Ogran, A. | Search bioRxiv

bioRxiv2022

Polysome-CAGE of TCL1-driven chronic lymphocytic leukemia revealed multiple N-terminally altered epigenetic regulators and a translation stress signature

The transformation of normal to malignant cells is accompanied by substantial changes in gene expression programs through diverse mechanisms. Here we examined the changes in the landscape of transcription start sites (TSSs) and alternative promoter (AP) usage and their impact on the translatome in TCL1-driven chronic lymphocytic leukemia (CLL). Our findings revealed a marked elevation of APs in CLL cells from E{micro}-Tcl1 transgenic mice, which are particularly enriched with intragenic promoters that generate N-terminally truncated or modified proteins. Intragenic promoter activation is mediated by (i) loss of function of closed chromatin epigenetic regulators due to the generation of inactive N-terminally modified isoforms or reduced expression; (ii) upregulation of transcription factors, including c-Myc, targeting the intragenic promoters and associated enhancers. Exogenous expression of Tcl1 in MEFs is sufficient to induce intragenic promoters of epigenetic regulators and promote c- Myc expression. We further found a dramatic translation downregulation of transcripts bearing CNY cap-proximal tri-nucleotides, reminiscent of cells undergoing metabolic stress. These findings uncovered the role of Tcl1 oncogenic function in altering promoter usage and mRNA translation in leukemogenesis.

molecular biology↗

bioRxiv2021

Cap-independent translation and a precisely localized RNA sequence enable SARS-CoV-2 to control host translation and escape anti-viral response

Translation of SARS-CoV-2-encoded mRNAs by the host ribosomes is essential for its propagation. Following infection, the early expressed viral protein NSP1 binds the ribosome, represseses translation and induces mRNA degradation, while the host elicits anti-viral response. The mechanisms enabling viral mRNAs to escape this multifaceted repression remain obscure. Here we show that expression of NSP1 leads to destabilization of multi-exon cellular mRNAs, while intron-less transcripts, such as viral mRNAs and anti-viral interferon genes, remain relatively stable. We identified a conserved and precisely located cap-proximal RNA element devoid of guanosines that confers resistance to NSP1-meidated translation inhibition. Importantly, the primary sequence rather than the secondary structure is critical for protection. We further show that the genomic 5UTR of SARS-CoV-2 exhibits an IRES-like activity and promotes expression of NSP1 in an eIF4E-independent and Torin-1 resistant manner. Upon expression, NSP1 enhances cap-independent translation. However, the sub-genomic 5UTRs are highly sensitive to eIF4E availability, rendering viral propagation partially sensitive to Torin-1. The combined NSP1-mediated degradation of spliced mRNAs and translation inhibition of single-exon genes, along with the unique features present in the viral 5UTRs, ensure robust expression of viral mRNAs. These features can be exploited as potential therapeutic targets.

molecular biology↗