Determining the role of alternative mRNA polyadenylation in SARS-Cov-2 replication and the host
innate immune response
SARS-CoV-2 infection has caused the COVID-19 pandemic, and understanding the molecular
mechanisms leading to its pathophysiology is a top biomedical priority. In spite of intense research over the
last year, we still have much to learn about host factors that promote or restrict SARS-CoV-2 infection and
how manipulating them might enable new antiviral treatments. Changes within the infected cell are often
mediated by changes in mRNA synthesis that affect not only transcription but also mRNA processing.
mRNA precursor is cleaved at its 3’ end and a poly(A) tail added in a process called cleavage and
polyadenylation (C/P). If C/P is blocked, mRNA is degraded, poorly exported from the nucleus, and poorly
translated. Changing the poly(A) site position, or alternative polyadenylation (APA), affects the type and
amount of protein produced from an mRNA. Many viruses have found ways to manipulate C/P and APA to
promote viral replication, to interfere with the host antiviral response, or to hijack C/P proteins to augment
viral activities. Several screens have demonstrated interaction of C/P proteins with SARS-Cov2 proteins
and RNA and identified some C/P proteins as antiviral factors. However, it remains unknown whether
SARS-CoV-2 causes changes in poly(A) site usage that support its replication and/or lead to the
dysregulation of innate immunity that might contribute to the pathogenic inflammatory response seen in
severe COVID-19 cases.
By analyzing global pA site usage in cells infected with SARS-CoV-2 using published mRNA-seq data, we
found that SARS-CoV-2 infection changes APA of genes involved in immunity, apoptosis, vesicle transport,
metabolism, and cell cycle. Based on this preliminary observation, we hypothesize that alterations in
C/P caused by SARS-CoV-2 infection influence viral replication and the host antiviral response. To
investigate how SARS-CoV-2 affects C/P in host cells and whether targeting the C/P proteins might alter
the progression of viral infection, we will 1) determine if C/P is inhibited across the genome during SARS-
CoV-2 infection, 2) determine the effects of overexpressing or depleting C/P proteins that regulate APA,
and 3) determine if specific viral proteins known to interact with C/P proteins affect 3' end processing.
Successful completion of this study will determine if manipulation of C/P has potential as a novel
therapeutic target for COVID-19.