NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE231738 Query DataSets for GSE231738
Status Public on Jan 23, 2024
Title N6-methyladenosine modification is not a general trait of viral RNA genomes [Dengue]
Organisms Homo sapiens; Dengue virus
Experiment type Other
Summary N6-methyladenosine (m6A), the most common internal RNA modification in eukaryotic mRNAs, is described to be abundantly present in the genomes of cytoplasmic-replicating RNA viruses. Yet, how the host nuclear m6A writer has access to the viral RNAs in the cytoplasm and what are the associated biological consequences remain unknown. Here, we comprehensively addressed these questions by combining antibody-dependent (m6A-seq) and antibody-independent (SELECT and nanopore direct RNA sequencing) methods on the cytoplasmic-replicating Chikungunya virus (CHIKV) RNA, and found no evidence of m6A modifications. Moreover, depletion of m6A modification machinery components did not affect CHIKV infection, and CHIKV infection did not alter their cellular localization. Consistent with these observations, no m6A modifications were found in the RNA genome of the dengue virus (DENV), another cytoplasmic-replicating virus. Our results challenge the idea that m6A modification is a general trait of cytoplasmic-replicating RNA viruses and stress the need of confirming antibody-dependent detection of m6A modifications with orthogonal antibody-independent methods.
 
Overall design m6A-RIP on Dengue-infected HEK293T cells, made up of two input and two IP samples, used to perform downstream peakcalling analysis.
 
Contributor(s) Baquero-Perez B, Yonchev ID, Delgado-Tejedor A, Medina R, Puig-Torrents M, Sudbery I, Begik O, Wilson SA, Novoa EM, Diez J
Citation(s) 38467633
Submission date May 05, 2023
Last update date Mar 20, 2024
Contact name Juana Diez
E-mail(s) juana.diez@upf.edu
Organization name Pompeu Fabra University
Street address Dr. Aiguader, 88
City Barcelona
ZIP/Postal code 08003
Country Spain
 
Platforms (1)
GPL33380 Illumina NextSeq 500 (Dengue virus; Homo sapiens)
Samples (4)
GSM7299915 HEK293T, Dengue-infected, Input, replicate 1
GSM7299916 HEK293T, Dengue-infected, Input, replicate 2
GSM7299917 HEK293T, Dengue-infected, m6AIP, replicate 1
This SubSeries is part of SuperSeries:
GSE231739 N6-methyladenosine modification is not a general trait of viral RNA genomes.
Relations
BioProject PRJNA967597

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
GSE231738_DENV-conserved-m6aViewer-peaks.txt.gz 4.2 Mb (ftp)(http) TXT
GSE231738_RAW.tar 755.6 Mb (http)(custom) TAR (of BW, NARROWPEAK)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap