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Conserved roles of mouse DUX and human DUX4 in activating cleavage-stage genes and MERVL/HERVL retrotransposons

Nature Genetics volume 49, pages 925934 (2017) | Download Citation

Abstract

To better understand transcriptional regulation during human oogenesis and preimplantation development, we defined stage-specific transcription, which highlighted the cleavage stage as being highly distinctive. Here, we present multiple lines of evidence that a eutherian-specific multicopy retrogene, DUX4, encodes a transcription factor that activates hundreds of endogenous genes (for example, ZSCAN4, KDM4E and PRAMEF-family genes) and retroviral elements (MERVL/HERVL family) that define the cleavage-specific transcriptional programs in humans and mice. Remarkably, mouse Dux expression is both necessary and sufficient to convert mouse embryonic stem cells (mESCs) into 2-cell-embryo-like ('2C-like') cells, measured here by the reactivation of '2C' genes and repeat elements, the loss of POU5F1 (also known as OCT4) protein and chromocenters, and the conversion of the chromatin landscape (as assessed by transposase-accessible chromatin using sequencing (ATAC–seq)) to a state strongly resembling that of mouse 2C embryos. Thus, we propose mouse DUX and human DUX4 as major drivers of the cleavage or 2C state.

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Acknowledgements

We thank S. Kuerten (NuGen) for assistance with preparing the RNA-seq libraries, B. Dalley for sequencing services, and T. Parnell for bioinformatic assistance. We give special thanks to M.-E. Torres-Padilla (IGBMC) for generously providing the MERVL::GFP reporter mESC line, and we thank D. Root (Broad Institute) for providing materials. Functional genomics work was supported by HHMI. J.A.D. was further supported by Eunice Kennedy Shriver NIH NICHD K12HD000849. S.J.T. and J.-W.L. were supported by NIH NIAMS R01AR045203, NIH NINDS P01NS069539, and the Friends of FSH Research. J.L.W. was supported by the National Science Foundation Graduate Research Fellowship Program DGE-1256082 and the University of Washington Interdisciplinary Training in Genome Sciences grant T32 HG00035 from NHGRI. Finally, we acknowledge CA042014 for support of the University of Utah core facilities.

Author information

Affiliations

  1. Department of Oncological Sciences, Huntsman Cancer Institute and Howard Hughes Medical Institute, Salt Lake City, Utah, USA.

    • Peter G Hendrickson
    • , Jessie A Doráis
    • , Edward J Grow
    • , Candice L Wike
    • , Bradley D Weaver
    • , Christian Pflueger
    • , David A Nix
    •  & Bradley R Cairns
  2. Departments of Obstetrics and Gynecology, and Surgery, University of Utah School of Medicine, Salt Lake City, Utah, USA.

    • Jessie A Doráis
    • , Benjamin R Emery
    • , Aaron L Wilcox
    • , C Matthew Peterson
    •  & Douglas T Carrell
  3. Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.

    • Jennifer L Whiddon
    • , Jong-Won Lim
    •  & Stephen J Tapscott

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Contributions

IRB processing, patient consent, patient management, and sample selection/processing were overseen by J.A.D., D.T.C., and C.M.P., with processing by clinical staff (B.R.E. and A.L.W.) in clinical (non-federally funded) facilities. After cDNA and library preparation, subsequent sequencing and transcriptome analyses, along with all molecular and functional approaches were overseen by B.R.C., with contributions from S.J.T. Experiments were performed, analyzed, and statistically evaluated by P.G.H., with contributions from E.J.G., J.L.W., J.-W.L., C.L.W., B.D.W., C.P., B.R.E., and D.A.N. The manuscript was written by P.G.H. and B.R.C.

Competing interests

B.R.C., E.J.G., P.G.H., J.L.W., and S.J.T. have filed a provisional patent application, ‘Compositions and methods for reprogramming cells and for somatic cell nuclear transfer using DUXC expression’ (US provisional application no. 62/410,078, US Patent and Trademark Office), which is based in part on this work.

Corresponding authors

Correspondence to Stephen J Tapscott or Douglas T Carrell or Bradley R Cairns.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–6

Excel files

  1. 1.

    Supplementary Table 1

    Egg/Embryo RNA-Seq quality control - Read depth (sheet 1) and quality control metrics (sheet 2) of human oocyte and embryo RNA sequencing.

  2. 2.

    Supplementary Table 2

    Egg/Embryo RNA-seq gene and repeat expression- Full expression analysis of all genes (sheet1) and repetitive elements (sheet 2) in the human oocytes and embryos.

  3. 3.

    Supplementary Table 3

    Egg/Embryo heatmap- A list of all 9,734 ensembl genes comprising the heatmap in Fig.1 with cluster and FPKM information.

  4. 4.

    Supplementary Table 4

    Egg/Embryo novel transcription- Full list of all novel transcription fragments (transfrags) and their differential expression.

  5. 5.

    Supplementary Table 5

    Egg/Embryo isoform expression- Expression data (TPM) for all ensembl gene isoforms in human oocytes/embryos estimated by Sailfish (Patro et al.,2014).

  6. 6.

    Supplementary Table 6

    RNA-seq in iPSCs - Full expression analysis of all genes (sheet1) and repetitive elements (sheet 2) in human induced pluripotent stem cells (iPSCs) following hDUX4 or luciferase expression.

  7. 7.

    Supplementary Table 7

    hDUX4 ChIP-seq in iPSCs- All hDUX4 ChIP-seq peaks in iPSCs (qval<10-20) called by MACS2 (over hDUX4 ChIP control) for replicates 1 (sheet 1) and 2 (sheet 2).

  8. 8.

    Supplementary Table 8

    RNA-seq in non-clonal mESCs- Full expression analysis of all genes (sheet1) and repetitive elements (sheet 2) in non-clonal mESCs post transient mDux expression.

  9. 9.

    Supplementary Table 9

    RNA-seq in clonal mESCs- Full expression analysis of all genes (sheet1) and repetitive elements (sheet 2) in a clonal, unsorted population of mESCs plus/minus 24hrs of dox-inducible mDux expression.

  10. 10.

    Supplementary Table 10

    RNA-seq in sorted '2C-like' cells- Full expression analysis of all genes (sheet1) and repetitive elements (sheet 2) in a clonal, sorted (GFPpos and GFPneg) population of mESCs after 24hrs of doxinducible mDux expression.

  11. 11.

    Supplementary Table 11

    RNA-seq in siRNA-treated mESCs- Full expression analysis of all genes (sheet1) and repetitive elements (sheet 2) in mESCs treated with siRNAs against Chaf1a alone or in combination with siRNAs against mDux (si308 and si309).

  12. 12.

    Supplementary Table 12

    ATAC-seq in sorted '2C-like' cells- a list of regions pertaining to the MACS2 ATAC-seq peaks gained in GFPpos mESCs (sheet 1), lost in GFPpos mESCs (sheet 2), or found in common between GFPpos and GFPneg mESCs (sheet3) induced with 24hrs of mDux expression.

  13. 13.

    Supplementary Table 13

    mDUX ChIP-seq in mESCs- All mDUX ChIP-seq peaks in mESCs (qval<0.05]) called by MACS2 (over input) for replicates 1 (sheet 1) and 2 (sheet 2).

  14. 14.

    Supplementary Table 14

    Primer sequences- A list of all primers used for RT-qPCR experiments (sheet 1) and generation of siRNA pools (sheet 2).

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DOI

https://doi.org/10.1038/ng.3844

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