RNA-seq, ChIP-seq and TERRA CHIRT-seq from p53-/- iPS infected with a lentiviral virus carrying a control scrambled shRNA or shRNA against TRF1

The mechanisms that regulate pluripotency and cell fate are still largely unknown. Here, we show that the Telomere Repeat Binding Factor 1 (TRF1), a component of the shelterin telomere protection complex, regulates genome-wide binding of polycomb to stem cell and pluripotency genes, thereby exerting vast epigenetic changes that contribute to maintain embryonic stem cells in a naïve state. We further show that TRF1 mediates these effects by regulating TERRA, the long-non-coding RNAs transcribed from telomeres and that are part of the telomeric chromatin. In particular, we find that TERRAs are enriched at polycomb and stem cell genes in pluripotent cells and that TRF1 abrogation results in increased TERRA levels and a higher binding of TERRA to those genes, an event that is coincidental with TRF1-dependent induction of cell-fate programs and loss of the naïve state. These results are consistent with a model in which TERRA recruits polycomb to genes important for pluripotency and differentiation in a manner that is dependent on TRF1. These unprecedented findings explain the long-standing observation that TRF1 is one of the most upregulated genes during induction of pluripotency and it is essential for the induction and maintenance of pluripotency. p53-/- iPS cells were infected with lentivirus encoding a control shRNA or a shRNA against TRF1. After two days selection with puromycin, RNA or chromatin was obtained to perform the next techniques. From RNA-seqs, two independent experiments were performed so 2 different control samples and two different condition samples were analyzed. A single experiment was analyzed for the ChIP-seqs, sending one sample for the control and one for the condition sample. The ChIPs against the following proteins were performed: Suz12, H3K27me3 and TRF1. As control, a mix of the input of the control and the condition samples was sequenced. For the CHIRT-seq against TERRA, the sample from the control condition and the original input were sequenced.