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Series GSE86964 Query DataSets for GSE86964
Status Public on May 10, 2017
Title Target enrichment followed by high throughput sequencing of telomeric DDRNAs in telomere-deprotected mouse cells
Organism Mus musculus
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary 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
Contributor(s) Iannelli F, Nguyen Q, Aguado J, Rossiello F, Carninci P, d'Adda di Fagagna F
Citation(s) 28239143
Submission date Sep 15, 2016
Last update date May 15, 2019
Contact name Fabrizio d'Adda di Fagagna
Organization name IFOM - The FIRC Institute of Molecular Oncology
Lab DNA Damage Response and Cellular Senescence
Street address Via Adamello 16
City Milan
State/province Mi
ZIP/Postal code 20139
Country Italy
Platforms (1)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (6)
GSM2311149 TRF2 F/F exp1
GSM2311150 TRF2 F/+ exp1
GSM2311151 TRF2 F/F exp2
BioProject PRJNA343104
SRA SRP089939

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Supplementary file Size Download File type/resource
GSE86964_RAW.tar 20.0 Kb (http)(custom) TAR (of BEDGRAPH)
GSE86964_telomere.fa.gz 61 b (ftp)(http) FA
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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