ARS2 instructs early transcription termination-coupled RNA decay by recruiting ZC3H4 to nascent transcripts.

The RNA-binding ARS2 protein is centrally involved in both early RNA polymerase II (RNAPII) transcription termination and transcript decay. Despite its essential nature, the mechanisms by which ARS2 enacts these functions have remained unclear. Here, we show that a conserved basic domain of ARS2 binds a corresponding acidic-rich, short linear motif (SLiM) in the transcription restriction factor ZC3H4. This interaction recruits ZC3H4 to chromatin to elicit RNAPII termination, independent of other early termination pathways defined by the cleavage and polyadenylation (CPA) and Integrator (INT) complexes. We find that ZC3H4, in turn, forms a direct connection to the nuclear exosome targeting (NEXT) complex, hereby facilitating rapid degradation of the nascent RNA. Hence, ARS2 instructs the coupled transcription termination and degradation of the transcript onto which it is bound. This contrasts with ARS2 function at CPA-instructed termination sites where the protein exclusively partakes in RNA suppression via post-transcriptional decay.

Integrator is a genome-wide attenuator of non-productive transcription.

Termination of RNA polymerase II (RNAPII) transcription in metazoans relies largely on the cleavage and polyadenylation (CPA) and integrator (INT) complexes originally found to act at the ends of protein-coding and small nuclear RNA (snRNA) genes, respectively. Here, we monitor CPA- and INT-dependent termination activities genome-wide, including at thousands of previously unannotated transcription units (TUs), producing unstable RNA. We verify the global activity of CPA occurring at pA sites indiscriminately of their positioning relative to the TU promoter. We also identify a global activity of INT, which is largely sequence-independent and restricted to a ~3-kb promoter-proximal region. Our analyses suggest two functions of genome-wide INT activity: it dampens transcriptional output from weak promoters, and it provides quality control of RNAPII complexes that are unfavorably configured for transcriptional elongation. We suggest that the function of INT in stable snRNA production is an exception from its general cellular role, the attenuation of non-productive transcription.

Nonsense-mediated mRNA decay: an intricate machinery that shapes transcriptomes.

Nonsense-mediated mRNA decay (NMD) is probably the best characterized eukaryotic RNA degradation pathway. Through intricate steps, a set of NMD factors recognize and degrade mRNAs with translation termination codons that are positioned in abnormal contexts. However, NMD is not only part of a general cellular quality control system that prevents the production of aberrant proteins. Mammalian cells also depend on NMD to dynamically adjust their transcriptomes and their proteomes to varying physiological conditions. In this Review, we discuss how NMD targets mRNAs, the types of mRNAs that are targeted, and the roles of NMD in cellular stress, differentiation and maturation processes.

The time course of feature-selective attention inside and outside the focus of spatial attention.

Research on attentional selection of stimulus features has yielded seemingly contradictory results. On the one hand, many experiments in humans and animals have observed a "global" facilitation of attended features across the entire visual field, even when spatial attention is focused on a single location. On the other hand, several event-related potential studies in humans reported that attended features are enhanced at the attended location only. The present experiment demonstrates that these conflicting results can be explained by differences in the timing of attentional allocation inside and outside the spatial focus of attention. Participants attended to fields of either red or blue randomly moving dots on either the left or right side of fixation with the task of detecting brief coherent motion targets. Recordings of steady-state visual evoked potentials elicited by the flickering stimuli allowed concurrent measurement of the time course of feature-selective attention in visual cortex on both the attended and the unattended sides. The onset of feature-selective attentional modulation on the attended side occurred around 150 ms earlier than on the unattended side. This finding that feature-selective attention is not spatially global from the outset but extends to unattended locations after a temporal delay resolves previous contradictions between studies finding global versus hierarchical selection of features and provides insight into the fundamental relationship between feature-based and location-based (spatial) attention mechanisms.

Box C/D snoRNP Autoregulation by a cis-Acting snoRNA in the NOP56 Pre-mRNA.

Box C/D snoRNAs constitute a class of abundant noncoding RNAs that associate with common core proteins to form catalytic snoRNPs. Most of these operate in trans to assist the maturation of rRNAs by guiding and catalyzing the 2'-O-methylation of specific nucleotides. Here, we report that the human intron-hosted box C/D snoRNA snoRD86 acts in cis as a sensor and master switch controlling levels of the limiting snoRNP core protein NOP56, which is important for proper ribosome biogenesis. Our results support a model in which snoRD86 adopts different RNP conformations that dictate the usage of nearby alternative splice donors in the NOP56 pre-mRNA. Excess snoRNP core proteins prevent further production of NOP56 and instead trigger the generation of a cytoplasmic snoRD86-containing NOP56-derived lncRNA via the nonsense-mediated decay pathway. Our findings reveal a feedback mechanism based on RNA structure that controls the precise coordination between box C/D snoRNP core proteins and global snoRNA levels.

Division and spreading of attention across color.

Biological systems must allocate limited perceptual resources to relevant elements in their environment. This often requires simultaneous selection of multiple elements from the same feature dimension (e.g. color). To establish the determinants of divided attentional selection of color, we conducted an experiment that used multicolored displays with four overlapping random dot kinematograms that differed only in hue. We manipulated (i) requirement to focus attention to a single color or divide it between two colors; (ii) distances of distractor hues from target hues in a perceptual color space. We conducted a behavioral and an electroencephalographic experiment, in which each color was tagged by a specific flicker frequency and driving its own steady-state visual evoked potential. Behavioral and neural indices of attention showed several major consistencies. Concurrent selection halved the neural signature of target enhancement observed for single targets, consistent with an approximately equal division of limited resources between two hue-selective foci. Distractors interfered with behavioral performance in a context-dependent fashion but their effects were asymmetric, indicating that perceptual distance did not adequately capture attentional distance. These asymmetries point towards an important role of higher-level mechanisms such as categorization and grouping-by-color in determining the efficiency of attentional allocation in complex, multicolored scenes.

Attentional Modulation in Early Visual Cortex: A Focused Reanalysis of Steady-state Visual Evoked Potential Studies.

Steady-state visual evoked potentials (SSVEPs) are a powerful tool for investigating selective attention. Here, we conducted a combined reanalysis of multiple studies employing this technique in a variety of attentional experiments to, first, establish benchmark effect sizes of attention on amplitude and phase of SSVEPs and, second, harness the power of a large data set to test more specific hypotheses. Data of eight published SSVEP studies were combined, in which human participants (n = 135 in total) attended to flickering random dot stimuli based on their defining features (e.g., location, color, luminance, or orientation) or feature conjunctions. The reanalysis established that, in all the studies, attention reliably enhanced amplitudes, with color-based attention providing the strongest effect. In addition, the latency of SSVEPs elicited by attended stimuli was reduced by ∼4 msec. Next, we investigated the modulation of SSVEP amplitudes in a subset of studies where two different features were attended concurrently. Although most models assume that attentional effects of multiple features are combined additively, our results suggest that neuronal enhancement provided by concurrent attention is better described by multiplicative integration. Finally, we used the combined data set to demonstrate that the increase in trial-averaged SSVEP amplitudes with attention cannot be explained by increased synchronization of single-trial phases. Contrary to the prediction of the phase-locking account, the variance across trials of complex Fourier coefficients increases with attention, which is more consistent with boosting of a largely phase-locked signal embedded in non-phase-locked noise.

Familywise error for multiple time-to-event endpoints in a group sequential design.

We investigate the familywise error rate (FWER) for time-to-event endpoints evaluated using a group sequential design with a hierarchical testing procedure for secondary endpoints. We show that, in this setup, the correlation between the log-rank test statistics at interim and at end of study is not congruent with the canonical correlation derived for normal-distributed endpoints. We show, both theoretically and by simulation, that the correlation also depends on the level of censoring, the hazard rates of the endpoints, and the hazard ratio. To optimize operating characteristics in this complex scenario, we propose a simulation-based method to assess the FWER which, better than the alpha-spending approach, can inform the choice of critical values for testing secondary endpoints.

Identification of a Nuclear Exosome Decay Pathway for Processed Transcripts.

The RNA exosome is fundamental for the degradation of RNA in eukaryotic nuclei. Substrate targeting is facilitated by its co-factor Mtr4p/hMTR4, which links to RNA-binding protein adaptors. One example is the trimeric human nuclear exosome targeting (NEXT) complex, which is composed of hMTR4, the Zn-finger protein ZCCHC8, and the RNA-binding factor RBM7. NEXT primarily targets early and unprocessed transcripts, which demands a rationale for how the nuclear exosome recognizes processed RNAs. Here, we describe the poly(A) tail exosome targeting (PAXT) connection, which comprises the ZFC3H1 Zn-knuckle protein as a central link between hMTR4 and the nuclear poly(A)-binding protein PABPN1. Individual depletion of ZFC3H1 and PABPN1 results in the accumulation of common transcripts that are generally both longer and more extensively polyadenylated than NEXT substrates. Importantly, ZFC3H1/PABPN1 and ZCCHC8/RBM7 contact hMTR4 in a mutually exclusive manner, revealing that the exosome targets nuclear transcripts of different maturation status by substituting its hMTR4-associating adaptors.

Attentional Enhancement of Tracked Stimuli in Early Visual Cortex Has Limited Capacity.

Keeping track of the location of multiple moving objects is one of the well documented functions of visual attention. However, the mechanism of attentional selection that supports such continuous tracking is unclear. In particular, it has been proposed that target selection in early visual cortex occurs in parallel, with tracking errors arising because of attentional limitations at later processing stages. Here, we examine whether, instead, total attentional capacity for enhancement of early visual processing of tracked targets is shared between all attended stimuli. If the magnitude of attentional facilitation of multiple tracked targets was a key limiting factor of tracking ability, then one should expect it to drop systematically with increasing set-size of tracked targets. Human observers (male and female) were instructed to track two, four, or six moving objects among a pool of identical distractors. Steady-state visual evoked potentials (SSVEPs) recorded during the tracking period revealed that the processing of tracked targets was consistently amplified compared with the processing of the distractors. The magnitude of this amplification decreased with increasing set size, and at lateral occipital electrodes it closely followed inverse proportionality to the number of tracked items, suggesting that limited attentional resources must be shared among the tracked stimuli. Accordingly, the magnitude of attentional facilitation predicted the behavioral outcome at the end of the trial. Together, these findings demonstrate that the limitations of multiple object tracking (MOT) across set-sizes stem from the limitations of top-down selective attention already at the early stages of visual processing.SIGNIFICANCE STATEMENT The ability to selectively attend to relevant features or objects is the key to flexibility of perception and action in the continuously changing environment. This ability is demonstrated in the multiple object tracking (MOT) task where observers monitor multiple independently moving objects at different locations in the visual field. The role of early attentional enhancement in tracking was previously acknowledged in the literature, however, the limitations on tracking were thought to arise during later stages of processing. Here, we demonstrate that the strength of attentional facilitation depends on the number of tracked objects and predicts successful tracking performance. Thus, it is the limitations of attentional enhancement at the early stages of visual processing that determine behavioral performance limits.

Attentional modulation as a mechanism for enhanced facial emotion discrimination: The case of action video game players.

Action video game players (AVGPs) outperform nonvideo game players (NVGPs) on a wide variety of attentional tasks, mediating benefits to perceptual and cognitive decision processes. A key issue in the literature is the extent to which such benefits transfer beyond cognition. Using steady-state visual evoked potentials (SSVEP) as a neural measure of attentional resource allocation, we investigated whether the attentional benefit of AVGPs generalizes to the processing of rapidly presented facial emotions. AVGPs (n = 36) and NVGPs (n = 32) performed a novel, attention-demanding emotion discrimination task, requiring the identification of a target emotion in one of two laterally presented streams of emotional faces. The emotional faces flickered at either 2.0 Hz or 2.5 Hz. AVGPs outperformed NVGPs at detecting the target emotions regardless of the type of emotion. Correspondingly, attentional modulation of the SSVEP at parieto-occipital recording sites was larger in AVGPs compared with NVGPs. This difference appeared to be driven by a larger response to attended information, as opposed to a reduced response to irrelevant distractor information. Exploratory analyses confirmed that this novel paradigm elicited the expected pattern of event-related potentials associated with target detection and error processing. These components did not, however, differ between groups. Overall, the results indicate enhanced discrimination of facial emotions in AVGPs arising from enhanced attentional processing of emotional information. This presents evidence for the attentional advantage of AVGPs to extend beyond perceptual and cognitive processes.

Control of non-productive RNA polymerase II transcription via its early termination in metazoans.

Transcription establishes the universal first step of gene expression where RNA is produced by a DNA-dependent RNA polymerase. The most versatile of eukaryotic RNA polymerases, RNA polymerase II (Pol II), transcribes a broad range of DNA including protein-coding and a variety of non-coding transcription units. Although Pol II can be configured as a durable enzyme capable of transcribing hundreds of kilobases, there is reliable evidence of widespread abortive Pol II transcription termination shortly after initiation, which is often followed by rapid degradation of the associated RNA. The molecular details underlying this phenomenon are still vague but likely reflect the action of quality control mechanisms on the early Pol II complex. Here, we summarize current knowledge of how and when such promoter-proximal quality control is asserted on metazoan Pol II.

Changes in perceived social support and PTSD symptomatology among Danish army military personnel.

PURPOSE: Previous research has identified social support to be associated with risk of posttraumatic stress disorder (PTSD) symptoms among military personnel. While the lack of social support influences PTSD symptomatology, it is unknown how changes in perceived social support affect the PTSD symptom level in the aftermath of deployment. Furthermore, the influence of specific sources of social support from pre- to post-deployment on level of PTSD symptoms is unknown. We aim to examine how changes in perceived social support (overall and from specific sources) from pre- to 2.5 year post-deployment are associated with the level of post-deployment PTSD symptoms. METHODS: Danish army military personnel deployed to Afghanistan in 2009 and 2013 completed questionnaires at pre-deployment and at 2.5 year post-deployment measuring perceived social support and PTSD symptomatology and sample characteristics of the two cohorts. Data were analyzed using univariate and multivariate nominal logistic regression. RESULTS: Negative changes in perceived social support from pre- to post-deployment were associated with both moderate (OR 1.99, CI 1.51-2.57) and high levels (OR 2.71, CI 1.94-3.78) of PTSD symptoms 2.5 year post-deployment (adjusted analysis). Broadly, the same direction was found for specific sources of social support and level of PTSD symptoms. In the adjusted analyses, pre-deployment perceived social support and military rank moderated the associations. CONCLUSIONS: Deterioration in perceived social support (overall and specific sources) from pre- to 2.5 year post-deployment increases the risk of an elevated level of PTSD symptoms 2.5 year post-deployment.

Human nonsense-mediated RNA decay initiates widely by endonucleolysis and targets snoRNA host genes.

Eukaryotic RNAs with premature termination codons (PTCs) are eliminated by nonsense-mediated decay (NMD). While human nonsense RNA degradation can be initiated either by an endonucleolytic cleavage event near the PTC or through decapping, the individual contribution of these activities on endogenous substrates has remained unresolved. Here we used concurrent transcriptome-wide identification of NMD substrates and their 5'-3' decay intermediates to establish that SMG6-catalyzed endonucleolysis widely initiates the degradation of human nonsense RNAs, whereas decapping is used to a lesser extent. We also show that a large proportion of genes hosting snoRNAs in their introns produce considerable amounts of NMD-sensitive splice variants, indicating that these RNAs are merely by-products of a primary snoRNA production process. Additionally, transcripts from genes encoding multiple snoRNAs often yield alternative transcript isoforms that allow for differential expression of individual coencoded snoRNAs. Based on our findings, we hypothesize that snoRNA host genes need to be highly transcribed to accommodate high levels of snoRNA production and that the expression of individual snoRNAs and their cognate spliced RNA can be uncoupled via alternative splicing and NMD.

Dynamic Interplay between Reward and Voluntary Attention Determines Stimulus Processing in Visual Cortex.

Reward enhances stimulus processing in the visual cortex, but the mechanisms through which this effect occurs remain unclear. Reward prospect can both increase the deployment of voluntary attention and increase the salience of previously neutral stimuli. In this study, we orthogonally manipulated reward and voluntary attention while human participants performed a global motion detection task. We recorded steady-state visual evoked potentials to simultaneously measure the processing of attended and unattended stimuli linked to different reward probabilities, as they compete for attentional resources. The processing of the high rewarded feature was enhanced independently of voluntary attention, but this gain diminished once rewards were no longer available. Neither the voluntary attention nor the salience account alone can fully explain these results. Instead, we propose how these two accounts can be integrated to allow for the flexible balance between reward-driven increase in salience and voluntary attention.

ARS2/SRRT: at the nexus of RNA polymerase II transcription, transcript maturation and quality control.

ARS2/SRRT is an essential eukaryotic protein that has emerged as a critical factor in the sorting of functional from non-functional RNA polymerase II (Pol II) transcripts. Through its interaction with the Cap Binding Complex (CBC), it associates with the cap of newly made RNAs and acts as a hub for competitive exchanges of protein factors that ultimately determine the fate of the associated RNA. The central position of the protein within the nuclear gene expression machinery likely explains why its depletion causes a broad range of phenotypes, yet an exact function of the protein remains elusive. Here, we consider the literature on ARS2/SRRT with the attempt to garner the threads into a unifying working model for ARS2/SRRT function at the nexus of Pol II transcription, transcript maturation and quality control.

Conscious awareness modulates processing speed in the redundant signal effect.

Evidence for the influence of unaware signals on behaviour has been reported in both patient groups and healthy observers using the Redundant Signal Effect (RSE). The RSE refers to faster manual reaction times to the onset of multiple simultaneously presented target than those to a single stimulus. These findings are robust and apply to unimodal and multi-modal sensory inputs. A number of studies on neurologically impaired cases have demonstrated that RSE can be found even in the absence of conscious experience of the redundant signals. Here, we investigated behavioural changes associated with awareness in healthy observers by using Continuous Flash Suppression to render observers unaware of redundant targets. Across three experiments, we found an association between reaction times to the onset of a consciously perceived target and the reported level of visual awareness of the redundant target, with higher awareness being associated with faster reaction times. However, in the absence of any awareness of the redundant target, we found no evidence for speeded reaction times and even weak evidence for an inhibitory effect (slowing down of reaction times) on response to the seen target. These findings reveal marked differences between healthy observers and blindsight patients in how aware and unaware information from different locations is integrated in the RSE.

Too little, too late, and in the wrong place: Alpha band activity does not reflect an active mechanism of selective attention.

Selective attention focuses visual processing on relevant stimuli in order to allow for adaptive behaviour despite an abundance of distracting information. It has been proposed that increases in alpha band (8-12 â€‹Hz) amplitude reflect an active mechanism for distractor suppression. If this were the case, increases in alpha band amplitude should be succeeded by a decrease in distractor processing. Surprisingly, this connection has not been tested directly; specifically, studies that have investigated changes in alpha band after attention-directing cues have not directly assessed the neuronal processing of distractors. We concurrently recorded alpha activity and steady-state visual evoked potentials (SSVEPs) to assess the processing of target and distractor stimuli. In two experiments, participants covertly shifted attention to one of two letter streams (left or right) to detect infrequent target letters 'X' while ignoring the other stream. In line with previous findings, alpha band amplitudes contralateral to the unattended location increased compared to a pre-cue baseline. However, there was no suppression of SSVEP amplitudes elicited by unattended stimuli, while there was a pronounced enhancement of SSVEPs elicited by attended stimuli. Furthermore, and crucially, changes in alpha band amplitude during attention shifts did not precede those in SSVEPs and hit rates in both experiments, indicating that changes in alpha band amplitudes are likely to be a consequence of attention shifts rather than the other way around. We conclude that these findings contradict the notion that alpha band activity reflects mechanisms that have a causal role in the allocation of selective attention.

Retraction: Andersen S. S. L. Real time large scale in vivo observations reveal intrinsic synchrony, plasticity and growth cone dynamics of midline crossing axons at the ventral floor plate of the zebrafish spinal cord. J. Integr. Neurosci. 18(4), 351-368.

The above-mentioned article (Andersen,2019), published online on December 30, 2019 has been withdrawn by Dr. Andersen. The retraction has been issued following additional information received by IMR Press and reviewed by the Chief Editor.

Promoter-proximal polyadenylation sites reduce transcription activity.

Gene expression relies on the functional communication between mRNA processing and transcription. We previously described the negative impact of a point-mutated splice donor (SD) site on transcription. Here we demonstrate that this mutation activates an upstream cryptic polyadenylation (CpA) site, which in turn causes reduced transcription. Functional depletion of U1 snRNP in the context of the wild-type SD triggers the same CpA event accompanied by decreased RNA levels. Thus, in accordance with recent findings, U1 snRNP can shield premature pA sites. The negative impact of unshielded pA sites on transcription requires promoter proximity, as demonstrated using artificial constructs and supported by a genome-wide data set. Importantly, transcription down-regulation can be recapitulated in a gene context devoid of splice sites by placing a functional bona fide pA site/transcription terminator within ~500 base pairs of the promoter. In contrast, promoter-proximal positioning of a pA site-independent histone gene terminator supports high transcription levels. We propose that optimal communication between a pA site-dependent gene terminator and its promoter critically depends on gene length and that short RNA polymerase II-transcribed genes use specialized termination mechanisms to maintain high transcription levels.