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An RNA interference screen uncovers a new molecule in stem cell self-renewal and long-term regeneration

Nature volume 485, pages 104–108 (2012)Cite this article

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Abstract

Adult stem cells sustain tissue maintenance and regeneration throughout the lifetime of an animal1,2. These cells often reside in specific signalling niches that orchestrate the stem cell’s balancing act between quiescence and cell-cycle re-entry based on the demand for tissue regeneration2,3,4. How stem cells maintain their capacity to replenish themselves after tissue regeneration is poorly understood. Here we use RNA-interference-based loss-of-function screening as a powerful approach to uncover transcriptional regulators that govern the self-renewal capacity and regenerative potential of stem cells. Hair follicle stem cells provide an ideal model. These cells have been purified and characterized from their native niche in vivo and, in contrast to their rapidly dividing progeny, they can be maintained and passaged long-term in vitro5,6,7. Focusing on the nuclear proteins and/or transcription factors that are enriched in stem cells compared with their progeny5,6, we screened ∼2,000 short hairpin RNAs for their effect on long-term, but not short-term, stem cell self-renewal in vitro. To address the physiological relevance of our findings, we selected one candidate that was uncovered in the screen: TBX1. This transcription factor is expressed in many tissues but has not been studied in the context of stem cell biology. By conditionally ablating Tbx1 in vivo, we showed that during homeostasis, tissue regeneration occurs normally but is markedly delayed. We then devised an in vivo assay for stem cell replenishment and found that when challenged with repetitive rounds of regeneration, the Tbx1-deficient stem cell niche becomes progressively depleted. Addressing the mechanism of TBX1 action, we discovered that TBX1 acts as an intrinsic rheostat of BMP signalling: it is a gatekeeper that governs the transition between stem cell quiescence and proliferation in hair follicles. Our results validate the RNA interference screen and underscore its power in unearthing new molecules that govern stem cell self-renewal and tissue-regenerative potential.

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Figure 1: In vitro RNAi screen for genes involved in stem cell long-term self-renewal.
Figure 2: The transcription factor TBX1 is highly enriched in stem cells in vivo and in vitro.
Figure 3: Tbx1 -null stem cells fail in an in vivo assay for stem cell self-renewal and long-term tissue regeneration.
Figure 4: TBX1 controls stem cell proliferation in part by fine-tuning the response to BMP signalling.

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Gene Expression Omnibus

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Microarray data have been deposited in the Gene Expression Omnibus database under accession number GSE35575.

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Acknowledgements

We are grateful to A. Baldini for the Tbx1fl/fl mice, the Comparative Biology Centre (AAALAC-accredited) for expert handling and care of the mice, The Rockefeller University FCRC for FACS sorting (supported by NYSTEM funds through NYSDOH, contract C023046), S. Dewell and The Rockefeller University Genomic Resource Centre for high-throughput sequencing, The Memorial Sloan Kettering Genomics Core Facility for RNA and microarray processing, Fuchs’ lab members Y. Hsu, B. Keyes, X. Wu, D. Devenport and L. Zhang for comments and suggestions, W. H. Lien for providing epigenetic ChIP-seq data for the Tbx1 gene in vivo and P. Janki for assisting in the production of the pooled virus for screening. This work was supported by grants from the National Institutes of Health (R01-AR050452; E.F.), the Empire State Stem Cell (NYSTEM N09G074; E.F.), a New York Stem Cell Foundation-Druckenmiller Fellowship (T.C.) and a NYSTEM Scholar Award (C026722; T.C.). E.F. is an Investigator of the Howard Hughes Medical Institute.

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  1. Howard Hughes Medical Institute, The Rockefeller University, New York, 10065, New York, USA

    Ting Chen, Evan Heller, Slobodan Beronja, Naoki Oshimori, Nicole Stokes & Elaine Fuchs

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  1. Ting Chen
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  2. Evan Heller
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  3. Slobodan Beronja
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  6. Elaine Fuchs
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Contributions

T.C. and E.F. designed the study. T.C. carried out the experiments and analysed the data. E.H. analysed the sequencing data. S.B. contributed to optimizing and testing methods used in the screen. N.O. carried out the Smad1 shRNA-related experiments. N.S. participated in the experiments involving mouse handling. T.C. and E.F. co-wrote the paper. E.F. supervised the research.

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Correspondence to Elaine Fuchs.

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The authors declare no competing financial interests.

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Chen, T., Heller, E., Beronja, S. et al. An RNA interference screen uncovers a new molecule in stem cell self-renewal and long-term regeneration. Nature 485, 104–108 (2012). https://doi.org/10.1038/nature10940

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