Biology subjects

Veeman, M. T.

Publications and source records attributed to Veeman, M. T..

4 recordsLinked to original sources

bioRxiv2025

Tissue-specificity of gene expression in the Ciona embryo is subtly bimodal

Expressed genes potentially fall into two distinct categories: tissue-specific genes expressed in a subset of cell types that carry out the distinctive functions of those cells; and housekeeping genes that are broadly expressed across all cell types and carry out the basic functions of life. It is unclear, however, whether these are actually two distinct classes or whether they represent an intuitive but false dichotomy imposed upon gene expression patterns that vary widely and continuously in how specific they are to particular tissues. We address this question using a high-coverage, whole-embryo single cell RNAseq atlas of the model invertebrate chordate Ciona robusta. There is a major complication in that quantitative measures of tissue-specificity such as the Tau and Gini metrics show a strong negative correlation with expression level. We show here that this correlation is the result of sampling error and not a fundamental biological relationship. Raw Tau scores are bimodal, but this is largely an artifact of Taus sigmoidal relationship with expression level for uniformly expressed genes. Simulations and statistical analyses indicate that the Tau metric is badly confounded by expression level for ubiquitously and/or weakly expressed genes but is relatively accurate for genes that have statistical evidence of differential expression. The distribution of tissue-specificity scores for these differentially expressed genes is broad and flat, spanning from near-binary to near-uniform. While only subtly bimodal, ubiquitously expressed and tissue-specific genes are clearly distinguishable, especially at higher expression levels. We explore the use of pseudocounts to shrink the high tissue-specificity scores of weakly expressed genes and find that they are effective at separating tissue-specific from ubiquitously expressed genes but distort rankings of tissue-specificity. Gene ontology code analysis indicates that the most tissue-specific genes are strongly enriched for predicted roles as transcriptional regulators and tissue-specific effector molecules, whereas the most ubiquitously expressed genes are enriched for predicted housekeeping functions. We conclude that the tissue-specific vs housekeeping dichotomy is meaningful in the Ciona embryo despite the broad range of Tau scores for tissue-specific genes. These findings provide a framework for formally assessing the tissue-specificity of gene expression across a broad range of taxa and developmental stages.

genomics↗

bioRxiv2020

Single-cell analysis of cell fate bifurcation in the chordate Ciona

Inductive signaling interactions between different cell types are a major mechanism for the further diversification of embryonic cell fates. Most blastomeres in the model chordate Ciona robusta become restricted to a single predominant fate between the 64-cell and mid-gastrula stages. We used single-cell RNAseq spanning this period to identify 53 distinct cell states, 25 of which are dependent on a MAPK-mediated signal critical to early Ciona patterning. Divergent gene expression between newly bifurcated sibling cell types is dominated by upregulation in the induced cell type. These upregulated genes typically include numerous transcription factors and not just one or two key regulators. The Ets family transcription factor Elk1/3/4 is upregulated in almost all the putatively direct inductions, indicating that it may act in an FGF-dependent feedback loop. We examine several bifurcations in detail and find support for a broad-hourglass model of cell fate specification in which many genes are induced in parallel to key tissue-specific transcriptional regulators via the same set of transcriptional inputs.

developmental biology↗

bioRxiv2020

Ciona Brachyury proximal and distal enhancers have different FGF dose-response relationships

Many genes are regulated by two or more enhancers that drive similar expression patterns. Evolutionary theory suggests that these seemingly redundant enhancers must have functionally important differences. In the simple ascidian chordate Ciona, the transcription factor Brachyury is induced exclusively in the presumptive notochord downstream of lineage specific regulators and FGF-responsive Ets family transcription factors. Here we exploit the ability to finely titrate FGF signaling activity via the MAPK pathway using the MEK inhibitor U0126 to quantify the dependence of transcription driven by different Brachyury reporter constructs on this direct upstream regulator. We find that the more powerful promoter-adjacent proximal enhancer and a weaker distal enhancer have fundamentally different dose-response relationships to MAPK inhibition. The Distal enhancer is more sensitive to MAPK inhibition but shows a less cooperative response, whereas the Proximal enhancer is less sensitive and more cooperative. A longer construct containing both enhancers has a complex dose-response curve that supports the idea that the proximal and distal enhancers are moderately super-additive. We show that the overall expression loss from intermediate doses of U0126 is not only a function of the fraction of cells expressing these reporters, but also involves graded decreases in expression at the single-cell level. Expression of the endogenous gene shows a comparable dose-response relationship to the full length reporter, and we find that different notochord founder cells are differentially sensitive to MAPK inhibition. Together, these results indicate that although the two Brachyury enhancers have qualitatively similar expression patterns, they respond to FGF in quantitatively different ways and act together to drive high levels of Brachyury expression with a characteristic input/output relationship. This indicates that they are fundamentally not redundant genetic elements.

developmental biology↗

bioRxiv2020

Brachyury controls Ciona notochord fate as part of a feedforward network and not as a unitary master regulator

The notochord is a defining feature of the chordates. The transcription factor Brachyury (Bra) is a key regulator of notochord fate but here we show that it is not a unitary master regulator in the model chordate Ciona. Ectopic Bra expression only partially reprograms other cell types to a notochord-like transcriptional profile and a subset of notochord-enriched genes are unaffected by CRISPR Bra disruption. We identify Foxa.a and Mnx as potential co-regulators and find that combinatorial cocktails are more effective at reprograming other cell types than Bra alone. We reassess the network relationships between Bra, Foxa.a and other components of the notochord gene regulatory network and find that Foxa.a expression in the notochord is regulated by vegetal FGF signaling. It is a direct activator of Bra expression and has a binding motif that is significantly enriched in the regulatory regions of notochord-enriched genes. These and other results indicate that Bra and Foxa.a act together in a regulatory network dominated by positive feed-forward interactions, with neither being a classically-defined master regulator.

developmental biology↗