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Series GSE48831 Query DataSets for GSE48831
Status Public on Nov 19, 2013
Title Viral small RNAs in Sindbis virus-infected mammalian cells
Organisms Chlorocebus aethiops; Homo sapiens
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary Small RNAs play a critical role in host-pathogen interaction. In insects, for instance, small RNA-mediated silencing or RNA interference (RNAi) represents the main antiviral defense system. However, the antiviral role of RNAi has not been clearly proven in higher vertebrates. On the contrary, it is well established that the cell response relies on the recognition of viral RNAs by host pattern recognition receptors (PRR) to trigger the activation of the interferon pathway. Based on this evidence, we wished to contribute to this research field by identifying and characterizing small non-coding RNAs produced in mammalian cells upon RNA virus infection. We focused on Sindbis virus (SINV), the prototypical arbovirus, which by definition, is able to infect both vertebrate hosts and invertebrate vectors and triggers the interferon pathway or RNAi, respectively.
Overall design Taking advantage of large scale sequencing, we cloned and sequenced small RNAs from both mock and SINV-infected mammalian cells (HEK 293 and VERO). We identified a novel population of viral small RNAs (vsRNAs) that accumulate as 20 to 30 nt species during infection. We assessed that this viral small RNA population is modified in 3'end and derived from the activation of the cellular antiviral endoribonuclease RNaseL. Altogether our results indicate a potential role for the SINV-derived small RNAs in the host defense mechanism.
Contributor(s) Girardi E, Chane-Woon-Ming B, Messmer M, Kaukinen P, Pfeffer S
Citation(s) 24255120
Submission date Jul 12, 2013
Last update date May 15, 2019
Contact name Sébastien Pfeffer
Organization name CNRS - Institut de Biologie Moléculaire et Cellulaire (IBMC)
Department UPR 9002 - Architecture et Réactivité de l'ARN
Lab RNA regulation in viral infections
Street address 2 allée Konrad Roentgen
City Strasbourg
ZIP/Postal code 67084
Country France
Platforms (4)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL16397 Illumina Genome Analyzer IIx (Chlorocebus aethiops)
Samples (10)
GSM1185387 sRNAs from non-infected HEK293 cells
GSM1185388 sRNAs from SINV-infected HEK293 cells
GSM1185389 sRNAs from non-infected VERO cells
BioProject PRJNA211869
SRA SRP027345

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Supplementary file Size Download File type/resource
GSE48831_RAW.tar 510.0 Kb (http)(custom) TAR (of BED)
GSE48831_Summary.txt.gz 995.4 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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