Transcriptome profiling of single cells resident in their natural microenvironment depends upon RNA capture methods that are both noninvasive and spatially precise. We engineered a transcriptome in vivo analysis (TIVA) tag, which upon photoactivation enables mRNA capture from single cells in live tissue. Using the TIVA tag in combination with RNA sequencing (RNA-seq), we analyzed transcriptome variance among single neurons in culture and in mouse and human tissue in vivo. Our data showed that the tissue microenvironment shapes the transcriptomic landscape of individual cells. The TIVA methodology is, to our knowledge, the first noninvasive approach for capturing mRNA from live single cells in their natural microenvironment.
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We thank J. Cheung-Lau for assistance with in vitro FRET measurements. Funding was provided by the PhRMA foundation to D.L., US National Institutes of Health (NIH) R01 GM083030 to I.J.D., McKnight Foundation Technology Innovations Award to I.J.D. and J.E., U01MH098953 to J.K. and J.E. and NIH DP004117 to J.E. This project is funded, in part, by the Penn Genome Frontiers Institute under a grant with the Pennsylvania Department of Health, which disclaims responsibility for any analyses, interpretations or conclusions.
The authors declare no competing financial interests.
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Lovatt, D., Ruble, B., Lee, J. et al. Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue. Nat Methods 11, 190–196 (2014). https://doi.org/10.1038/nmeth.2804
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