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Series GSE106764 Query DataSets for GSE106764
Status Public on Oct 22, 2018
Title Next-generation sequencing reveals two populations of damage-induced small RNAs at endogenous DNA double-strand breaks
Organisms Homo sapiens; Mus musculus
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary Recent studies suggest that the repair of DNA double-strand breaks (DSBs) is supported by damage-induced small RNAs (diRNAs) that are generated by Drosha and Dicer from transcripts that originate from the regions flanking the break. However, transcription and diRNA production at naturally occurring DSBs in mammalian genomes remain controversial. We have used the homing endonuclease I-PpoI to produce DSBs in human and mouse cells, and we have analyzed the biogenesis of diRNAs at I-PpoI induced breaks in the 28S rDNA and the Ryr2 gene. We provide direct evidence that RNA polymerase II transcribes the sequences that flank the DSBs. Our results also reveal that the resulting transcripts are processed into two types of diRNAs with characteristic length and terminal nucleotide signatures. Furthermore, diRNA production is independent of Drosha and DGCR8, and only a subset of diRNAs depends on Dicer, as shown by small RNA analyses of knock-out cells that lack specific RNA processing enzymes. Our findings are compatible with previous observations of a general transcription inhibition at DSBs and provide novel insights into the mechanisms of RNA synthesis and processing at DSBs.
 
Overall design Cells (either mESCs or HeLa) were transfected with a plasmid coding for the homing endonuclease I-PpoI that induces a double strand break in the 28S rDNA. After transfection the small RNA fraction was sequenced using standard Illumina sequencing and analyzed for reads mapping to the 28S rDNA.
 
Contributor(s) Bonath F, Domingo-Prim J, Tarbier M, Friedländer M, Visa N
Citation(s) 30418607
Submission date Nov 10, 2017
Last update date Mar 26, 2019
Contact name Franziska Bonath
E-mail(s) franziska.bonath@scilifelab.se
Organization name Stockholm University
Department Department for Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratories
Lab Visa/Friedländer
Street address Tomtebodavägen 23A
City Solna
State/province Stockholm
ZIP/Postal code 17165
Country Sweden
 
Platforms (2)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (80)
GSM2850016 Dicer KO mESC, no I-PpoI [19_DcrKO_unc]
GSM2850017 Dicer KO mESC, no I-PpoI [20_DcrKO_unc]
GSM2850018 Dicer KO mESC, I-PpoI [22_DcrKO_cut]
Relations
BioProject PRJNA417936
SRA SRP124771

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE106764_RAW.tar 44.8 Mb (http)(custom) TAR (of BOWTIE)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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