RNA-seq and Ribo-seq analysis of the effects of METTL3/14 depletion on gene expression during the interferon response in Huh7 cells

UID: 10672

Author(s): McFadden, Michael J., Mourelatos, Haralambos, Mason, Christopher E, Horner, Stacy M.

Description: Summary from the GEO: "The RNA modification N6-methyladenosine (m6A) regulates gene expression through various transcript-specific effects. The overall goal of these experiments was to determine the effects of the m6A methyltransferase complex proteins METTL3 and METTL14 on the expression of interferon stimulated genes. First, we depleted METTL3 and METTL14 in Huh7 cells using siRNAs and treated with Mock or IFN-β to analyze the regulatory effects of METTL3/14 on interferon-stimulated genes' transcript abundance. We then used Ribo-seq following METTL3/14 siRNA depletion and IFN treatment to quantify its effect on the translation of ISGs and other genes. Overall, we found that METTL3/14 exerts transcript-specific regulatory effects on a subset of interferon-stimulated genes. Overall, METTL3/14 appeared to enhance the translation of a subset of interferon-stimulated genes. We characterized the molecular effects of METTL3/14 and m6A on certain ISGs and determined that m6A augments the antiviral effects of the interferon response."

Overall design from the GEO: "siRNA transfections were performed for 36 hours in Huh7 cells prior to IFN-β treatment (50 units/mL) for 8 hours, after which cells were harvested and RNA-seq or Ribo-seq protocols were performed. For RNA-seq, 3 replicates of each condition were performed and for Ribo-seq, 4 replicates for each condition were performed."

Subject of Study

Subject(s)

Access via GEO
Plain Text Data of expression profiling by high throughput sequencing
Accession #: GSE155447

Access via SRA
RNA and Ribo Sequence reads for 20 samples
Accession #: SRP274360

Access via BioProject
Additional information about overall initiative.
Accession #: PRJNA649776
Access Restrictions: Free to All
Access Instructions: The NCBI Gene Expression Omnibus, SRA, and BioProject databases provide open access to these files.
Associated Publications: McFadden MJ, McIntyre ABR, Mourelatos H, et al. Post-transcriptional regulation of antiviral gene expression by N6-methyladenosine. Cell Rep. 2021;34(9):108798.
Data Type: Genomic
Equipment Used: Illumina HiSeq 4000
High throughput gene sequencing system

Illumina NextSeq 500
Software Used: SRA Toolkit
The NCBI SRA Toolkit enables reading ("dumping") of sequencing files from the SRA database and writing ("loading") files into the .sra format.
Dataset Format(s): Plain Text, SRA
Data Tool(s): RNA Seq

Ribo Seq
Dataset Size: 6.6 MB (TXT), 42.2 Gb (SRA)

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