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PEER-REVIEWED
Published: January 5, 2023
Kristoffer E. Leon ,Mir M. Khalid ,Ryan A. Flynn,Krystal A. Fontaine,Thong T. Nguyen,G. Renuka Kumar,
Camille R. Simoneau,Sakshi Tomar,David Jimenez-Morales,Mariah Dunlap,Julia Kaye,Priya S. Shah, Steven Finkbeiner, [ ... ], Melanie Ott [ view all ]
Abstract
Zika virus (ZIKV) infects fetal neural progenitor cells (NPCs) causing severe neurodevelopmental disorders in utero. Multiple pathways involved in normal brain development are dysfunctional in infected NPCs but how ZIKV centrally reprograms these pathways remains unknown. Here we show that ZIKV infection disrupts subcellular partitioning of host transcripts critical for neurodevelopment in NPCs and functionally link this process to the up-frameshift protein 1 (UPF1). UPF1 is an RNA-binding protein known to regulate decay of cellular and viral RNAs and is less expressed in ZIKV-infected cells. Using infrared crosslinking immunoprecipitation and RNA sequencing (irCLIP-Seq), we show that a subset of mRNAs loses UPF1 binding in ZIKV-infected NPCs, consistent with UPF1’s diminished expression. UPF1 target transcripts, however, are not altered in abundance but in subcellular localization, with mRNAs accumulating in the nucleus of infected or UPF1 knockdown cells. This leads to diminished protein expression of FREM2, a protein required for maintenance of NPC identity. Our results newly link UPF1 to the regulation of mRNA transport in NPCs, a process perturbed during ZIKV infection.
Author summary
The outbreak of Zika Virus (ZIKV) led to an epidemic of microcephaly and other congenital abnormalities. ZIKV is typically spread by mosquitoes, but it can also cross the placenta and infect the fetus of pregnant individuals. During the infection of the fetus, ZIKV targets neural progenitor cells (NPCs), leading to disruptions in brain development. In this study, we infect NPCs with ZIKV to better understand changes in the host cell during infection. In particular, we focus on the protein UPF1, a key player on the nonsense mediated mRNA decay pathway. We found that during ZIKV infection, UPF1 interacts with fewer transcripts, and these transcripts are associated with neurodevelopment. Furthermore, it appears that UPF1 is involved in mRNA transport out of the nucleus. We identify FREM2 as one of the transcripts with the greatest loss of UPF1 interaction and find that perturbation of this gene leads to upregulation of proteins associated with neural progenitor cell differentiation. Our study provides new insights into both the molecular pathogenesis of ZIKV and highlights another role that UPF1 plays in the cell.
PEER-REVIEWED
Published: January 5, 2023
Kristoffer E. Leon ,Mir M. Khalid ,Ryan A. Flynn,Krystal A. Fontaine,Thong T. Nguyen,G. Renuka Kumar,
Camille R. Simoneau,Sakshi Tomar,David Jimenez-Morales,Mariah Dunlap,Julia Kaye,Priya S. Shah, Steven Finkbeiner, [ ... ], Melanie Ott [ view all ]
Abstract
Zika virus (ZIKV) infects fetal neural progenitor cells (NPCs) causing severe neurodevelopmental disorders in utero. Multiple pathways involved in normal brain development are dysfunctional in infected NPCs but how ZIKV centrally reprograms these pathways remains unknown. Here we show that ZIKV infection disrupts subcellular partitioning of host transcripts critical for neurodevelopment in NPCs and functionally link this process to the up-frameshift protein 1 (UPF1). UPF1 is an RNA-binding protein known to regulate decay of cellular and viral RNAs and is less expressed in ZIKV-infected cells. Using infrared crosslinking immunoprecipitation and RNA sequencing (irCLIP-Seq), we show that a subset of mRNAs loses UPF1 binding in ZIKV-infected NPCs, consistent with UPF1’s diminished expression. UPF1 target transcripts, however, are not altered in abundance but in subcellular localization, with mRNAs accumulating in the nucleus of infected or UPF1 knockdown cells. This leads to diminished protein expression of FREM2, a protein required for maintenance of NPC identity. Our results newly link UPF1 to the regulation of mRNA transport in NPCs, a process perturbed during ZIKV infection.
Author summary
The outbreak of Zika Virus (ZIKV) led to an epidemic of microcephaly and other congenital abnormalities. ZIKV is typically spread by mosquitoes, but it can also cross the placenta and infect the fetus of pregnant individuals. During the infection of the fetus, ZIKV targets neural progenitor cells (NPCs), leading to disruptions in brain development. In this study, we infect NPCs with ZIKV to better understand changes in the host cell during infection. In particular, we focus on the protein UPF1, a key player on the nonsense mediated mRNA decay pathway. We found that during ZIKV infection, UPF1 interacts with fewer transcripts, and these transcripts are associated with neurodevelopment. Furthermore, it appears that UPF1 is involved in mRNA transport out of the nucleus. We identify FREM2 as one of the transcripts with the greatest loss of UPF1 interaction and find that perturbation of this gene leads to upregulation of proteins associated with neural progenitor cell differentiation. Our study provides new insights into both the molecular pathogenesis of ZIKV and highlights another role that UPF1 plays in the cell.