Biology subjects

Koulena, N.

Publications and source records attributed to Koulena, N..

4 recordsLinked to original sources

bioRxiv2024

A Spatiotemporal Atlas of Mouse Gastrulation and Early Organogenesis to Explore Axial Patterning and Project In Vitro Models onto In Vivo Space

At the onset of murine gastrulation, pluripotent epiblast cells migrate through the primitive streak, generating mesodermal and endodermal precursors, while the ectoderm arises from the remaining epiblast. Together, these germ layers establish the body plan, defining major body axes and initiating organogenesis. Although comprehensive single cell transcriptional atlases of dissociated mouse embryos across embryonic stages have provided valuable insights during gastrulation, the spatial context for cell differentiation and tissue patterning remain underexplored. In this study, we employed spatial transcriptomics to measure gene expression in mouse embryos at E6.5 and E7.5 and integrated these datasets with previously published E8.5 spatial transcriptomics1 and a scRNA-seq2 atlas spanning E6.5 to E9.5. This approach resulted in a comprehensive spatiotemporal atlas, comprising over 150,000 cells with 88 refined cell type annotations as well as genome-wide transcriptional imputation during mouse gastrulation and early organogenesis. The atlas facilitates exploration of gene expression dynamics along anterior-posterior and dorsal-ventral axes at cell type, tissue, and organismal scales, revealing insights into mesodermal fate decisions within the primitive streak. Moreover, we developed a bioinformatics pipeline to project additional scRNA-seq datasets into a spatiotemporal framework and demonstrate its utility by analysing cardiovascular models of gastrulation3. To maximise impact, the atlas is publicly accessible via a user-friendly web portal empowering the wider developmental and stem cell biology communities to explore mechanisms of early mouse development in a spatiotemporal context.

developmental biology↗

bioRxiv2020

Highly multiplexed spatially resolved gene expression profiling of mouse organogenesis

Transcriptional and epigenetic profiling of single-cells has advanced our knowledge of the molecular bases of gastrulation and early organogenesis. However, current approaches rely on dissociating cells from tissues, thereby losing the crucial spatial context that is necessary for understanding cell and tissue interactions during development. Here, we apply an image-based single-cell transcriptomics method, seqFISH, to simultaneously and precisely detect mRNA molecules for 387 selected target genes in 8-12 somite stage mouse embryo tissue sections. By integrating spatial context and highly multiplexed transcriptional measurements with two single-cell transcriptome atlases we accurately characterize cell types across the embryo and demonstrate how spatially-resolved expression of genes not profiled by seqFISH can be imputed. We use this high-resolution spatial map to characterize fundamental steps in the patterning of the midbrain-hindbrain boundary and the developing gut tube. Our spatial atlas uncovers axes of resolution that are not apparent from single-cell RNA sequencing data - for example, in the gut tube we observe early dorsal-ventral separation of esophageal and tracheal progenitor populations. In sum, by computationally integrating high-resolution spatially-resolved gene expression maps with single-cell genomics data, we provide a powerful new approach for studying how and when cell fate decisions are made during early mammalian development.

developmental biology↗

bioRxiv2020

Imaging cell lineage with a synthetic digital recording system

Multicellular development depends on the differentiation of cells into specific fates with precise spatial organization. Lineage history plays a pivotal role in cell fate decisions, but is inaccessible in most contexts. Engineering cells to actively record lineage information in a format readable in situ would provide a spatially resolved view of lineage in diverse developmental processes. Here, we introduce a serine integrase-based recording system that allows in situ readout, and demonstrate its ability to reconstruct lineage relationships in cultured stem cells and flies. The system, termed intMEMOIR, employs an array of independent three-state genetic memory elements that can recombine stochastically and irreversibly, allowing up to 59,049 distinct digital states. intMEMOIR accurately reconstructed lineage trees in stem cells and enabled simultaneous analysis of single cell clonal history, spatial position, and gene expression in Drosophila brain sections. These results establish a foundation for microscopy-readable clonal analysis and recording in diverse systems. One sentence summaryA new genetic editing system termed intMEMOIR reveals the lineage histories of individual cells directly within their native tissue context.

synthetic biology↗

bioRxiv2018

Dynamics and spatial genomics of the nascent transcriptome in single mESCs by intron seqFISH

Recent single cell experiments have revealed significant heterogeneities at the levels of transcription, DNA methylation and chromosome organization in individual cells. However, existing method of profiling mRNAs effectively averages transcriptional dynamics over many hours due to hours-long life time of most mRNAs. To capture the instantaneous activity of the transcriptome that reflects the rapid regulatory changes in cells, we imaged up to 10,421 nascent transcription active sites (TAS) in single mouse embryonic stem cells using seqFISH followed by multiple rounds of single molecule FISH and immunofluorescence. We observed that nascent transcription active sites appear to be distributed on the surface of individual chromosome territories and are dispersed throughout the nucleus. In addition, there are significant variability in the number of active transcription sites in single cells, representing globally more active to quiescent states. These states interconverted on the time scale of 2 hours as determined by a single cell pulse-chase experiment. Thus, transcriptome level seqFISH experiments provide an unprecedented spatial and dynamic view of chromosome organization and global nascent transcription activity in single cells.

systems biology↗