Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Technical Report
  • Published:

Large-scale analysis of the regulatory architecture of the mouse genome with a transposon-associated sensor

Nature Genetics volume 43, pages 379–386 (2011)Cite this article

Subjects

Abstract

We present here a Sleeping Beauty–based transposition system that offers a simple and efficient way to investigate the regulatory architecture of mammalian chromosomes in vivo. With this system, we generated several hundred mice and embryos, each with a regulatory sensor inserted at a random genomic position. This large sampling of the genome revealed the widespread presence of long-range regulatory activities along chromosomes, forming overlapping blocks with distinct tissue-specific expression potentials. The presence of tissue-restricted regulatory activities around genes with widespread expression patterns challenges the gene-centric view of genome regulation and suggests that most genes are modulated in a tissue-specific manner. The local hopping property of Sleeping Beauty provides a dynamic approach to map these regulatory domains at high resolution and, combined with Cre-mediated recombination, allows for the determination of their functions by engineering mice with specific chromosomal rearrangements.

Access through your institution
Buy or subscribe

This is a preview of subscription content, access via your institution

Access options

Access through your institution

Buy this article

  • Purchase on SpringerLink
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: The GROMIT strategy.
Figure 2: Genomic distribution and transcriptional activity of the different insertions.
Figure 3: Examples of patterns of activities associated with different insertions.
Figure 4: Short- and long-range activities detected by transposons inserted into the same loci.
Figure 5: Comparison between the genomic regulatory potential and intrinsic activities of nearby enhancers.
Figure 6: Mapping genomic regulatory domains with sequential tranposition and/or recombination.

Similar content being viewed by others

References

  1. ENCODE Project Consortium. et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799–816 (2007).

  2. Pennacchio, L.A. et al. In vivo enhancer analysis of human conserved non-coding sequences. Nature 444, 499–502 (2006).

    Article  CAS  Google Scholar 

  3. Kleinjan, D.A. et al. Long-range downstream enhancers are essential for Pax6 expression. Dev. Biol. 299, 563–581 (2006).

    Article  CAS  Google Scholar 

  4. Spitz, F., Gonzalez, F. & Duboule, D. A global control region defines a chromosomal regulatory landscape containing the HoxD cluster. Cell 113, 405–417 (2003).

    Article  CAS  Google Scholar 

  5. Nobrega, M.A., Ovcharenko, I., Afzal, V. & Rubin, E.M. Scanning human gene deserts for long-range enhancers. Science 302, 413 (2003).

    Article  CAS  Google Scholar 

  6. Sagai, T. et al. A cluster of three long-range enhancers directs regional Shh expression in the epithelial linings. Development 136, 1665–1674 (2009).

    Article  CAS  Google Scholar 

  7. Libioulle, C. et al. Novel Crohn disease locus identified by genome-wide association maps to a gene desert on 5p13.1 and modulates expression of PTGER4. PLoS Genet. 3, e58 (2007).

    Article  Google Scholar 

  8. Wang, K. et al. Common genetic variants on 5p14.1 associate with autism spectrum disorders. Nature 459, 528–533 (2009).

    Article  CAS  Google Scholar 

  9. Visel, A., Rubin, E.M. & Pennacchio, L.A. Genomic views of distant-acting enhancers. Nature 461, 199–205 (2009).

    Article  CAS  Google Scholar 

  10. Hallikas, O. et al. Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity. Cell 124, 47–59 (2006).

    Article  CAS  Google Scholar 

  11. Visel, A. et al. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457, 854–858 (2009).

    Article  CAS  Google Scholar 

  12. Heintzman, N.D. et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459, 108–112 (2009).

    Article  CAS  Google Scholar 

  13. Tuupanen, S. et al. The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling. Nat. Genet. 41, 885–890 (2009).

    Article  CAS  Google Scholar 

  14. Lettice, L.A. et al. A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly. Hum. Mol. Genet. 12, 1725–1735 (2003).

    Article  CAS  Google Scholar 

  15. Jeong, Y. et al. Regulation of a remote Shh forebrain enhancer by the Six3 homeoprotein. Nat. Genet. 40, 1348–1353 (2008).

    Article  CAS  Google Scholar 

  16. Benko, S. et al. Highly conserved non-coding elements on either side of SOX9 associated with Pierre Robin sequence. Nat. Genet. 41, 359–364 (2009).

    Article  CAS  Google Scholar 

  17. D'haene, B. et al. Disease-causing 7.4 kb cis-regulatory deletion disrupting conserved non-coding sequences and their interaction with the FOXL2 promotor: implications for mutation screening. PLoS Genet. 5, e1000522 (2009).

    Article  Google Scholar 

  18. Kurth, I. et al. Duplications of noncoding elements 5′ of SOX9 are associated with brachydactyly-anonychia. Nat. Genet. 41, 862–863 (2009).

    Article  CAS  Google Scholar 

  19. Klopocki, E. et al. A microduplication of the long range SHH limb regulator (ZRS) is associated with triphalangeal thumb-polysyndactyly syndrome. J. Med. Genet. 45, 370–375 (2008).

    Article  CAS  Google Scholar 

  20. Dathe, K. et al. Duplications involving a conserved regulatory element downstream of BMP2 are associated with brachydactyly type A2. Am. J. Hum. Genet. 84, 483–492 (2009).

    Article  CAS  Google Scholar 

  21. Sun, M. et al. Triphalangeal thumb-polysyndactyly syndrome and syndactyly type IV are caused by genomic duplications involving the long-range, limb-specific SHH enhancer. J. Med. Genet. 45, 589–595 (2008).

    Article  CAS  Google Scholar 

  22. Conrad, D.F. et al. Origins and functional impact of copy number variation in the human genome. Nature 464, 704–712 (2010).

    Article  CAS  Google Scholar 

  23. Kidd, J.M. et al. Mapping and sequencing of structural variation from eight human genomes. Nature 453, 56–64 (2008).

    Article  CAS  Google Scholar 

  24. Kokubu, C. et al. A transposon-based chromosomal engineering method to survey a large cis-regulatory landscape in mice. Nat. Genet. 41, 946–952 (2009).

    Article  CAS  Google Scholar 

  25. Kondo, T. & Duboule, D. Breaking colinearity in the mouse HoxD complex. Cell 97, 407–417 (1999).

    Article  CAS  Google Scholar 

  26. Nakatani, J. et al. Abnormal behavior in a chromosome-engineered mouse model for human 15q11–13 duplication seen in autism. Cell 137, 1235–1246 (2009).

    Article  Google Scholar 

  27. Visel, A. et al. Targeted deletion of the 9p21 non-coding coronary artery disease risk interval in mice. Nature 464, 409–412 (2010).

    Article  CAS  Google Scholar 

  28. Spitz, F., Herkenne, C., Morris, M.A. & Duboule, D. Inversion-induced disruption of the Hoxd cluster leads to the partition of regulatory landscapes. Nat. Genet. 37, 889–893 (2005).

    Article  CAS  Google Scholar 

  29. Hérault, Y., Rassoulzadegan, M., Cuzin, F. & Duboule, D. Engineering chromosomes in mice through targeted meiotic recombination (TAMERE). Nat. Genet. 20, 381–384 (1998).

    Article  Google Scholar 

  30. Wu, S., Ying, G., Wu, Q. & Capecchi, M.R. Toward simpler and faster genome-wide mutagenesis in mice. Nat. Genet. 39, 922–930 (2007).

    Article  CAS  Google Scholar 

  31. Yee, S.P. & Rigby, P.W. The regulation of myogenin gene expression during the embryonic development of the mouse. Genes Dev. 7, 1277–1289 (1993).

    Article  CAS  Google Scholar 

  32. Ivics, Z., Hackett, P.B., Plasterk, R.H. & Izsvak, Z. Molecular reconstruction of Sleeping Beauty, a Tc1-like transposon from fish, and its transposition in human cells. Cell 91, 501–510 (1997).

    Article  CAS  Google Scholar 

  33. Luo, G., Ivics, Z., Izsvák, Z. & Bradley, A. Chromosomal transposition of a Tc1/mariner-like element in mouse embryonic stem cells. Proc. Natl. Acad. Sci. USA 95, 10769–10773 (1998).

    Article  CAS  Google Scholar 

  34. Horie, K. et al. Characterization of Sleeping Beauty transposition and its application to genetic screening in mice. Mol. Cell. Biol. 23, 9189–9207 (2003).

    Article  CAS  Google Scholar 

  35. Baus, J., Liu, L., Heggestad, A.D., Sanz, S. & Fletcher, B.S. Hyperactive transposase mutants of the Sleeping Beauty transposon. Mol. Ther. 12, 1148–1156 (2005).

    Article  CAS  Google Scholar 

  36. Peschon, J.J., Behringer, R.R., Palmiter, R.D. & Brinster, R.L. Expression of mouse protamine 1 genes in transgenic mice. Ann. NY Acad. Sci. 564, 186–197 (1989).

    Article  CAS  Google Scholar 

  37. Geurts, A.M. et al. Gene mutations and genomic rearrangements in the mouse as a result of transposon mobilization from chromosomal concatemers. PLoS Genet. 2, e156 (2006).

    Article  Google Scholar 

  38. Reymond, A. et al. Human chromosome 21 gene expression atlas in the mouse. Nature 420, 582–586 (2002).

    Article  CAS  Google Scholar 

  39. Wurst, W. et al. A large-scale gene-trap screen for insertional mutations in developmentally regulated genes in mice. Genetics 139, 889–899 (1995).

    CAS  PubMed  PubMed Central  Google Scholar 

  40. Pauler, F.M. et al. H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome. Genome Res. 19, 221–233 (2009).

    Article  CAS  Google Scholar 

  41. Geurts, A.M. et al. Conditional gene expression in the mouse using a Sleeping Beauty gene-trap transposon. BMC Biotechnol. 6, 30 (2006).

    Article  Google Scholar 

  42. Yae, K. et al. Sleeping Beauty transposon-based phenotypic analysis of mice: lack of Arpc3 results in defective trophoblast outgrowth. Mol. Cell. Biol. 26, 6185–6196 (2006).

    Article  CAS  Google Scholar 

  43. Korn, R. et al. Enhancer trap integrations in mouse embryonic stem cells give rise to staining patterns in chimaeric embryos with a high frequency and detect endogenous genes. Mech. Dev. 39, 95–109 (1992).

    Article  CAS  Google Scholar 

  44. Kikuta, H. et al. Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates. Genome Res. 17, 545–555 (2007).

    Article  CAS  Google Scholar 

  45. Dimas, A.S. et al. Common regulatory variation impacts gene expression in a cell type–dependent manner. Science 325, 1246–1250 (2009).

    Article  CAS  Google Scholar 

  46. Schmidt, D. et al. Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science 21, 1036–1040 (2010).

    Article  Google Scholar 

  47. Wunderle, V.M., Critcher, R., Hastie, N., Goodfellow, P.N. & Schedl, A. Deletion of long-range regulatory elements upstream of SOX9 causes campomelic dysplasia. Proc. Natl. Acad. Sci. USA 95, 10649–10654 (1998).

    Article  CAS  Google Scholar 

  48. Gordon, J., Bennett, A.R., Blackburn, C.C. & Manley, N.R. Gcm2 and Foxn1 mark early parathyroid- and thymus-specific domains in the developing third pharyngeal pouch. Mech. Dev. 103, 141–143 (2001).

    Article  CAS  Google Scholar 

  49. Sumiyama, K. et al. Genomic structure and functional control of the Dlx3–7 bigene cluster. Proc. Natl. Acad. Sci. USA 99, 780–785 (2002).

    Article  CAS  Google Scholar 

  50. Lefèvre, C. & Mann, J.R. RNA expression microarray analysis in mouse prospermatogonia: identification of candidate epigenetic modifiers. Dev. Dyn. 237, 1082–1089 (2008).

    Article  Google Scholar 

Download references

Acknowledgements

We thank all the members of the EMBL mouse and transgenic facilities for pronuclear injections of the transgenes and mouse husbandry, particularly C. Klasen, A. Schultz and S. Feller; B. Fletcher (University of Florida) for the Sleeping Beauty transposon and transposase plasmids; A. Ephrussi and A. Aulehla for discussions and comments on the manuscript; and A. Hermelin and EMBL information technology service for helping with the TRACER website. We are grateful to all the members of the Spitz lab and students of the EMBL PhD classes of 2008 and 2009 who contributed to embryo dissection and staining. O.S. is funded by a Louis-Jeantet Foundation PhD fellowship. This work was supported by funding from the European Molecular Biology Laboratory (to F.S.) and from the European Community's Seventh Framework Programme (FP7/ 2007-2013) under the grant agreement n°FP7-211868 (to L.E. and F.S.).

Author information

Authors and Affiliations

  1. Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany

    Sandra Ruf, Orsolya Symmons, Veli Vural Uslu, Chloé Hot & François Spitz

  2. Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany

    Dirk Dolle & Laurence Ettwiller

Authors
  1. Sandra Ruf
    View author publications

    You can also search for this author inPubMed Google Scholar

  2. Orsolya Symmons
    View author publications

    You can also search for this author inPubMed Google Scholar

  3. Veli Vural Uslu
    View author publications

    You can also search for this author inPubMed Google Scholar

  4. Dirk Dolle
    View author publications

    You can also search for this author inPubMed Google Scholar

  5. Chloé Hot
    View author publications

    You can also search for this author inPubMed Google Scholar

  6. Laurence Ettwiller
    View author publications

    You can also search for this author inPubMed Google Scholar

  7. François Spitz
    View author publications

    You can also search for this author inPubMed Google Scholar

Contributions

F.S. conceived and designed the GROMIT strategy. S.R., O.S., V.V.U., C.H. and F.S. performed the experiments. O.S., D.D. and L.E. performed the statistical analyses. All authors discussed the results and contributed to the writing of the manuscript.

Corresponding author

Correspondence to François Spitz.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Note, Supplementary Figures 1–9 and Supplementary Tables 1–3. (PDF 8467 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Ruf, S., Symmons, O., Uslu, V. et al. Large-scale analysis of the regulatory architecture of the mouse genome with a transposon-associated sensor. Nat Genet 43, 379–386 (2011). https://doi.org/10.1038/ng.790

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/ng.790

Search

Advanced search

Quick links

Nature Briefing: Translational Research

Sign up for the Nature Briefing: Translational Research newsletter — top stories in biotechnology, drug discovery and pharma.

Get what matters in translational research, free to your inbox weekly. Sign up for Nature Briefing: Translational Research