Mammalian Rap1 controls telomere function and gene expression through binding to telomeric and extratelomeric sites

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Abstract

Rap1 is a component of the shelterin complex at mammalian telomeres, but its in vivo role in telomere biology has remained largely unknown to date. Here we show that Rap1 deficiency is dispensable for telomere capping but leads to increased telomere recombination and fragility. We generated cells and mice deleted for Rap1; mice with Rap1 deletion in stratified epithelia were viable but had shorter telomeres and developed skin hyperpigmentation in adulthood. By performing chromatin immunoprecipitation coupled with ultrahigh-throughput sequencing, we found that Rap1 binds to both telomeres and to extratelomeric sites through the (TTAGGG)2 consensus motif. Extratelomeric Rap1-binding sites were enriched at subtelomeric regions, in agreement with preferential deregulation of subtelomeric genes in Rap1-deficient cells. More than 70% of extratelomeric Rap1-binding sites were in the vicinity of genes, and 31% of the genes deregulated in Rap1-null cells contained Rap1-binding sites, suggesting a role for Rap1 in transcriptional control. These findings place a telomere protein at the interface between telomere function and transcriptional regulation.

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Figure 1: Generation of Rap1Δ/Δ cells.
Figure 2: Rap1 deletion does not affect the binding of other shelterins to telomeres.
Figure 3: Rap1-deleted MEFs show increased fragility (MTSs) and recombination but no fusions.
Figure 4: Deletion of Rap1 in stratified epithelia leads to telomere shortening and skin hyperpigmentation in adulthood.
Figure 5: Role for RAP1 in subtelomeric silencing.
Figure 6: Differentially expressed genes on abrogation of Rap1.
Figure 7: Genome-wide mapping of RAP1-binding sites.
Figure 8: De novo identification of a consensus RAP1-binding site.

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Acknowledgements

We are indebted to L. Harrington for Tert-deficient MEFs; S. West for Rap1 antibodies; and R. Serrano for animal care. P.M. is funded by a 'Ramón y Cajal' grant from the Spanish Ministry of Innovation and Science. M.A.B.'s laboratory is funded by the Spanish Ministry of Innovation and Science, the European Union (FP7-Genica, Telomarker), the European Research Council (ERC Advance Grants), the Spanish Association Against Cancer (AECC) and a Körber European Science Award to M.A.B. The work in M.T.'s laboratory is funded by Cancer Research UK.

Author information

M.A.B. conceived the original idea. M.A.B. and P.M. designed experiments and wrote the manuscript. P.M. performed most of the experiments. M.T.A., A.R.C. and M.T. contributed results in Figs 2a, b and 3a–f. A.T. performed experiments in Fig. 2c, d and Supplementary Information, Fig. S2e. S.S. designed the knockout allele. O.D. performed DNA methylation analysis, microarray and ChIP-seq experiments. G.G. and D.G.P. performed microarray and ChIP-seq data analysis.

Correspondence to Maria A. Blasco.

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Martinez, P., Thanasoula, M., Carlos, A. et al. Mammalian Rap1 controls telomere function and gene expression through binding to telomeric and extratelomeric sites. Nat Cell Biol 12, 768–780 (2010) doi:10.1038/ncb2081

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