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Nature DOI:10.1038/nature12172

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells.

Publication TypeJournal Article
Year of Publication2013
AuthorsShalek, AK, Satija, R, Adiconis, X, Gertner, RS, Gaublomme, JT, Raychowdhury, R, Schwartz, S, Yosef, N, Malboeuf, C, Lu, D, Trombetta, JJ, Gennert, D, Gnirke, A, Goren, A, Hacohen, N, Levin, JZ, Park, H, Regev, A
Date Published2013 Jun 13
KeywordsAnimals, Bone Marrow Cells, Dendritic Cells, Gene Expression Profiling, Gene Expression Regulation, In Situ Hybridization, Fluorescence, Interferon Regulatory Factor-7, Interferons, Lipopolysaccharides, Mice, Mice, Knockout, Protein Isoforms, Reproducibility of Results, RNA Splicing, RNA, Messenger, Sequence Analysis, RNA, Single-Cell Analysis, STAT2 Transcription Factor, Transcriptome, Viruses

Recent molecular studies have shown that, even when derived from a seemingly homogenous population, individual cells can exhibit substantial differences in gene expression, protein levels and phenotypic output, with important functional consequences. Existing studies of cellular heterogeneity, however, have typically measured only a few pre-selected RNAs or proteins simultaneously, because genomic profiling methods could not be applied to single cells until very recently. Here we use single-cell RNA sequencing to investigate heterogeneity in the response of mouse bone-marrow-derived dendritic cells (BMDCs) to lipopolysaccharide. We find extensive, and previously unobserved, bimodal variation in messenger RNA abundance and splicing patterns, which we validate by RNA-fluorescence in situ hybridization for select transcripts. In particular, hundreds of key immune genes are bimodally expressed across cells, surprisingly even for genes that are very highly expressed at the population average. Moreover, splicing patterns demonstrate previously unobserved levels of heterogeneity between cells. Some of the observed bimodality can be attributed to closely related, yet distinct, known maturity states of BMDCs; other portions reflect differences in the usage of key regulatory circuits. For example, we identify a module of 137 highly variable, yet co-regulated, antiviral response genes. Using cells from knockout mice, we show that variability in this module may be propagated through an interferon feedback circuit, involving the transcriptional regulators Stat2 and Irf7. Our study demonstrates the power and promise of single-cell genomics in uncovering functional diversity between cells and in deciphering cell states and circuits.


Alternate JournalNature
PubMed ID23685454
PubMed Central IDPMC3683364
Grant ListF32 HD075541 / HD / NICHD NIH HHS / United States
1F32HD075541-01 / HD / NICHD NIH HHS / United States
5DP1OD003893-03 / OD / NIH HHS / United States
U54 AI057159 / AI / NIAID NIH HHS / United States
DP1OD003958-01 / OD / NIH HHS / United States
DP1 CA174427 / CA / NCI NIH HHS / United States
DP2 OD002230 / OD / NIH HHS / United States
/ / Howard Hughes Medical Institute / United States
P50 HG006193 / HG / NHGRI NIH HHS / United States
DP1 DA035083 / DA / NIDA NIH HHS / United States
DP1 OD003893 / OD / NIH HHS / United States
1P50HG006193-01 / HG / NHGRI NIH HHS / United States
DP1 OD003958 / OD / NIH HHS / United States