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Probing long-distance regulatory interactions in the Drosophila melanogaster bithorax complex using Dam identification


A cis-regulatory region of nearly 300 kb controls the expression of the three bithorax complex (BX-C) homeotic genes: Ubx, abd-A and Abd-B1,2. Interspersed between the numerous enhancers and silencers within the complex are elements called domain boundaries. Recently, many pieces of evidence have suggested that boundaries function to create autonomous domains by interacting among themselves and forming chromatin loops3,4,5,6. In order to test this hypothesis, we used Dam identification to probe for interactions between the Fab-7 boundary and other regions in the BX-C7. We were surprised to find that the targeting of Dam methyltransferase (Dam) to the Fab-7 boundary results in a strong methylation signal at the Abd-Bm promoter, 35 kb away. Moreover, this methylation pattern is found primarily in the tissues where Abd-B is not expressed and requires an intact Fab-7 boundary. Overall, our work provides the first documented example of a dynamic, long-distance physical interaction between distal regulatory elements within a living, multicellular organism.

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We thank P. Rorth, B. van Steensel and S. Henikoff for providing plasmids, fly strains and advices. We are indebted to C. Barraclough, M. Docquier and P. Descombes of the NCCR Frontiers in Genetics genomics group for their advice and assistance in quantitative PCR. We also thank A. Mutero for her critical reading and comments on the manuscript. Finally, we wish to thank P. Verrijzer and H.Gyurkovics for stimulating discussions. This work was supported by the Swiss National Foundation, by the NCCR Frontiers in Genetics and by the State of Geneva.

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Competing interests

The authors declare no competing financial interests.

Correspondence to François Karch.

Supplementary information

  1. Supplementary Fig. 1

    Boundary tethering model. (PDF 344 kb)

  2. Supplementary Table 1

    Primers used in this study and their positions in the bithorax complex. (PDF 48 kb)

  3. Supplementary Table 2

    Summary of two-way ANOVA analysis. (PDF 68 kb)

  4. Supplementary Table 3

    Tables summarizing two-way ANOVA analysis. (PDF 76 kb)

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Figure 1: Experimental setup.
Figure 2: Graph marking relative methylation levels above background (RMoB) in DGL (red) and DGLΔFab-7 (blue).
Figure 3: Graphs marking relative methylation levels above background (RMoB).