Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems.

Methods for highly multiplexed RNA imaging are limited in spatial resolution and thus in their ability to localize transcripts to nanoscale and subcellular compartments. We adapt expansion microscopy, which physically expands biological specimens, for long-read untargeted and targeted in situ RNA sequencing. We applied untargeted expansion sequencing (ExSeq) to the mouse brain, which yielded the readout of thousands of genes, including splice variants. Targeted ExSeq yielded nanoscale-resolution maps of RNAs throughout dendrites and spines in the neurons of the mouse hippocampus, revealing patterns across multiple cell types, layer-specific cell types across the mouse visual cortex, and the organization and position-dependent states of tumor and immune cells in a human metastatic breast cancer biopsy. Thus, ExSeq enables highly multiplexed mapping of RNAs from nanoscale to system scale.

Physical modeling of the cellular arrangement in C. elegans early embryo: effect of rounding and stiffening of the cells.

The ultimate goal of bioinformatics is to reconstruct biological systems in a computer. Biological systems have a multi-scale and multi-level biological hierarchy. The cellular level of the hierarchy is appropriate and practicable for reconstructing biological systems by computer modeling. In our first application of computer modeling to development of the nematode C. elegans, we focus on the cellular arrangement in early embryos. This plays a very important role in cell fate determination by cell-cell interaction, which is largely restricted by physical conditions. We have already constructed a computer model of a C. elegans embryo, currently up to the 4-cell stage, using deformable and dividable geometric graphics. Modeling components of the embryo are based solely on cellular-level dynamics. Here, we modeled new physical phenomena of cell division, cell rounding and stiffening; we then combined them with already modeled phenomena, contractile ring contraction and cell elongation. We investigated effectiveness of the new model on cellular arrangement by computer simulations. We found that cell rounding and stiffening only during the period of cell division were effective to generate almost identical cellular arrangements to in real embryos. Since cells could be soft during the period between cell divisions, implementation of the new model resulted in cell shapes similar to real embryos. The nature of the model and its relationship to real embryos are discussed.

Computer simulation of the cellular arrangement using physical model in early cleavage of the nematode Caenorhabditis elegans.

MOTIVATION: The ultimate goal of bioinformatics is to reconstruct biological systems in the computer. Since biological systems have many levels, it is important to focus on an appropriate level. In our first application of computer modeling to the early development of the nematode Caenorhabditis elegans, we focus on the cellular arrangement in early embryos. This plays a very important role in cell fate determination by cell-cell interaction, and is regarded as a system, one level higher than the system of gene regulation within cells. It is largely restricted by physical conditions that seemed feasible to model by computer. RESULTS: We constructed a computer model of the C.elegans embryo, currently up to the 4-cell stage, using a deformable and dividable triangulated network. The model is based solely on cellular-level dynamics. We found that the optimal ranges of three parameters that affect the elongation of dividing cells led, in computer simulations, to almost the same cellular arrangements as in real embryos. The nature of the model and the relationship with real embryos are discussed.