Biology subjects

Renvoise, E.

Publications and source records attributed to Renvoise, E..

3 recordsLinked to original sources

bioRxiv2025

Six million years of vole dental evolution driven by tooth development

Morphological change occurs over macroevolutionary timescales under the action of natural selection and genetic drift combined with developmental processes shaping organogenesis1-3. Although determining their relative weight is made difficult by discrepancies between palaeontological and neontological data4, mammalian tooth morphology may bridge the gap between fossil record and laboratory observations. Fossils indicate that placentals and marsupials diversified after evolving molars bearing more cusps5-7, which emerge through the iterative signalling of enamel knots8,9. However, this theoretical evo-devo model of mammalian tooth evolution has not been explicitly assessed on empirical data. Here, by combining the fossil record with laboratory experiments, we identify a shared developmental basis for the convergent, ratcheted evolution of increasingly complex molars in arvicoline rodents (voles, lemmings, muskrats). Longer, narrower molars lead to more cusps throughout development and deep time, suggesting a developmental driver for tooth evolution. Both the arvicoline fossil record and vole tooth development show slower transitions toward the highest cusp counts. This newly identified pattern suggests that the developmental processes fuelling the evolution of increasingly complex molars may also limit the potential for further complexity increases. Integrating palaeontological and developmental data shows that long-term evolutionary trends can be accurately explained by the simple tinkering of developmental pathways.

evolutionary biology↗

bioRxiv2020

DELocal: Chromosomal neighbourhoods having genes of diverse functions allow improved identification of differentially expressed genes

Although most genes share their chromosomal neighbourhood with other genes, distribution of genes has not been explored in the context of individual organ development; the common focus of developmental biology studies. Because developmental processes are often associated with initially subtle changes in gene expression, here we explored whether neighbouring genes are informative in the identification of differentially expressed genes. First, we quantified the chromosomal neighbourhood patterns of genes having related functional roles in the mammalian genome. Although the majority of protein coding genes have at least five neighbours within 1 Mb window around each gene, very few of these neighbours regulate development of the same organ. Analyses of transcriptomes of developing mouse molar teeth revealed that whereas expression of genes regulating tooth development changes, their neighbouring genes show no marked changes, irrespective of their level of expression. Finally, we test whether inclusion of gene neighbourhood in the analyses of differential expression could provide additional benefits. For the analyses, we developed an algorithm, called DELocal that identifies differentially expressed genes by comparing their expression changes to changes in adjacent genes in their chromosomal regions. Our results show that DELocal removes detection bias towards large changes in expression, thereby allowing identification of even subtle changes in development. Future studies, including the detection of differential expression, may benefit from, and further characterize the significance of gene-gene neighbour relationships. Author SummaryDevelopment of organs is typically associated with small and hard to detect changes in gene expression. Here we examined how often genes regulating specific organs are neighbours to each other in the genome, and whether this gene neighbourhood helps in the detection of changes in gene expression. We found that genes regulating individual organ development are very rarely close to each other in the mouse and human genomes. We built an algorithm, called DELocal, to detect changes in gene expression that incorporates information about neighbouring genes. Using transcriptomes of developing mouse molar teeth containing gene expression profiles of thousands of genes, we show how genes regulating tooth development are ranked high by DELocal even if their expression level changes are subtle. We propose that developmental biology studies can benefit from gene neighbourhood analyses in the detection of differential expression and identification of organ specific genes.

bioinformatics↗

bioRxiv2019

Keystone genes of mammalian tooth patterning and quantification of their expression

When a null mutation of a gene causes a complete developmental arrest, the gene is typically considered essential for life. Yet, in most cases null mutations have more subtle effects on the phenotype. Here we used the phenotypic severity of mutations as a tool to examine system-level dynamics of gene expression. We classify genes required for the normal development of the mouse molar into different categories that range from essential to subtle modification of the phenotype. Collectively, we call these the developmental keystone genes. Transcriptome profiling using microarray and RNAseq analyses of patterning stage mouse molars show highly elevated expression levels for genes essential for the progression of tooth development, a result reminiscent of essential genes in single cell organisms. Elevated expression levels of progression genes were also detected in developing rat molars, suggesting evolutionary conservation of this system-level dynamics. Single-cell RNAseq analyses of developing mouse molars reveal that even though the size of the expression domain, measured in number of cells, is the main driver of organ-level expression, progression genes show high cell-level transcript abundances. Progression genes are also upregulated within their pathways, which themselves are highly expressed. In contrast, a high proportion of the genes required for normal tooth patterning are secreted ligands that are expressed in fewer cells than their receptors and intracellular components. Overall, even though expression patterns of individual genes can be highly different, conserved system-level principles of gene expression can be detected using phenotypically defined gene categories.

developmental biology↗