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bioRxiv · 10.1101/2024.05.07.592900

Embryo spatial 3D genomics

Ma, Y.·Gou, B.·Xu, Y.·Shu, M.·Lu, F.·Li, X.
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Abstract

The 3D architecture of the genome is crucial for controlling gene expression and organ development. Here, we introduce a spatial 3D genomics approach for assessing chromatin conformation in-situ in tissue sections, by integrating microfluidic deterministic barcoding and SPRITE procedures. This method was applied to mouse embryo sections, revealing a hierarchical model of chromatin interactions within and between compartments in various organs. The intra-compartment interactions vary among organs to orchestrate gene expressions, while the inter-compartment interactions remain identical in the most organs. Beyond this, the liver exhibits overwhelmingly packed chromatin with enhanced adjacent-compartment interactions, possibly related to its physiology. These findings highlight the importance of tissue-spatial information in understanding embryonic chromatin organization. The approach presents a powerful tool for investigating these processes in tissues with high heterogeneity. One Sentence SummaryA spatial 3D genomics approach was developed that accesses hierarchical chromatin conformation in-situ in tissue sections.

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Ma, Y., Gou, B., Xu, Y., Shu, M., Lu, F., Li, X.. 2024-05-10. Embryo spatial 3D genomics. https://doi.org/10.1101/2024.05.07.592900

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