Computational Mapping of the Human-SARS-CoV-2 Protein-RNA Interactome

Abstract

It is well known that viruses make extensive use of the host cell's machinery, hijacking it for the purpose of viral replication and interfere with the activity of master regulatory proteins - including RNA binding proteins (RBPs). RBPs recognize and bind RNA molecules to control several steps of cellular RNA metabolism, such as splicing, transcript stability, translation and others, and recognize their targets by means of sequence or structure motifs. Host RBPs are critical factors for viral replication, especially for RNA viruses, and have been shown to influence viral RNA stability, replication and escape of host immune response. While current research efforts have been centered around identifying mechanisms of host cell-entry, the role of host RBPs in the context of SARS-CoV-2 replication remains poorly understood. Few experimental studies have started mapping the SARS-CoV-2 RNA-protein interactome in infected human cells, but they are limited in the resolution and exhaustivity of their output. On the other hand, computational approaches enable screening of large numbers of human RBPs for putative interactions with the viral RNA, and are thus crucial to prioritize candidates for further experimental investigation. Here, we investigate the role of RBPs in the context of SARS-CoV-2 by constructing a first single-nucleotide \textit{in silico} map of human RBP / viral RNA interactions by using deep learning models trained on RNA sequences. Our framework is based on Pysster and DeepRiPe, two deep learning method which use a convolutional neural network to learn sequence-structure preferences of a specific RBP. Models were trained using eCLIP and PAR-CLIP datasets for >150 RBP generated on human cell lines and applied cross-species to predict the propensity of each RBP to bind the SARS-CoV-2 genome. After extensive validation of predicted binding sites, we generate RBP binding profiles across different SARS-CoV-2 variants and 6 other betacoronaviruses. We address the questions of (1) conservation of binding between pathogenic betacoronaviruses, (2) differential binding across viral strains and (3) gain and loss of binding events in novel mutants which can be linked to disease severity and spread in the population. In addition, we explore the specific pathways hijacked by the virus, by integrating host factors linked to these virus-binding RBPs through protein-protein interaction networks or genome wide CRISPR screening. We believe that identifying viral RBP binding sites will give valuable insights into the mechanisms of host-virus interaction, thus giving us a deeper understanding of the life cycle of SARS-CoV-2 but also opening new avenues for the development of new therapeutics.

Single cell phototransfection of mRNAs encoding SARS-CoV2 spike and nucleocapsid into human astrocytes results in RNA dependent translation interference

“…Further the impact of Spike mRNA presence and translation in increasing Nuc immunoreactivity suggests that the translational status of Nuc mRNA is enhanced perhaps by suppressing activity of a Nuc mRNA translation inhibitory RBP through the Spike mRNA competing for its binding. Computational analysis of the primary sequence of SARS-CoV-2 Spike and Nuc RNA sequences shows the presence of RNA sequences that are predicted canonical binding sites for various RBPs (Horlacher et al, 2023). The combination of the translation data presented herein and computational predictions from others (Horlacher et al, 2023) suggests that cells will differ in their ability to harbor or propagate SARS-CoV-2 virus based upon the host cells RBP complement.…”

Discovering host protein interactions specific for SARS-CoV-2 RNA genome

“…3D ). Among them, i) FAM120A, LSG1 and RPS6 that were already reported as host proteins reproducibly interacting with SARS-CoV-2 RNA (32); ii) the splicing factors GPKOW, SF3A1, NOP58 and the NDM factor SMG7 that were computationally predicted to specifically associate to the genomic viral RNA (34, 35); iii) the RNA modifier PUS7, that catalyzes the isomerisation of uridine into pseudouridine in cellular tRNAs and mRNAs, reported here for the first time. In the RaPID-MS dataset, PUS7 specifically associates with fragments 1, 4, 7 and 10, all harboring a PUS7 consensus sequence.…”

Systematic analysis of alternative splicing in time course data using Spycone

“…ILF3 plays a role in antiviral response by inducing the expression of interferon-stimulated genes ( Watson et al , 2020 ). In another computational analysis, SRSF7 is also predicted to have binding potential with SARS-CoV-2 RNA ( Horlacher et al , 2021 ).…”