GSE132725
Transcriptome and ribosome profiling of XRN1-null HEK293T human cell line generated by CRISPR/Cas9 gene editing
XRN1 is the major cytoplasmic exoribonuclease in eukaryotes, which degrades deadenylated and decapped mRNAs in the last step of the 5'–3' mRNA decay pathway. Metazoan XRN1 interacts with decapping factors coupling the final stages of decay. Ribosome profiling revealed that XRN1 loss impacts not only on mRNA levels but also on the translational efficiency of many cellular transcripts likely as a consequence of incomplete decay. We compared differentially expressed genes derived from the analysis of the transcriptome and the translatome of HEK293T wild-type (WT) and XRN1-null cells by RNA-Seq and Ribo-Seq, respectively. Two biological replicates of each cell line were analyzed. The RNA-Seq analysis indicated that a substantial fraction of the total 10,105 genes showed significant differences between the two cell lines. 2,906 genes were significantly upregulated whilst 2,900 genes were downregulated using a fold change >0 on log2 scale with an FDR<0.005 to determine abundance. Significantly fewer genes showed differences between the WT and the XRN1-null cells at the level of translation with 433 genes showing an increase in abundance of ribosomal footprints whilst 560 genes were decreased as indicated by the Ribo-Seq analysis. Comparative analysis of translational efficiency (TE) in WT and XRN1-null cells on a genome-wide scale as a ratio of ribosomal occupancy to mRNA abundance identified an increase in TE for 102 genes but a decrease for 598 genes with most of the genes showing no evidence of change in the TE. Overall design: Two cell types with two biological replicates analysed using two methods.