Identifying cellular RNA-binding proteins during infection uncovers a role for MKRN2 in influenza mRNA trafficking
Cite this dataset
Bonazza, Stefano et al. (2024). Identifying cellular RNA-binding proteins during infection uncovers a role for MKRN2 in influenza mRNA trafficking [Dataset]. Dryad. https://doi.org/10.5061/dryad.k98sf7mf5
Abstract
Utilisation of RNA-binding proteins (RBPs) is an important aspect of post-transcriptional regulation of viral RNA. Viruses such as influenza A viruses (IAV) interact with RBPs to regulate processes including splicing, nuclear export and trafficking, while also encoding RBPs within their genomes, such as NP and NS1. But with almost 1000 RBPs encoded within the human genome it is still unclear what role, if any, many of these proteins play during viral replication. Using the RNA interactome capture (RIC) technique, we isolated RBPs from IAV infected cells to unravel the RBPome of mRNAs from IAV infected human cells. This led to the identification of one particular RBP, MKRN2, that associates with and positively regulates IAV mRNA. Through further validation, we determined that MKRN2 is involved in the nuclear-cytoplasmic trafficking of IAV mRNA potentially through an association with the RNA export mediator GLE1. In the absence of MKRN2, IAV mRNAs accumulate in the nucleus of infected cells, which may lead to their degradation by the nuclear RNA exosome complex. MKRN2, therefore, appears to be required for the efficient nuclear export of IAV mRNAs in human cells.
README: Identifying cellular RNA-binding proteins during infection uncovers a role for MKRN2 in influenza mRNA trafficking.
https://doi.org/10.5061/dryad.k98sf7mf5
Description of the data and file structure
The raw_data.xls contains all the data used to generate each graph within the referenced manuscript. Each excel tab corresponds to a different panel in a figure, and is named after the figure panel. All replicate data is contained within the tab and labelled appropriately for each condition.
The MKRN2.zip file contains all the image files used for quantification of MKRN2 localisation during an influenza A virus time course, with nuclear and cytoplasmic fractions quantified to generate Figure 5B of the referenced publication. The parent folder contains 4 subfolders, 3 correspond to the 3 biological replicates of the experiment and a 4th folder named 'For figure' which are the representative images selected for Figure 5A. Within each replicate folder are .tif files containing series of z-collapsed images for conditions of Mock, 4 h and 8 h post infection.
The MKRN2_smiFISH.zip file contains all the image files used for the quantification of NP mRNA localisation in Figure 5D of the referenced manuscript. The parent folder contains 4 subfolders, 3 correspond to the 3 biological replicates of the experiment and are named Replicate 1, Replicate 2 and Replicate 3. Within each of these folders are .lif files containing sets of images and can be opened using the free ImageJ software for image processing. The files are titled Mock.lif, NSC.lif and MKRN2.lif, corresponding to the Mock infection, cells treated with an Non-Specific Control siRNA and infected, or cell treated with a MKRN2-specific siRNA and infected, respectively. The 4th folder contains the representative images selected for Figure 5C within sub folder for each condition, labeled mock, NSC and MKRN2.
Sharing/Access information
This data is not available anywhere else.
Code/Software
This is a compilation of raw unprocessed images and raw data used to generate graphs for the referenced manuscript.
Methods
Funding
European Research Council, Award: PTFLU 949506, StG