Eukaryotic Initiation Factor 4G Suppresses Nonsense-Mediated mRNA Decay by Two Genetically Separable Mechanisms

Nonsense-mediated mRNA decay (NMD), which is best known for degrading mRNAs with premature termination codons (PTCs), is thought to be triggered by aberrant translation termination at stop codons located in an environment of the mRNP that is devoid of signals necessary for proper termination. In mammals, the cytoplasmic poly(A)-binding protein 1 (PABPC1) has been reported to promote correct termination and therewith antagonize NMD by interacting with the eukaryotic release factors 1 (eRF1) and 3 (eRF3). Using tethering assays in which proteins of interest are recruited as MS2 fusions to a NMD reporter transcript, we show that the three N-terminal RNA recognition motifs (RRMs) of PABPC1 are sufficient to antagonize NMD, while the eRF3-interacting C-terminal domain is dispensable. The RRM1-3 portion of PABPC1 interacts with eukaryotic initiation factor 4G (eIF4G) and tethering of eIF4G to the NMD reporter also suppresses NMD. We identified the interactions of the eIF4G N-terminus with PABPC1 and the eIF4G core domain with eIF3 as two genetically separable features that independently enable tethered eIF4G to inhibit NMD. Collectively, our results reveal a function of PABPC1, eIF4G and eIF3 in translation termination and NMD suppression, and they provide additional evidence for a tight coupling between translation termination and initiation.

Search for displaced muonic lepton jets from light Higgs boson decay in proton-proton collisions at sqrts TeV with the ATLAS detector

A search is performed for collimated muon pairs displaced from the primary vertex produced in the decay of long-lived neutral particles in proton-proton collisions at root s = 7 TeV centre-of-mass energy, with the ATLAS detector at the LHC. In a 1.9 fb(-1) event sample collected during 2011, the observed data are consistent with the Standard Model background expectations. Limits on the product of the production cross section and the branching ratio of a Higgs boson decaying to hidden-sector neutral long-lived particles are derived as a function of the particles' mean lifetime.

Search for resonant diboson production in the lvjj decay channels with the ATLAS detector at 7 TeV

A search for resonant diboson production using a data sample corresponding to 4.7 fb(-1) of integrated luminosity collected by the ATLAS experiment at the Large Hadron Collider in pp collisions at root s = 7 TeV is presented. The search for a narrow resonance in the WW or WZ mass distribution is conducted in a final state with an electron or a muon, missing transverse momentum, and at least two jets. No significant excess is observed and limits are set using three benchmark models: WW resonance masses below 940 and 710 GeV are excluded at 95% confidence level for spin-2 Randall-Sundrum and bulk Randall-Sundrum gravitons, respectively; WZ resonance masses below 950 GeV are excluded at 95% confidence level for a spin-1 extended gauge model W' boson.

Search for a light charged Higgs boson in the decay channel H⁺ o c ars in t art events using collisions at sqrts = 7 TeV with the ATLAS detector

A search for a charged Higgs boson (H+) in t (t) over bar decays is presented, where one of the top quarks decays via t -> H(+)b, followed by H+ -> two jets (c (s) over bar). The other top quark decays to Wb, where the W boson then decays into a lepton (e/mu) and a neutrino. The data were recorded in pp collisions at root s = 7 TeV by the ATLAS detector at the LHC in 2011, and correspond to an integrated luminosity of 4.7 fb(-1). With no observation of a signal, 95 % confidence level (CL) upper limits are set on the decay branching ratio of top quarks to charged Higgs bosons varying between 5 % and 1 % for H+ masses between 90 GeV and 150 GeV, assuming B(H+ -> c (s) over bar) = 100 %.

The Host Nonsense-Mediated mRNA Decay Pathway Restricts Mammalian RNA Virus Replication

In addition to classically defined immune mechanisms, cell-intrinsic processes can restrict virus infection and have shaped virus evolution. The details of this virus-host interaction are still emerging. Following a genome-wide siRNA screen for host factors affecting replication of Semliki Forest virus (SFV), a positive-strand RNA (+RNA) virus, we found that depletion of nonsense-mediated mRNA decay (NMD) pathway components Upf1, Smg5, and Smg7 led to increased levels of viral proteins and RNA and higher titers of released virus. The inhibitory effect of NMD was stronger when virus replication efficiency was impaired by mutations or deletions in the replicase proteins. Consequently, depletion of NMD components resulted in a more than 20-fold increase in production of these attenuated viruses. These findings indicate that a cellular mRNA quality control mechanism serves as an intrinsic barrier to the translation of early viral proteins and the amplification of +RNA viruses in animal cells.

Michel decay spectrum for a muon bound to a nucleus

The spectrum of electrons from muons decaying in an atomic bound state is significantly modified by their interaction with the nucleus. Somewhat unexpectedly, its first measurement, at the Canadian laboratory TRIUMF, differed from basic theory. We show, using a combination of techniques developed in atomic, nuclear, and high-energy physics, that radiative corrections eliminate the discrepancy. In addition to solving that outstanding problem, our more precise predictions are potentially useful for interpreting future high-statistics muon experiments that aim to search for exotic interactions at 10−16 sensitivity.

Nonsense-mediated mRNA decay (NMD) restricts replication of mammalian RNA viruses

A genome-wide siRNA screen against host factors that affect the infection of Semliki Forest virus (SFV), a positive-strand (+)RNA virus, revealed that components of the nonsense-mediated mRNA decay (NMD) pathway restrict early, post-entry steps of the infection cycle. In HeLa cells and primary human fibroblasts, knockdown of UPF1, SMG5 and SMG7 leads to increased levels of viral proteins and RNA and to higher titers of released virus. The inhibitory effect of NMD was stronger when the efficiency of virus replication was impaired by mutations or deletions in the replicase proteins. Accordingly, impairing NMD resulted in a more than 20-fold increased production of these attenuated viruses. Our data suggest that intrinsic features of genomic and sub-genomic viral mRNAs, most likely the extended 3'-UTR length, make them susceptible to NMD. The fact that SFV replication is entirely cytoplasmic strongly suggests that degradation of the viral RNA occurs through the exon junction complex (EJC)-independent mode of NMD. Collectively, our findings uncover a new biological function for NMD as an intrinsic barrier to the translation of early viral proteins and the amplification of (+)RNA viruses in animal cells. Thus, in addition to its role in mRNA surveillance and post-transcriptional gene regulation, NMD also contributes to protect cells from RNA viruses.

Investigation of premature termination codon recognition in nonsense-mediated mRNA decay

Nonsense-mediated mRNA decay (NMD) is best known for its role in quality control of mRNAs, where it recognizes premature translation termination codons (PTCs) and rapidly degrades the corresponding mRNA. The basic mechanism of NMD appears to be conserved among eukaryotes: aberrant translation termination triggers NMD. According to the current working model, correct termination requires the interaction of the ribosome with the poly(A)-binding protein (PABPC1) mediated through the eukaryotic release factors 1 (eRF1) and 3 (eRF3). The model predicts that in the absence of this interaction, the NMD core factor UPF1 binds to eRF3 instead and initiates the events ultimately leading to mRNA degradation. However, the exact mechanism of how the decision between proper and aberrant (i.e. NMD-inducing) translation termination occurs is not yet well understood. We address this question using a tethering approach in which proteins of interest are bound to a reporter transcript into the vicinity of a PTC. Subsequently, the ability of the tethered proteins to inhibit NMD and thus stabilize the reporter transcript is assessed. Our results revealed that the C-terminal domain interacting with eRF3 seems not to be necessary for tethered PABPC1 to suppress NMD. In contrast, the N-terminal part of PABPC1, consisting of 4 RNA recognition motifs (RRMs) and interacting with eukaryotic initiation factor 4G (eIF4G), retains the ability to inhibit NMD. We find that eIF4G is able to inhibit NMD in a similar manner as PABPC1 when tethered to the reporter mRNA. This stabilization by eIF4G depends on two key interactions. One of these interactions is to PABPC1, the other is to eukaryotic initiation factor 3 (eIF3). These results confirm the importance of PABPC1 in inhibiting NMD but additionally reveal a role of translation initiation factors in the distinction between bona fide termination codons and PTCs.

Trying to make sense in nonsense-mediated mRNA decay

Despite over 30 years of research, the molecular mechanisms of nonsense-mediated mRNA decay (NMD) are still not well understood. NMD appears to exist in most eukaryotes and is intensively studied in S. cerevisiae, C. elegans, D. melanogaster and in mammalian cells. Current evidence suggests that the core of NMD – involving UPF1, UPF2 and UPF3 – is evolutionarily conserved, but that different species may have evolved slightly different ways to identify target mRNAs for NMD and to degrade them. Our lab has shown that the exon junction complex (EJC) is not absolutely required for NMD in human cells (Bühler et al., NSMB 2006) and that it is neither restricted to CBP80-bound mRNAs as classical models claim (Rufener & Mühlemann, NSMB 2013). Together with the finding that long 3’ UTRs often are an NMD-inducing feature (Eberle et al, PLoS Biol 2008; Yepiskoposyan et al., RNA 2011), our data is consistent with much of the data from other species and hence has led to a “unified” working model for NMD (Stalder & Mühlemann, Trends Cell Biol 2008; Schweingruber et al., Biochim Biophys Acta 2013). Our recent iCLIP experiments with endogenous UPF1 indicate that UPF1 binds mRNAs indiscriminately with respect to being an NMD target or not before they engage with ribosomes (Zünd et al., NSMB 2013). After onset of translation, UPF1 is cleared from the coding region but remains bound to the 3’ UTR of mRNAs. Why this 3’ UTR-associated in some cases induces NMD and in others not is currently being investigated and not yet understood. Following assembly of a phospho-UPF1-containing NMD complex, decay adaptors (SMG5, SMG7, PNRC2) and/or the endonuclease SMG6 are recruited. While the latter cleaves the mRNA in the vicinity of the termination codon, the former proteins induce deadenylation, decapping and exonucleolytic degradation of the mRNA. In my talk, I will give an overview about the latest developments in NMD – with a focus on our own work – and try to integrate the bits and pieces into a somewhat coherent working model.

One-loop SQCD corrections to the decay of top squarks to charm and neutralino in the generic MSSM

In this article we calculate the one-loop supersymmetric QCD (SQCD) corrections to the decay u˜1→cχ˜01 in the minimal supersymmetric standard model with generic flavor structure. This decay mode is phenomenologically important if the mass difference between the lightest squark u˜1 (which is assumed to be mainly stoplike) and the neutralino lightest supersymmetric particle χ˜01 is smaller than the top mass. In such a scenario u˜1→tχ˜01 is kinematically not allowed and searches for u˜1→Wbχ˜01 and u˜1→cχ˜01 are performed. A large decay rate for u˜1→cχ˜01 can weaken the LHC bounds from u˜1→Wbχ01 which are usually obtained under the assumption Br[u˜1→Wbχ01]=100%. We find the SQCD corrections enhance Γ[u˜1→cχ˜01] by approximately 10% if the flavor violation originates from bilinear terms. If flavor violation originates from trilinear terms, the effect can be ±50% or more, depending on the sign of At. We note that connecting a theory of supersymmetry breaking to LHC observables, the shift from the DR¯¯¯¯¯ to the on-shell mass is numerically very important for light stop decays.

Search for pair and single production of new heavy quarks that decay to a ℤ boson and a third-generation quark in pp collisions at √ s=8 TeV with the ATLAS detector

A search is presented for the production of new heavy quarks that decay to a Z boson and a third-generation Standard Model quark. In the case of a new charge +2/3 quark (T), the decay targeted is T → Zt, while the decay targeted for a new charge −1/3 quark (B) is B → Zb. The search is performed with a dataset corresponding to 20.3 fb−1 of pp collisions at √ s = 8TeV recorded in 2012 with the ATLAS detector at the CERN Large Hadron Collider. Selected events contain a high transverse momentum Z boson candidate reconstructed from a pair of oppositely charged same-flavor leptons (electrons or muons), and are analyzed in two channels defined by the absence or presence of a third lepton. Hadronic jets, in particular those with properties consistent with the decay of a b-hadron, are also required to be present in selected events. Different requirements are made on the jet activity in the event in order to enhance the sensitivity to either heavy quark pair production mediated by the strong interaction, or single production mediated by the electroweak interaction. No significant excess of events above the Standard Model expectation is observed, and lower limits are derived on the mass of vector-like T and B quarks under various branching ratio hypotheses, as well as upper limits on the agnitude of electroweak coupling parameters.

Measurement of Higgs boson production in the diphoton decay channel in pp collisions at center-of-mass energies of 7 and 8 TeV with the ATLAS detector

A measurement of the production processes of the recently discovered Higgs boson is performed in the two-photon final state using 4.5  fb −1 of proton-proton collisions data at s √ =7  TeV and 20.3  fb −1 at s √ =8  TeV collected by the ATLAS detector at the Large Hadron Collider. The number of observed Higgs boson decays to diphotons divided by the corresponding Standard Model prediction, called the signal strength, is found to be μ=1.17±0.27 at the value of the Higgs boson mass measured by ATLAS, m H =125.4  GeV . The analysis is optimized to measure the signal strengths for individual Higgs boson production processes at this value of m H . They are found to be μ ggF =1.32±0.38 , μ VBF =0.8±0.7 , μ WH =1.0±1.6 , μ ZH =0.1 +3.7 −0.1 , and μ tt ¯ H =1.6 +2.7 −1.8 , for Higgs boson production through gluon fusion, vector-boson fusion, and in association with a W or Z boson or a top-quark pair, respectively. Compared with the previously published ATLAS analysis, the results reported here also benefit from a new energy calibration procedure for photons and the subsequent reduction of the systematic uncertainty on the diphoton mass resolution. No significant deviations from the predictions of the Standard Model are found.

Search for the lepton flavor violating decay Z→eμ in pp collisions at √s =8 TeV with the ATLAS detector

The ATLAS detector at the Large Hadron Collider is used to search for the lepton flavor violating process Z→eμ in pp collisions using 20.3  fb −1 of data collected at s √ =8  TeV . An enhancement in the eμ invariant mass spectrum is searched for at the Z -boson mass. The number of Z bosons produced in the data sample is estimated using events of similar topology, Z→ee and μμ , significantly reducing the systematic uncertainty in the measurement. There is no evidence of an enhancement at the Z -boson mass, resulting in an upper limit on the branching fraction, B(Z→eμ)<7.5×10 −7 at the 95% confidence level.