Posttranscriptional Gene Regulation by Spatial Rearrangement of the 3′ Untranslated Region

Translation termination at premature termination codons (PTCs) triggers degradation of the aberrant mRNA, but the mechanism by which a termination event is defined as premature is still unclear. Here we show that the physical distance between the termination codon and the poly(A)-binding protein PABPC1 is a crucial determinant for PTC recognition in human cells. “Normal” termination codons can trigger nonsense-mediated mRNA decay (NMD) when this distance is extended; and vice versa, NMD can be suppressed by folding the poly(A) tail into proximity of a PTC or by tethering of PABPC1 nearby a PTC, indicating an evolutionarily conserved function of PABPC1 in promoting correct translation termination and antagonizing activation of NMD. Most importantly, our results demonstrate that spatial rearrangements of the 3′ untranslated region can modulate the NMD pathway and thereby provide a novel mechanism for posttranscriptional gene regulation

Journal- or article-based citation measure? A study of academic promotion at a Swiss university [version 1].

In academia, decisions on promotions are influenced by the citation impact of the works published by the candidates. The Medical Faculty of the University of Bern used a measure based on the journal impact factor (JIF) for this purpose: the JIF of the papers submitted for promotion should rank in the upper third of journals in the relevant discipline (JIF rank >0.66). The San Francisco Declaration on Research Assessment (DORA) aims to eliminate the use of journal-based metrics in academic promotion. We examined whether the JIF rank could be replaced with the relative citation ratio (RCR), an article-level measure of citation impact developed by the National Institutes of Health (NIH). An RCR percentile >0.66 corresponds to the upper third of citation impact of articles from NIH-sponsored research. We examined 1525 publications submitted by 64 candidates for academic promotion at University of Bern. There was only a moderate correlation between the JIF rank and RCR percentile (Pearson correlation coefficient 0.34, 95% CI 0.29-0.38). Among the 1,199 articles (78.6%) published in journals ranking >0.66 for the JIF, less than half (509, 42.5%) were in the upper third of the RCR percentile. Conversely, among the 326 articles published in journals ranking <0.66 regarding the JIF, 72 (22.1%) ranked in the upper third of the RCR percentile. Our study demonstrates that the rank of the JIF is a bad proxy measure for the actual citation impact of individual articles. The Medical Faculty of University of Bern has signed DORA and replaced the JIF rank with the RCR percentile to assess the citation impact of papers submitted for academic promotion

Processing bodies are not required for mammalian nonsense-mediated mRNA decay

Nonsense-mediated mRNA decay (NMD) is a eukaryotic quality-control mechanism that recognizes and degrades mRNAs with premature termination codons (PTCs). In yeast, PTC-containing mRNAs are targeted to processing bodies (P-bodies), and yeast strains expressing an ATPase defective Upf1p mutant accumulate P-bodies. Here we show that in human cells, an ATPase-deficient UPF1 mutant and a fraction of UPF2 and UPF3b accumulate in cytoplasmic foci that co-localize with P-bodies. Depletion of the P-body component Ge-1, which prevents formation of microscopically detectable P-bodies, also impairs the localization of mutant UPF1, UPF2, and UPF3b in cytoplasmic foci. However, the accumulation of the ATPase-deficient UPF1 mutant in P-bodies is independent of UPF2, UPF3b, or SMG1, and the ATPase-deficient UPF1 mutant can localize into the P-bodies independent of its phosphorylation status. Most importantly, disruption of P-bodies by depletion of Ge-1 affects neither the mRNA levels of PTC-containing reporter genes nor endogenous NMD substrates. Consistent with the recently reported decapping-independent SMG6-mediated endonucleolytic decay of human nonsense mRNAs, our results imply that microscopically detectable P-bodies are not required for mammalian NMD

Transcriptional silencing of nonsense codon-containing immunoglobulin micro genes requires translation of its mRNA

Eukaryotes have evolved quality control mechanisms that prevent the expression of genes in which the protein coding potential is crippled by the presence of a premature translation-termination codon (PTC). In addition to nonsense-mediated mRNA decay (NMD), a well documented posttranscriptional consequence of the presence of a PTC in an mRNA, we recently reported the transcriptional silencing of PTC-containing immunoglobulin (Ig) mu and gamma minigenes when they are stably integrated into the genome of HeLa cells. Here we demonstrate that this transcriptional silencing of PTC-containing Ig-mu constructs requires active translation of the cognate mRNA, as it is not observed under conditions where translation of the PTC-containing mRNA is inhibited through an iron-responsive element in the 5'-untranslated region. Furthermore, RNA interference-mediated depletion of the essential NMD factor Upf1 not only abolishes NMD but also reduces the extent of nonsense-mediated transcriptional gene silencing (NMTGS). Collectively, our data indicate that NMTGS and NMD are linked, relying on the same mechanism for PTC recognition, and that the NMTGS pathway branches from the NMD pathway at a step after Upf1 function