Target enrichment followed by high throughput sequencing of telomeric DDRNAs in telomere-deprotected mouse cells. Mus musculus

Telomeres are the nucleoprotein complexes located at the tips of eukaryotic chromosomes, composed of repetitive DNA (TTAGGG in vertebrates), and coated by a set of proteins collectively known as the shelterin complex. Dysfunctional telomeres resemble DSBs and they have been observed during ageing and cancer and a number of pathological conditions. Apart from telomeric repeat-containing RNA (TERRA), a non-coding UUAGGG-rich transcript starting from promoters located in the subtelomeric region, in mammals no other transcripts at telomeres have been characterized so far. Here we show that in mammals telomere dysfunction (analysed using TRF2+/- and TRF2-/- mouse embryonic fibroblasts) induces the transcription of telomeric DDRNAs (tDDRNAs) from both DNA strands. To characterize the length and sequence of tDDRNAs, we devised and employed an innovative method for target enrichment of RNA, based on in solution capture of low abundance small RNA species followed by next generation sequencing, developed in our laboratories. By this approach, we observed that telomere deprotection induced the accumulation of small RNA species generated from the transcription of both telomere strands and including the expected DDRNA size range products. Importantly, 20-23 nucleotide RNAs displayed a base bias at both 5’ and 3’ ends significantly different from the telomeric locus suggesting a regulated processing. Overall design: RNA extracted from mouse embryonic fibroblasts, induced or uninduced for TRF2 knock out, were used for target enrichment and MiSeq sequencing. The experiment was carried out in 3 replicates