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

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.

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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.

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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.).

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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.

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The authors declare no competing financial interests.

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

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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

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