Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue

• Published in: Nature methods Vol. 11; no. 2; pp. 190 - 196
• Main Authors: Lovatt, Ditte, Ruble, Brittani K, Lee, Jaehee, Dueck, Hannah, Kim, Tae Kyung, Fisher, Stephen, Francis, Chantal, Spaethling, Jennifer M, Wolf, John A, Grady, M Sean, Ulyanova, Alexandra V, Yeldell, Sean B, Griepenburg, Julianne C, Buckley, Peter T, Kim, Junhyong, Sul, Jai-Yoon, Dmochowski, Ivan J, Eberwine, James
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.02.2014; Nature Publishing Group
• Subjects: 631/1647/2017; 631/1647/2217/2018; 631/208/200; 631/92/96; Animals; Bioinformatics; Biological Microscopy; Biological Techniques; Biomedical Engineering/Biotechnology; Brain - metabolism; Computational Biology; Gene expression; Gene Expression Profiling; Gene Library; Genetic research; Genetic variation; High-Throughput Nucleotide Sequencing - methods; Hippocampus - metabolism; Humans; Identification and classification; Life Sciences; Messenger RNA; Mice; Mice, Inbred C57BL; Neurons - metabolism; Photoactivation; Photobiology; Proteins; Proteomics; Ribonucleic acid; RNA; RNA, Messenger - genetics; Sequence Analysis, RNA - methods; Tissues; Transcription factors
• ISSN: 1548-7091; 1548-7105
• DOI: 10.1038/nmeth.2804

A noninvasive method is reported for the isolation and profiling of the transcriptome from a single cell in the context of intact tissue. 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.