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Variegated gene expression caused by cell-specific long-range DNA interactions

Nature Cell Biology volume 13, pages 944–951 (2011)Cite this article

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Abstract

Mammalian genomes contain numerous regulatory DNA sites with unknown target genes. We used mice with an extra β-globin locus control region (LCR) to investigate how a regulator searches the genome for target genes. We find that the LCR samples a restricted nuclear subvolume, wherein it preferentially contacts genes controlled by shared transcription factors. No contacted gene is detectably upregulated except for endogenous β-globin genes located on another chromosome. This demonstrates genetically that mammalian trans activation is possible, but suggests that it will be rare. Trans activation occurs not pan-cellularly, but in ‘jackpot’ cells enriched for the interchromosomal interaction. Therefore, cell-specific long-range DNA contacts can cause variegated expression.

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Figure 1: An ectopic LCR does not activate a natural target gene on the homologous chromosome.
Figure 2: Contacts of 8C3–C4 with and without the LCR are similar.
Figure 3: Within a predetermined genomic environment the ectopic LCR shows preferential interactions with specific genes.
Figure 4: The ectopic LCR on chromosome 8 enhances the expression of the endogenous βh1 gene on chromosome 7.
Figure 5: Increased βh1 mRNA levels in cells showing interchromosomal LCR–βh1 interactions.
Figure 6: Increased βh1 and β-major mRNA levels in cells showing interchromosomal LCR–βh1 interactions.

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Acknowledgements

We thank J. Marteijn and W. Vermeulen for providing Rad23a knockout material, Y. Oz for counting FISH slides, V. Buckle for providing BAC probes, J. van Rheenen and the Hubrecht Imaging Center for help with image analysis and E. Splinter and other members of the group for assistance. This work was financially supported by grants from the Dutch Scientific Organization (NWO) (91204082 and 935170621) and a European Research Council Starting Grant (209700, ‘4C’) to W.d.L.

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Author notes

  1. Daan Noordermeer

    Present address: Present address: Laboratory of Developmental Genomics, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland,

  2. Daan Noordermeer, Elzo de Wit and Petra Klous: These authors contributed equally to this work

Authors and Affiliations

  1. Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands

    Daan Noordermeer, Elzo de Wit, Petra Klous, Harmen van de Werken, Marieke Simonis & Wouter de Laat

  2. Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA

    Melissa Lopez-Jones & Robert H. Singer

  3. Department of Clinical Genetics, Erasmus Medical Centre, 3000 CA Rotterdam, PO Box 2040, The Netherlands

    Bert Eussen & Annelies de Klein

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Contributions

D.N. and W.d.L. designed the experiments, analysed the data and, with help from E.d.W., wrote the manuscript. D.N. and P.K. carried out experiments. E.d.W. analysed 4C data and developed the automated FISH image analysis. H.v.d.W. analysed 4C and microarray expression data. M.S. carried out 4C experiments. M.L-J. and R.H.S. designed and synthesized RNA-FISH probes. B.E. and A.d.K. helped with the FISH experiments.

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Correspondence to Wouter de Laat.

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Noordermeer, D., de Wit, E., Klous, P. et al. Variegated gene expression caused by cell-specific long-range DNA interactions. Nat Cell Biol 13, 944–951 (2011). https://doi.org/10.1038/ncb2278

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