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Signaling pathways drive cell fate transitions largely by changing gene expression. However, the mechanisms for rapid and selective transcriptome rewiring in response to signaling cues remain elusive. Here we use deep learning to deconvolve both the sequence determinants and the trans-acting regulators that trigger extracellular signal-regulated kinase (ERK)-mitogen-activated protein kinase kinase (MEK)-induced decay of the naive pluripotency mRNAs. Timing of decay is coupled to embryo implantation through ERK-MEK phosphorylation of LIN28A, which repositions pLIN28A to the highly A+U-rich 3' untranslated region (3'UTR) termini of naive pluripotency mRNAs. Interestingly, these A+U-rich 3'UTR termini serve as poly(A)-binding protein (PABP)-binding hubs, poised for signal-induced convergence with LIN28A. The multivalency of AUU motifs determines the efficacy of pLIN28A-PABP convergence, which enhances PABP 3'UTR binding, decreases the protection of poly(A) tails and activates mRNA decay to enable progression toward primed pluripotency. Thus, the signal-induced convergence of LIN28A with PABP-RNA hubs drives the rapid selection of naive mRNAs for decay, enabling the transcriptome remodeling that ensures swift developmental progression., (© 2024. The Author(s).)

The cytoplasm is highly compartmentalized, but the extent and consequences of subcytoplasmic mRNA localization in non-polarized cells are largely unknown. We determined mRNA enrichment in TIS granules (TGs) and the rough endoplasmic reticulum (ER) through particle sorting and isolated cytosolic mRNAs by digitonin extraction. When focusing on genes that encode non-membrane proteins, we observed that 52% have transcripts enriched in specific compartments. Compartment enrichment correlates with a combinatorial code based on mRNA length, exon length, and 3' UTR-bound RNA-binding proteins. Compartment-biased mRNAs differ in the functional classes of their encoded proteins: TG-enriched mRNAs encode low-abundance proteins with strong enrichment of transcription factors, whereas ER-enriched mRNAs encode large and highly expressed proteins. Compartment localization is an important determinant of mRNA and protein abundance, which is supported by reporter experiments showing that redirecting cytosolic mRNAs to the ER increases their protein expression. In summary, the cytoplasm is functionally compartmentalized by local translation environments., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

The structure of mRNA molecules plays an important role in its interactions with trans-acting factors, notably RNA binding proteins (RBPs), thus contributing to the functional consequences of this interplay. However, current transcriptome-wide experimental methods to chart these interactions are limited by their poor sensitivity. Here we extend the hiCLIP atlas of duplexes bound by Staufen1 (STAU1) ∼10-fold, through careful consideration of experimental assumptions, and the development of bespoke computational methods which we apply to existing data. We present Tosca, a Nextflow computational pipeline for the processing, analysis and visualisation of proximity ligation sequencing data generally. We use our extended duplex atlas to discover insights into the RNA selectivity of STAU1, revealing the importance of structural symmetry and duplex-span-dependent nucleotide composition. Furthermore, we identify heterogeneity in the relationship between transcripts with STAU1-bound 3' UTR duplexes and metabolism of the associated RNAs that we relate to RNA structure: transcripts with short-range proximal 3' UTR duplexes have high degradation rates, but those with long-range duplexes have low rates. Overall, our work enables the integrative analysis of proximity ligation data delivering insights into specific features and effects of RBP-RNA structure interactions., (© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Variants of UNC13A, a critical gene for synapse function, increase the risk of amyotrophic lateral sclerosis and frontotemporal dementia 1-3 , two related neurodegenerative diseases defined by mislocalization of the RNA-binding protein TDP-43 4,5 . Here we show that TDP-43 depletion induces robust inclusion of a cryptic exon in UNC13A, resulting in nonsense-mediated decay and loss of UNC13A protein. Two common intronic UNC13A polymorphisms strongly associated with amyotrophic lateral sclerosis and frontotemporal dementia risk overlap with TDP-43 binding sites. These polymorphisms potentiate cryptic exon inclusion, both in cultured cells and in brains and spinal cords from patients with these conditions. Our findings, which demonstrate a genetic link between loss of nuclear TDP-43 function and disease, reveal the mechanism by which UNC13A variants exacerbate the effects of decreased TDP-43 function. They further provide a promising therapeutic target for TDP-43 proteinopathies., (© 2022. The Author(s).)

RNA-binding proteins (RBPs) act as posttranscriptional regulators controlling the fate of target mRNAs. Unraveling how RNAs are recognized by RBPs and in turn are assembled into neuronal RNA granules is therefore key to understanding the underlying mechanism. While RNA sequence elements have been extensively characterized, the functional impact of RNA secondary structures is only recently being explored. Here, we show that Staufen2 binds complex, long-ranged RNA hairpins in the 3'-untranslated region (UTR) of its targets. These structures are involved in the assembly of Staufen2 into RNA granules. Furthermore, we provide direct evidence that a defined Rgs4 RNA duplex regulates Staufen2-dependent RNA localization to distal dendrites. Importantly, disrupting the RNA hairpin impairs the observed effects. Finally, we show that these secondary structures differently affect protein expression in neurons. In conclusion, our data reveal the importance of RNA secondary structure in regulating RNA granule assembly, localization and eventually translation. It is therefore tempting to speculate that secondary structures represent an important code for cells to control the intracellular fate of their mRNAs.

Mutations causing amyotrophic lateral sclerosis (ALS) often affect the condensation properties of RNA-binding proteins (RBPs). However, the role of RBP condensation in the specificity and function of protein-RNA complexes remains unclear. We created a series of TDP-43 C-terminal domain (CTD) variants that exhibited a gradient of low to high condensation propensity, as observed in vitro and by nuclear mobility and foci formation. Notably, a capacity for condensation was required for efficient TDP-43 assembly on subsets of RNA-binding regions, which contain unusually long clusters of motifs of characteristic types and density. These "binding-region condensates" are promoted by homomeric CTD-driven interactions and required for efficient regulation of a subset of bound transcripts, including autoregulation of TDP-43 mRNA. We establish that RBP condensation can occur in a binding-region-specific manner to selectively modulate transcriptome-wide RNA regulation, which has implications for remodeling RNA networks in the context of signaling, disease, and evolution., Competing Interests: Declaration of interests J.S. is a consultant for Dewpoint Therapeutics, Maze Therapeutics, and Vivid Sciences. B.P. is an employee of Dewpoint Therapeutics., (Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.)

Objective: Long-term effects of hyperoxemia during acute exacerbation of chronic obstructive pulmonary disease (AECOPD) remained unknown. We aimed to explore these effects of hyperoxemia during AECOPD., Methods: This was an exploratory follow-up study of a cohort with AECOPD managed by Emergency Medical Service and two emergency departments (EDs). Patients were classified as hyperoxemic (PaO2 > 65 mmHg) or nonhyperoxemic (PaO2 ≤ 65 mmHg). Patients discharged from ED/inpatient care were followed up prospectively for 1 year. The primary outcome was 1-year all-cause mortality in hyperoxemic vs. nonhyperoxemic groups. Secondary outcomes were 3-month all-cause mortality and median number of repeat AECOPD hospitalizations within 1 year. We generated Kaplan-Meier curves and compared them using log-rank test. The primary outcome was also analyzed using Cox proportional-hazards model. We reported crude and adjusted hazard ratios, their 95% confidence intervals (CIs) and P values. We adjusted for two a priori predictors of delayed mortality; age ≥ 70 years and repeat AECOPD hospitalizations., Results: A total of 231 patients were analyzed. One-year mortality rates in hyperoxemic vs. nonhyperoxemic groups were 26/137 (19.0%) and 12/94 (12.8%), respectively (P = 0.693). Although Kaplan-Meier curves showed divergent courses favoring nonhyperoxemic group, log-rank test was not statistically significant (P = 0.203). The crude and adjusted hazard ratios (reference: nonhyperoxemic group) were 1.55 (95% CIs, 0.78-3.08; P = 0.207) and 1.57 (95% CIs, 0.79-3.13; P = 0.196), respectively. Secondary outcomes did not differ., Conclusions: Our study reported no effect on 1-year all-cause mortality associated with hyperoxemia during AECOPD. Further studies are needed to prove/disprove our findings.

Translation of ribosomal protein-coding mRNAs (RP-mRNAs) constitutes a key step in ribosome biogenesis, but the mechanisms that modulate RP-mRNA translation in coordination with other cellular processes are poorly defined. Here, we show that subcellular localization of RP-mRNAs acts as a key regulator of their translation during cell migration. As cells migrate into their surroundings, RP-mRNAs localize to the actin-rich cell protrusions. This localization is mediated by La-related protein 6 (LARP6), an RNA-binding protein that is enriched in protrusions. Protrusions act as hotspots of translation for RP-mRNAs, enhancing RP synthesis, ribosome biogenesis, and the overall protein synthesis in migratory cells. In human breast carcinomas, epithelial-to-mesenchymal transition (EMT) upregulates LARP6 expression to enhance protein synthesis and support invasive growth. Our findings reveal LARP6-mediated mRNA localization as a key regulator of ribosome biogenesis during cell migration and demonstrate a role for this process in cancer progression downstream of EMT., Competing Interests: Declaration of Interests The authors declare no competing interests., (Copyright © 2020 The Authors. Published by Elsevier Inc. All rights reserved.)

RNA-binding proteins (RBPs) and long non-coding RNAs (lncRNAs) are key regulators of gene expression, but their joint functions in coordinating cell fate decisions are poorly understood. Here we show that the expression and activity of the RBP TDP-43 and the long isoform of the lncRNA Neat1, the scaffold of the nuclear compartment "paraspeckles," are reciprocal in pluripotent and differentiated cells because of their cross-regulation. In pluripotent cells, TDP-43 represses the formation of paraspeckles by enhancing the polyadenylated short isoform of Neat1. TDP-43 also promotes pluripotency by regulating alternative polyadenylation of transcripts encoding pluripotency factors, including Sox2, which partially protects its 3' UTR from miR-21-mediated degradation. Conversely, paraspeckles sequester TDP-43 and other RBPs from mRNAs and promote exit from pluripotency and embryonic patterning in the mouse. We demonstrate that cross-regulation between TDP-43 and Neat1 is essential for their efficient regulation of a broad network of genes and, therefore, of pluripotency and differentiation., (Copyright © 2019 The Authors. Published by Elsevier Inc. All rights reserved.)

Introduction: Hyperoxemia in acute exacerbation of chronic obstructive pulmonary disease (AECOPD) leads to adverse outcomes. It remains prevalent in the pre-hospital Emergency Medical Services (EMS) and Emergency Department (ED)., Objective: To determine the key predictors for hyperoxemia in AECOPD in EMS and ED., Methods: This was a prospective observational study of AECOPD patients in EMS and two EDs. Hyperoxemia was defined as PaO 2 > 65 mm Hg (corresponds to SpO 2 > 92%). We determined apriori candidate factors in Patient, Organization and Staff domains. Primary outcomes were the key predictors for hyperoxemia. Secondary outcomes were in-hospital mortality and mechanical ventilation rates in hyperoxemic versus non-hyperoxemic groups. We generated a logistic regression model for each domain. We reported the adjusted odds ratios (AORs), 95% CIs and p values. We selected the output factors using AOR ≥2.0 and ≥2.5 for modifiable and non-modifiable factors, respectively. These selected factors were fed into a final model with eventual factors selected based on: threshold AORs as stated above and/or 95% CIs including these AORs., Results: Three hundred and twenty-six patients were analysed; 60.7% had hyperoxemia. We found three eventual modifiable factors; first, ED SpO 2 > 95% [AOR 2.62 (95% CIs: 1.61-4.33); P < 0.001], EMS non-rebreathing mask [AOR 2.01 (95% CIs: 1.06-3.97); P = 0.04]; and ED nasal cannula [AOR 1.69 (95% CIs: 1.05-2.72); P = 0.03]. Secondary outcomes did not differ between groups., Conclusion: We identified three key modifiable predictors. We intend to conduct an interventional study using them to reduce hyperoxemia rate in AECOPD., (© 2019 John Wiley & Sons Ltd.)

RNA binding proteins (RBPs) regulate all aspects in the life cycle of RNA molecules. To elucidate the elements that guide RNA specificity, regulatory mechanisms, and functions of RBPs, methods that identify direct endogenous protein-RNA interactions are particularly valuable. UV crosslinking and immunoprecipitation (CLIP) purifies short RNA fragments that crosslink to a specific protein and then identifies these fragments by sequencing. When combined with high-throughput sequencing, CLIP can produce transcriptome-wide maps of RNA crosslink sites. The protocol is comprised of several dozen biochemical steps, and improvements made over the last 15 years have increased its resolution, sensitivity, and convenience. Adaptations of CLIP are also emerging in the epitranscriptomic field to map the positions of RNA modifications accurately. Here, we describe the rationale for each step in the protocol and discuss the impact of variations to help users determine the most suitable option., (Crown Copyright © 2018. Published by Elsevier Inc. All rights reserved.)

The curtain sign (CS) is a sonographic artifact found in lung ultrasound studies. It is generally used to describe the appearance of an expanded and aerated lung, often in the context of pleural effusion diagnosis. In emergency and critical care ultrasound use, the recognition of changes to the CS is very useful in the detection of early pulmonary pathological processes occurring at the lateral lung bases and costophrenic recesses. The author suggests a simple standardisation of the CS description and describes its use in lung ultrasound., Competing Interests: Conflict of interest: I declare that I do not have any conflict of interests.

During brain wiring, cue-induced axon behaviors such as directional steering and branching are aided by localized mRNA translation. Different guidance cues elicit translation of subsets of mRNAs that differentially regulate the cytoskeleton, yet little is understood about how specific mRNAs are selected for translation. MicroRNAs (miRNAs) are critical translational regulators that act through a sequence-specific mechanism. Here, we investigate the local role of miRNAs in mRNA-specific translation during pathfinding of Xenopus laevis retinal ganglion cell (RGC) axons. Among a rich repertoire of axonal miRNAs, miR-182 is identified as the most abundant. Loss of miR-182 causes RGC axon targeting defects in vivo and impairs Slit2-induced growth cone (GC) repulsion. We find that miR-182 targets cofilin-1 mRNA, silencing its translation, and Slit2 rapidly relieves the repression without causing miR-182 degradation. Our data support a model whereby miR-182 reversibly gates the selection of transcripts for fast translation depending on the extrinsic cue., (Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.)