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Gene expression

One mouse to trap them all

Roh, H.C. et al. Cell Rep. 18, 1048–1061 (2017).

Broadly speaking, the epigenome regulates the transcriptome, and it is therefore desirable to profile chromatin states together with expression data. Doing so in pooled cells obscures cellular heterogeneity, and single-cell data derived from cultured cells may poorly reflect their in vivo counterparts. To isolate mRNA and nuclei from a desired cell type in vivo, Roh et al. developed a transgenic mouse line they call NuTRAP. It combines the TRAP (translating ribosome affinity purification) strategy—isolation of ribosome-bound mRNA from a cell type that expresses a GFP-tagged ribosomal protein—with nuclear tagging by a labeled nuclear membrane protein. The trapping cassette is activated by Cre-dependent removal of a STOP cassette. By breeding a NuTRAP mouse with a mouse expressing Cre only in adipocytes, the researchers were able to discover substantial differences in gene expression and epigenetic states between adipocytes in vivo and in vitro.

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One mouse to trap them all. Nat Methods 14, 340 (2017). https://doi.org/10.1038/nmeth.4247

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