Abstract
Human telomeres are bound and protected by protein complexes assembled around the six core telomeric proteins RAP1, TRF1, TRF2, TIN2, TPP1, and POT1. The function of these proteins on telomeres has been studied extensively. Recently, increasing evidence has suggested possible roles for these proteins outside of telomeres. However, the non-canonical (extra-telomeric) function of human telomeric proteins remains poorly understood. To this end, we systematically investigated the binding sites of telomeric proteins along human chromosomes, by performing whole-genome chromatin immunoprecipitation (ChIP) for RAP1 and TRF2. ChIP sequencing (ChIP-seq) revealed that RAP1 and TRF2 could be found on a small number of interstitial sites, including regions that are proximal to genes. Some of these binding sites contain short telomere repeats, suggesting that telomeric proteins could directly bind to interstitial sites. Interestingly, only a small fraction of the available interstitial telomere repeat-containing regions were occupied by RAP1 and TRF2. Ectopically expressed TRF2 was able to occupy additional interstitial telomere repeat sites, suggesting that protein concentration may dictate the selective targeting of telomeric proteins to interstitial sites. Reducing RAP1 and TRF2 expression by RNA interference led to altered transcription of RAP1- and TRF2-targeted genes. Our results indicate that human telomeric proteins could occupy a limited number of interstitial sites and regulate gene transcription.
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Acknowledgements
We would like to thank Dr Maria Blasco (Spanish National Cancer Center) for sharing with us the mouse RAP1 ChIP-seq data. We thank Yi Zhang (Baylor College of Medicine) for technical help with TRF2 knockdown and Dr Dan Liu (Baylor College of Medicine) for critical reading of this manuscript. This work is supported by NCI CA133249, NIGMS GM081627, the Welch Foundation Q-1673, and 2010CB945400. This work is also supported by 1S10RR026550-01 and 5U54HG003273 (RC). ZS is a Leukemia and Lymphoma Society Scholar.
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( Supplementary information is linked to the online version of the paper on the Cell Research website.)
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Supplementary information, Figure S1
Ectopically expressed RAP1-FLAG and TRF2-FLAG bind telomeres. (PDF 23 kb)
Supplementary information, Figure S2
Overexpression of TRF2 does not increase the binding of RAP1 at interstitial sites. (PDF 72 kb)
Supplementary information, Figure S3
Knockdown of TRF2 decreases its binding to target genes. (PDF 47 kb)
Supplementary information, Table S1
A list of primers used in real-time quantitative PCR (PDF 92 kb)
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Yang, D., Xiong, Y., Kim, H. et al. Human telomeric proteins occupy selective interstitial sites. Cell Res 21, 1013–1027 (2011). https://doi.org/10.1038/cr.2011.39
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DOI: https://doi.org/10.1038/cr.2011.39
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