The influenza A virus endoribonuclease PA-X usurps host mRNA processing machinery to limit host gene expression

Lea Gaucherand; Brittany K. Porter; Summer K. Schmaling; Christopher Harley Rycroft; Yuzo Kevorkian; Craig McCormick; Denys A. Khaperskyy; Marta Maria Gaglia

Clustering was carried out based on the relative RNA levels in PA-X-overexpressing vs. control 165 cells or IAV-infected vs. mock-infected cells in the eight datasets we collected ( Figures 1C, S1B , 166 2A). Two sets of RNAs, comprising 55% of the RNAs that were detected in all conditions, were 167 identified as true PA-X targets ( Figure 3A ). They were down-regulated in a PA-X-dependent 168 manner both during infection and by PA-X ectopic expression. The first group was completely 169 PA-X-specific, because their levels were largely unchanged in IAV PA(ΔX) infected cells 170 ( Figure 3A , left panel). The RNAs in the second group were PA-X-sensitive, but were partially 171 down-regulated by other mechanisms during IAV PA(ΔX) infection ( Figure 3A , right panel). By 172 contrast, 28% of the RNAs were host shutoff resistant and were not down-regulated by infection 173 or PA-X expression ( Figure 3B ). In addition, the k-means algorithm identified a group of RNAs 174 that were down-regulated during infection by a PA-X-independent mechanism, and yet were PA-175 X-sensitive in PA-X-expressing cells ( Figure 3C ). The levels of these transcripts may be 176 All rights reserved. No reuse allowed without permission.