Biology subjects

Waterston, R.

Publications and source records attributed to Waterston, R..

2 recordsLinked to original sources

bioRxiv2024

Lineage-resolved analysis of embryonic gene expression evolution in C. elegans and C. briggsae

What constraints govern the evolution of gene expression patterns across development remains a fundamental question of evolutionary biology. The advent of single-cell sequencing opens the possibility of learning these constraints by systematically profiling homologous cells across different organisms. The nematode C. elegans is a well-studied model for embryonic development, and its invariant lineage that is conserved with other Caenorhabditis species makes it an ideal model to directly compare gene expression between homologous progenitor and terminal cell types across evolution. We have measured the spatiotemporal divergence of gene expression across embryogenesis by collecting, annotating, and comparing the transcriptomes of homologous embryonic progenitors and terminal cell types, using a dataset comprising >200,000 C. elegans cells and >190,000 C. briggsae cells. We find a high level of similarity in gene expression programs between the species despite tens of millions of years of evolutionary divergence, consistent with their conserved developmental lineages. Even still, thousands of genes show divergence in their cell-type specific expression patterns, and these are enriched for categories involved in environmental response and behavior. Comparing the degree of expression conservation across cell types reveals that certain cell types such as neurons, have diverged more than others such as the intestine and body wall muscle. Taken together, this work identifies likely constraints on the evolution of developmental gene expression and provides a powerful resource for addressing diverse evolutionary questions.

evolutionary biology↗

bioRxiv2022

Whole-body gene expression atlas of an adult metazoan

Animals are integrated organ systems composed of interacting cells whose structure and function are in turn defined by their active genes. Understanding what distinguishes physiological and disease states therefore requires systemic knowledge of the gene activities that define the distinct cells that make up an animal. Towards this goal, this study reports the first single-cell resolution transcriptional atlas of a fertile multicellular organism: Caenorhabditis elegans. The scRNA-Seq compendium of wild-type young adult C. elegans comprises 159 distinct cell types with 18,033 genes expressed across cell types. Fewer than 300 of these genes are housekeeping genes as evidenced by their consistent expression across cell types and conditions, and by their basic and essential functions; 170 of these housekeeping genes are conserved across phyla. The 362 transcription factors with available ChIP-Seq data are linked to patterns of gene expression of different cell types. To identify potential interactions between cell types, we used the in silico tool cell2cell to predict molecular patterns reflecting both known and uncharacterized intercellular interactions across the C. elegans body. Finally, we present WormSeq (wormseq.org), a web interface that, among other functions, enables users to query gene expression across cell types, identify cell-type specific and potential housekeeping genes, analyze candidate ligand-receptors mediating communication between cells, and study promiscuous and cell-specific transcription factors. The datasets, analyses, and tools presented here will enable the generation of testable hypotheses about the cell and organ-specific function of genes in diverse biological contexts.

genomics↗