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Series GSE138730 Query DataSets for GSE138730
Status Public on Oct 11, 2019
Title Altered m6A Modification of Specific Cellular Transcripts Affects Flaviviridae Infection
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary The RNA modification N6-methyladenosine (m6A) can modulate mRNA fate and thus affect many biological processes. We analyzed m6A modification across the transcriptome following infection by dengue virus (DENV), Zika virus (ZIKV), West Nile virus (WNV), and hepatitis C virus (HCV). We found that infection by these viruses in the Flaviviridae family alters m6A modification of specific cellular transcripts, including RIOK3 and CIRBP. During viral infection, the addition of m6A to RIOK3 promotes its translation, while loss of m6A in CIRBP promotes alternative splicing. Importantly, we found that viral activation of innate immune sensing or the endoplasmic reticulum (ER) stress response contributes to the changes in m6A modification in RIOK3 and CIRBP, respectively. Further, several transcripts with infection-altered m6A profiles, including RIOK3 and CIRBP, encode proteins that influence DENV, ZIKV, and HCV infection. Overall, this work reveals that cellular signaling pathways activated during viral infection lead to alterations in m6A modification of host mRNAs to regulate infection.
Overall design Study of m6A changes in cellular RNA from Huh7 cells following 4 biological replicates of innate immune activation (HCV PAMP transfection, 8 hpt) or ER stress (thapsigargin (TG) treatment, 16 hpt).
Web link
Contributor(s) Gokhale NS, McIntyre AB, Mattocks MD, Holley CL, Lazear HM, Mason CE, Horner SM
Citation(s) 31810760
Submission date Oct 10, 2019
Last update date Jan 10, 2020
Contact name A McIntyre
Organization name University of Zurich
Department Molecular Life Sciences
Street address Winterthurerstrasse 190
City Zurich
ZIP/Postal code 8057
Country Switzerland
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (32)
GSM4117129 PAMP_IP_1
GSM4117130 PAMP_input_1
GSM4117131 PAMP_IP_2
BioProject PRJNA576915
SRA SRP225110

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
GSE138730_PAMP_1.macs2_peaks.narrowPeak.gz 217.3 Kb (ftp)(http) NARROWPEAK
GSE138730_PAMP_2.macs2_peaks.narrowPeak.gz 199.9 Kb (ftp)(http) NARROWPEAK
GSE138730_PAMP_3.macs2_peaks.narrowPeak.gz 204.3 Kb (ftp)(http) NARROWPEAK
GSE138730_PAMP_4.macs2_peaks.narrowPeak.gz 226.9 Kb (ftp)(http) NARROWPEAK
GSE138730_Pmock_1.macs2_peaks.narrowPeak.gz 221.6 Kb (ftp)(http) NARROWPEAK
GSE138730_Pmock_2.macs2_peaks.narrowPeak.gz 222.8 Kb (ftp)(http) NARROWPEAK
GSE138730_Pmock_3.macs2_peaks.narrowPeak.gz 237.7 Kb (ftp)(http) NARROWPEAK
GSE138730_Pmock_4.macs2_peaks.narrowPeak.gz 274.0 Kb (ftp)(http) NARROWPEAK
GSE138730_TG_1.macs2_peaks.narrowPeak.gz 118.7 Kb (ftp)(http) NARROWPEAK
GSE138730_TG_2.macs2_peaks.narrowPeak.gz 176.0 Kb (ftp)(http) NARROWPEAK
GSE138730_TG_3.macs2_peaks.narrowPeak.gz 216.1 Kb (ftp)(http) NARROWPEAK
GSE138730_TG_4.macs2_peaks.narrowPeak.gz 207.4 Kb (ftp)(http) NARROWPEAK
GSE138730_Tmock_1.macs2_peaks.narrowPeak.gz 156.4 Kb (ftp)(http) NARROWPEAK
GSE138730_Tmock_2.macs2_peaks.narrowPeak.gz 168.3 Kb (ftp)(http) NARROWPEAK
GSE138730_Tmock_3.macs2_peaks.narrowPeak.gz 228.1 Kb (ftp)(http) NARROWPEAK
GSE138730_Tmock_4.macs2_peaks.narrowPeak.gz 223.4 Kb (ftp)(http) NARROWPEAK
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Processed data are available on Series record

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