homogeneous, differentiating cell types? In our new study, out now in @nature.com, we show a more complex picture: two distinct cell states within root lineages, shaped in part by the environment. 🧵👇 www.nature.com/articles/s41...

nature.comAn environmentally regulated dichotomy in cell lineages of the root - NatureAn environment-regulated state is identified across multiple cell types at the root tip, revealing a shared dichotomy between cells with and without this state.

View full thread

Marina Oliva

@moliva.bsky.social

A big thank you to all my colleagues and collaborators who worked on this project, with a special shout out to @ryanlister.bsky.social, without whom none of this would have even happened!

Marina Oliva

@moliva.bsky.social

In other exciting news, I'll be starting my own lab at UWA next year! There will be opportunities for PhD students interested in exploring more about plant cell identity.

This increase was detected not only by scRNA-seq, but also directly in plants using whole-mount HCR and cell-by-cell quantification.

Marina Oliva

@moliva.bsky.social

Many exciting questions remain about the ERS, but our findings reveal an additional layer of cell identity in the root, beyond cell type and developmental stage, and highlight how the environment can shape the transcriptional states of cells across different lineages.

We tested the involvement of ABA by profiling ABA-deficient and ABA-insensitive mutants. In both cases, we found a significant decrease in the proportion of ERS+ cells, accompanied by downregulation of the ERS-specific gene modules.

Marina Oliva

@moliva.bsky.social

But is the ERS really regulated by the environment? Given the functions of its gene modules, we tested the effect of water deficit using the drought model developed by Gonzalez et al. and found that the proportion of ERS+ cells increased substantially under water deficit.

In the epidermis - the only layer where we identified a gene specific to the low-UMI branch - dual-marker HCR further confirmed the existence of two distinct cell populations!

Marina Oliva

@moliva.bsky.social

So, what does this state correspond to? The branch-specific genes were linked to environmental responses, including water and nutrients, with ABA as the only enriched signalling pathway. We named it the Environment-Regulated State (ERS): cells can either be ERS+ or ERS−.

In the snATAC-seq data from Farmer et al., we found further support for the hypothesis that one subpopulation was more transcriptionally active, with cells in this branch showing higher chromatin accessibility.

Marina Oliva

@moliva.bsky.social

Of course, to confirm that this reflected a biological reality, we went back to the bench and examined branch-specific gene expression using our whole-mount HCR method. We found striking heterogeneity within cell layers: up to a 20-fold difference in fluorescence between cells.

A subset of cells having more genes and transcripts detected than others... Couldn't that just be an artefact? We investigated potential experimental and computational explanations: cell cycle, protoplasting, cell quality and microenvironment (air vs agar). None could explain it.

Marina Oliva

@moliva.bsky.social

Importantly, we reexamined several published scRNA-seq and snRNA-seq datasets and found the same two branches, with the same branch-specific gene modules, in every case. In the atlas by Shahan et al., the authors had already noted a bifurcation in the outer root cell layers.

Even more surprisingly, this additional branch shared similarities across all cell types. By looking at modules of co-expressed genes, we found that the same sets of genes were preferentially expressed in one of the two branches, regardless of developmental identity.

Marina Oliva

@moliva.bsky.social

Consistent with this, cells in this branch always had more genes and transcripts detected. In other words, what created this dichotomy was that a subset of cells across all cell types expressed an additional, shared set of genes, on top of those defining their cell type identity.

We initially used scRNA-seq to uncover the finer details of linear differentiation trajectories in the root tip. Unexpectedly, we consistently found a striking dichotomy across all cell lineages above the root cap, as if cells could adopt one of two distinct states.

You are up to date.