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An allelic series of miR-17∼92–mutant mice uncovers functional specialization and cooperation among members of a microRNA polycistron

Nature Genetics volume 47, pages 766–775 (2015)Cite this article

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Abstract

Polycistronic microRNA (miRNA) clusters are a common feature of vertebrate genomes. The coordinated expression of miRNAs belonging to different seed families from a single transcriptional unit suggests functional cooperation, but this hypothesis has not been experimentally tested. Here we report the characterization of an allelic series of genetically engineered mice harboring selective targeted deletions of individual components of the miR-17∼92 cluster. Our results demonstrate the coexistence of functional cooperation and specialization among members of this cluster, identify a previously undescribed function for the miR-17 seed family in controlling axial patterning in vertebrates and show that loss of miR-19 selectively impairs Myc-driven tumorigenesis in two models of human cancer. By integrating phenotypic analysis and gene expression profiling, we provide a genome-wide view of how the components of a polycistronic miRNA cluster affect gene expression in vivo. The reagents and data sets reported here will accelerate exploration of the complex biological functions of this important miRNA cluster.

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Figure 1: Generation of an allelic series of miR-17∼92–mutant mice.
Figure 2: Feingold syndrome (FS2) features in miR-17∼92–mutant mice.
Figure 3: miR-17∼92 regulates axial patterning.
Figure 4: Analysis of B cell development in the miR-17∼92 allelic series.
Figure 5: Impaired Myc-driven lymphomagenesis in miR-19–deficient mice.
Figure 6: Genome-wide identification of genes regulated by members of the miR-17∼92 cluster.

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Acknowledgements

We thank J. Hollenstein for editing the manuscript and members of the Ventura laboratory for helpful discussions. The authors greatly acknowledge the contribution of the Weill Cornell Epigenomics Core. This work was funded by grants from the US National Institutes of Health/National Cancer Institute (R01CA149707 to A.V. and Core grant P30CA008748), the STARR Consortium (to A.V. and D.B.), the Geoffrey Beene Cancer Foundation (to A.V.), the Gabrielle's Angel Foundation (to A.V.), the Leukemia Lymphoma Society (to Y.-C.H.), the American Italian Cancer Foundation (to C.B.) and a US National Institutes of Health training grant (F31CA168356 to C.P.C.).

Author information

Author notes

  1. Yoon-Chi Han, Joana A Vidigal and Ping Mu: These authors contributed equally to this work.

Authors and Affiliations

  1. Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA

    Yoon-Chi Han, Joana A Vidigal, Ping Mu, Evelyn Yao, Carla P Concepcion, Ciro Bonetti, Paul Ogrodowski & Andrea Ventura

  2. Oncology Research Unit, Pfizer, Inc., Pearl River, New York, USA

    Yoon-Chi Han

  3. Weill Cornell Graduate School of Medical Sciences of Cornell University, New York, New York, USA

    Ping Mu, Evelyn Yao & Carla P Concepcion

  4. Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA

    Irtisha Singh, Alvaro J González & Christina Leslie

  5. Human Oncology and Pathogenesis Program. Memorial Sloan Kettering Cancer Center, New York, New York, USA

    Brett Carver

  6. Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA

    Brett Carver

  7. Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, New York, USA

    Licia Selleri

  8. Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, New York, USA

    Doron Betel

  9. Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, USA

    Doron Betel

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  1. Yoon-Chi Han
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Contributions

A.V., J.A.V., Y.-C.H. and P.M. conceived the project and designed the experiments. A.V., J.A.V. and Y.-C.H. wrote the manuscript. A.V., E.Y., P.O. and P.M. generated the mouse strains. Y.-C.H. characterized overall viability. Y.-C.H. and P.M. characterized the hematopoietic phenotypes. J.A.V., E.Y. and L.S. characterized the skeletal phenotypes. P.M., B.C. and C.B. characterized the oncogenic phenotypes. Y.-C.H., J.A.V. and C.P.C. generated the small-RNA libraries. Y.-C.H. and J.A.V. generated the RNA-seq libraries. A.V., D.B., C.L., I.S. and A.J.G. performed the computational analysis for the RNA-seq data. D.B. and C.L. contributed equally to the computational analysis.

Corresponding author

Correspondence to Andrea Ventura.

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Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–7, Supplementary Tables 1–4 and Supplementary Note. (PDF 23229 kb)

Supplementary Figure 8

High-resolution Scalable Vector Graphics (svg) format version of the tail bud Circos plot shown in Figure 6a. (XML 1619 kb)

Supplementary Figure 9

High-resolution Scalable Vector Graphics (svg) format version of the tail bud Circos plot shown in Figure 6a, modified to include genes differentially expressed in miR-17~92Δ17,18/Δ17,18 and miR-17~92Δ17,18,92/Δ17,18,92 embryos. To reduce the complexity of the plot, only links originating or ending at one of the four single-seed mutants are shown. (XML 3453 kb)

Supplementary Figure 10

High-resolution Scalable Vector Graphics (svg) format version of a Circos plot generated from the heart data set. (XML 337 kb)

Supplementary Figure 11

High-resolution Scalable Vector Graphics (svg) format version of the Circos plot generated from the heart data set, modified to include genes differentially expressed in miR-17~92Δ17,18/Δ17,18 and miR-17~92Δ17,18,92/Δ17,18,92 embryos. To reduce the complexity of the plot, only links originating or ending at one of the four single-seed mutants are shown. (XML 603 kb)

Supplementary Table 5

Gene expression data for heart and tail bud samples and information on the presence of miR-17~92–binding sites. (XLSX 5040 kb)

Supplementary Table 6

Gene Ontology enrichment analysis using genes deregulated in the tail buds and hearts of miR-17~92–null embryos. (XLSX 91 kb)

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Han, YC., Vidigal, J., Mu, P. et al. An allelic series of miR-17∼92–mutant mice uncovers functional specialization and cooperation among members of a microRNA polycistron. Nat Genet 47, 766–775 (2015). https://doi.org/10.1038/ng.3321

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