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1.
Nature ; 601(7891): 45-48, 2022 01.
Article in English | MEDLINE | ID: mdl-34987215

ABSTRACT

Stellar ejecta gradually enrich the gas out of which subsequent stars form, making the least chemically enriched stellar systems direct fossils of structures formed in the early Universe1. Although a few hundred stars with metal content below 1,000th of the solar iron content are known in the Galaxy2-4, none of them inhabit globular clusters, some of the oldest known stellar structures. These show metal content of at least approximately 0.2% of the solar metallicity [Formula: see text]. This metallicity floor appears universal5,6, and it has been proposed that protogalaxies that merged into the galaxies we observe today were simply not massive enough to form clusters that survived to the present day7. Here we report observations of a stellar stream, C-19, whose metallicity is less than 0.05% of the solar metallicity [Formula: see text]. The low metallicity dispersion and the chemical abundances of the C-19 stars show that this stream is the tidal remnant of the most metal-poor globular cluster ever discovered, and is significantly below the purported metallicity floor: clusters with significantly lower metallicities than observed today existed in the past and contributed their stars to the Milky Way halo.

2.
RNA ; 30(8): 1058-1069, 2024 Jul 16.
Article in English | MEDLINE | ID: mdl-38719745

ABSTRACT

Identification of splice sites is a critical step in pre-messenger RNA (pre-mRNA) splicing because the definition of the exon/intron boundaries controls what nucleotides are incorporated into mature mRNAs. The intron boundary with the upstream exon is initially identified through interactions with the U1 small nuclear ribonucleoprotein (snRNP). This involves both base-pairing between the U1 snRNA and the pre-mRNA as well as snRNP proteins interacting with the 5' splice site (5'ss)/snRNA duplex. In yeast, this duplex is buttressed by two conserved protein factors, Yhc1 and Luc7. Luc7 has three human paralogs (LUC7L, LUC7L2, and LUC7L3), which play roles in alternative splicing. What domains of these paralogs promote splicing at particular sites is not yet clear. Here, we humanized the zinc finger (ZnF) domains of the yeast Luc7 protein in order to understand their roles in splice site selection using reporter assays, transcriptome analysis, and genetic interactions. Although we were unable to determine a function for the first ZnF domain, humanization of the second ZnF domain to mirror that found in LUC7L or LUC7L2 resulted in altered usage of nonconsensus 5'ss. In contrast, the corresponding ZnF domain of LUC7L3 could not support yeast viability. Further, humanization of Luc7 can suppress mutation of the ATPase Prp28, which is involved in U1 release and exchange for U6 at the 5'ss. Our work reveals a role for the second ZnF of Luc7 in splice site selection and suggests that different ZnF domains may have different ATPase requirements for release by Prp28.


Subject(s)
Saccharomyces cerevisiae Proteins , Saccharomyces cerevisiae , Zinc Fingers , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , RNA, Small Nuclear/genetics , RNA, Small Nuclear/metabolism , RNA Splicing Factors/metabolism , RNA Splicing Factors/genetics , RNA Splice Sites , Humans , RNA-Binding Proteins/metabolism , RNA-Binding Proteins/genetics , RNA Splicing , RNA Precursors/genetics , RNA Precursors/metabolism , Alternative Splicing , Ribonucleoprotein, U1 Small Nuclear/metabolism , Ribonucleoprotein, U1 Small Nuclear/genetics , Introns/genetics
3.
J Biol Chem ; 300(11): 107820, 2024 Sep 27.
Article in English | MEDLINE | ID: mdl-39343004

ABSTRACT

Coenzyme Q (CoQ) is a redox-active lipid molecule that acts as an electron carrier in the mitochondrial electron transport chain. In Saccharomyces cerevisiae, CoQ is synthesized in the mitochondrial matrix by a multisubunit protein-lipid complex termed the CoQ synthome, the spatial positioning of which is coordinated by the endoplasmic reticulum-mitochondria encounter structure (ERMES). The MDM12 gene encoding the cytosolic subunit of ERMES is coexpressed with COQ10, which encodes the putative CoQ chaperone Coq10, via a shared bidirectional promoter. Deletion of COQ10 results in respiratory deficiency, impaired CoQ biosynthesis, and reduced spatial coordination between ERMES and the CoQ synthome. While Coq10 protein content is maintained upon deletion of MDM12, we show that deletion of COQ10 by replacement with a HIS3 marker results in diminished Mdm12 protein content. Since deletion of individual ERMES subunits prevents ERMES formation, we asked whether some or all of the phenotypes associated with COQ10 deletion result from ERMES dysfunction. To identify the phenotypes resulting solely due to the loss of Coq10, we constructed strains expressing a functionally impaired (coq10-L96S) or truncated (coq10-R147∗) Coq10 isoform using CRISPR-Cas9. We show that both coq10 mutants preserve Mdm12 protein content and exhibit impaired respiratory capacity like the coq10Δ mutant, indicating that Coq10's function is vital for respiration regardless of ERMES integrity. Moreover, the maintenance of CoQ synthome stability and efficient CoQ biosynthesis observed for the coq10-R147∗ mutant suggests these deleterious phenotypes in the coq10Δ mutant result from ERMES disruption. Overall, this study clarifies the role of Coq10 in modulating CoQ biosynthesis.

4.
J Biol Chem ; 300(1): 105557, 2024 Jan.
Article in English | MEDLINE | ID: mdl-38097186

ABSTRACT

Formins are large, multidomain proteins that nucleate new actin filaments and accelerate elongation through a processive interaction with the barbed ends of filaments. Their actin assembly activity is generally attributed to their eponymous formin homology (FH) 1 and 2 domains; however, evidence is mounting that regions outside of the FH1FH2 stretch also tune actin assembly. Here, we explore the underlying contributions of the tail domain, which spans the sequence between the FH2 domain and the C terminus of formins. Tails vary in length from ∼0 to >200 residues and contain a number of recognizable motifs. The most common and well-studied motif is the ∼15-residue-long diaphanous autoregulatory domain. This domain mediates all or nothing regulation of actin assembly through an intramolecular interaction with the diaphanous inhibitory domain in the N-terminal half of the protein. Multiple reports demonstrate that the tail can enhance both nucleation and processivity. In this study, we provide a high-resolution view of the alternative splicing encompassing the tail in the formin homology domain (Fhod) family of formins during development. While four distinct tails are predicted, we found significant levels of only two of these. We characterized the biochemical effects of the different tails. Surprisingly, the two highly expressed Fhod-tails inhibit processive elongation and diminish nucleation, while a third supports activity. These findings demonstrate a new mechanism of modulating actin assembly by formins and support a model in which splice variants are specialized to build distinct actin structures during development.


Subject(s)
Actins , Drosophila Proteins , Actin Cytoskeleton/metabolism , Actins/metabolism , Drosophila melanogaster , Drosophila Proteins/genetics , Drosophila Proteins/metabolism , Animals
5.
RNA ; 29(8): 1099-1107, 2023 08.
Article in English | MEDLINE | ID: mdl-37137666

ABSTRACT

RT-PCR and northern blots have long been used to study RNA isoforms usage for single genes. Recent advancements in long-read sequencing have yielded unprecedented information about the usage and abundance of these RNA isoforms. However, visualization of long-read sequencing data remains challenging due to the high information density. To alleviate these issues, we have developed NanoBlot, an open-source R-package that generates northern blot and RT-PCR-like images from long-read sequencing data. NanoBlot requires aligned, positionally sorted and indexed BAM files. Plotting is based around ggplot2 and is easily customizable. Advantages of NanoBlot include a robust system for designing probes to visualize isoforms including excluding reads based on the presence or absence of a specified region, an elegant solution to representing isoforms with continuous variations in length, and the ability to overlay multiple genes in the same plot using different colors. We present examples of nanoblots compared to actual northern blot data. In addition to traditional gel-like images, the NanoBlot package can also output other visualizations such as violin plots and 3'-RACE-like plots focused on 3'-end isoforms visualization. The use of the NanoBlot package should provide a simple answer to some of the challenges of visualizing long-read RNA-sequencing data.


Subject(s)
RNA Isoforms , RNA , RNA/genetics , RNA Isoforms/genetics , High-Throughput Nucleotide Sequencing/methods , Sequence Analysis, RNA/methods , Protein Isoforms/genetics , Alternative Splicing , Gene Expression Profiling/methods , Transcriptome
6.
Nucleic Acids Res ; 51(22): 12428-12442, 2023 Dec 11.
Article in English | MEDLINE | ID: mdl-37956322

ABSTRACT

The fidelity of splice site selection is critical for proper gene expression. In particular, proper recognition of 3'-splice site (3'SS) sequences by the spliceosome is challenging considering the low complexity of the 3'SS consensus sequence YAG. Here, we show that absence of the Prp18p splicing factor results in genome-wide activation of alternative 3'SS in S. cerevisiae, including highly unusual non-YAG sequences. Usage of these non-canonical 3'SS in the absence of Prp18p is enhanced by upstream poly(U) tracts and by their potential to interact with the first intronic nucleoside, allowing them to dock in the spliceosome active site instead of the normal 3'SS. The role of Prp18p in 3'SS fidelity is facilitated by interactions with Slu7p and Prp8p, but cannot be fulfilled by Slu7p, identifying a unique role for Prp18p in 3'SS fidelity. This fidelity function is synergized by the downstream proofreading activity of the Prp22p helicase, but is independent from another late splicing helicase, Prp43p. Our results show that spliceosomes exhibit remarkably relaxed 3'SS sequence usage in the absence of Prp18p and identify a network of spliceosomal interactions centered on Prp18p which are required to promote the fidelity of the recognition of consensus 3'SS sequences.


Subject(s)
RNA Splice Sites , Saccharomyces cerevisiae , Alternative Splicing , RNA Splicing , RNA Splicing Factors/genetics , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Spliceosomes/genetics , Saccharomyces cerevisiae Proteins/metabolism
7.
Proc Natl Acad Sci U S A ; 119(31): e2202473119, 2022 08 02.
Article in English | MEDLINE | ID: mdl-35878033

ABSTRACT

Many small nucleolar RNAs (snoRNA)s are processed from introns of host genes, but the importance of splicing for proper biogenesis and the fate of the snoRNAs is not well understood. Here, we show that inactivation of splicing factors or mutation of splicing signals leads to the accumulation of partially processed hybrid messenger RNA-snoRNA (hmsnoRNA) transcripts. hmsnoRNAs are processed to the mature 3' ends of the snoRNAs by the nuclear exosome and bound by small nucleolar ribonucleoproteins. hmsnoRNAs are unaffected by translation-coupled RNA quality-control pathways, but they are degraded by the major cytoplasmic exonuclease Xrn1p, due to their messenger RNA (mRNA)-like 5' extensions. These results show that completion of splicing is required to promote complete and accurate processing of intron-encoded snoRNAs and that splicing defects lead to degradation of hybrid mRNA-snoRNA species by cytoplasmic decay, underscoring the importance of splicing for the biogenesis of intron-encoded snoRNAs.


Subject(s)
RNA Splicing , RNA Stability , RNA, Messenger , RNA, Small Nucleolar , Introns , RNA, Messenger/genetics , RNA, Small Nucleolar/genetics
8.
RNA ; 27(12): 1545-1556, 2021 12.
Article in English | MEDLINE | ID: mdl-34497070

ABSTRACT

The expression of bromodomain-containing proteins that regulate chromatin structure and accessibility must be tightly controlled to ensure the appropriate regulation of gene expression. In the yeast S. cerevisiae, Bromodomain Factor 2 (BDF2) expression is extensively regulated post-transcriptionally during stress by RNase III-mediated decay (RMD), which is triggered by cleavage of the BDF2 mRNA in the nucleus by the RNase III homolog Rnt1p. Previous studies have shown that RMD-mediated down-regulation of BDF2 is hyperactivated in osmotic stress conditions, yet the mechanisms driving the enhanced nuclear cleavage of BDF2 RNA under these conditions remain unknown. Here, we show that RMD hyperactivation can be detected in multiple stress conditions that inhibit mRNA export, and that Rnt1p remains primarily localized in the nucleus during salt stress. We show that globally inhibiting mRNA nuclear export by anchoring away mRNA biogenesis or export factors out of the nucleus can recapitulate RMD hyperactivation in the absence of stress. RMD hyperactivation requires Rnt1p nuclear localization but does not depend on the BDF2 gene endogenous promoter, and its efficiency is affected by the structure of the stem-loop cleaved by Rnt1p. Because multiple stress conditions have been shown to mediate global inhibition of mRNA export, our results suggest that the hyperactivation of RMD is primarily the result of the increased nuclear retention of the BDF2 mRNA during stress.


Subject(s)
Cell Nucleus/metabolism , RNA Transport , RNA, Messenger/metabolism , Ribonuclease III/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/metabolism , Salt Stress , Transcription Factors/metabolism , Active Transport, Cell Nucleus , Cell Nucleus/genetics , RNA, Messenger/genetics , Ribonuclease III/genetics , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae Proteins/genetics , Transcription Factors/genetics
9.
J Environ Manage ; 342: 118034, 2023 Sep 15.
Article in English | MEDLINE | ID: mdl-37187070

ABSTRACT

Intense urbanisation in many coastal areas has led to intensification of groundwater consumption, while reducing permeable areas and increasing the frequency and magnitude of flooding. Among the potential strategies to compensate for these adverse effects, which are expected to become worse as a result of climate change, rooftop rainwater harvesting (RWH) in combination with managed aquifer recharge (MAR), may be indicated. This work investigated the performance of different configurations of such a system, tested as a twofold sustainable stormwater and domestic water management tool in a tropical metropole (João Pessoa, Brazil). This area located over a sedimentary aquifer system illustrates the water security challenges of densely urbanised areas in southern cities. To that end, several configurations of rooftop catchments and storage volumes were evaluated, by simulating a MAR-RWH system connected to the regional unconfined aquifer (Barreiras Formation) through a 6″ diameter injection well. Rainfall-runoff-recharge processes and water balances were simulated using monitored high-temporal resolution rainfall data. The results showed that catchments ranging from 180 to 810 m2, connected to tanks from 0.5 to 30.0 m³, are the optimal solutions in terms of efficient rainwater retention and peak flow reduction. These solutions provided mean annual estimates of aquifer recharge between 57 and 255 m³/yr from 2004 to 2019. The results of this study highlight the opportunity for MAR schemes to reconcile stormwater management and water supply goals.


Subject(s)
Groundwater , Water , Cities , Floods , Brazil
10.
BJU Int ; 130(3): 314-322, 2022 09.
Article in English | MEDLINE | ID: mdl-34674367

ABSTRACT

OBJECTIVE: To determine the prevalence of intra-patient inter-metastatic heterogeneity based on positron emission tomography (PET)/computed tomography (CT) in patients with metastatic castration-resistant prostate cancer (mCRPC) and to determine the prevalence of neuroendocrine disease in these patients and their eligibility for radioligand therapies (RLTs). PATIENTS AND METHODS: This multicentre observational prospective clinical study will include 100 patients with mCRPC from five Canadian academic centres. Patients with radiological or biochemical progression and harbouring at least three metastases by conventional imaging will be accrued. Intra-patient inter-metastatic heterogeneity will be determined with triple-tracer imaging using fluorine-18 fluorodeoxyglucose (18 F-FDG), gallium-68-(68 Ga)-prostate-specific membrane antigen (PSMA)-617 and 68 Ga-DOTATATE, which are a glucose analogue, a PSMA receptor ligand and a somatostatin receptor ligand, respectively. The 68 Ga-PSMA-617 and 18 F-FDG PET/CT scans will be performed first. If at least one PSMA-negative/FDG-positive lesion is observed, an additional PET/CT scan with 68 Ga-DOTATATE will be performed. The tracer uptake of individual lesions will be assessed for each PET tracer and patients with lesions presenting discordant uptake profiles will be considered as having inter-metastatic heterogeneous disease and may be offered a biopsy. EXPECTED RESULTS: The proposed triple-tracer approach will allow whole-body mCRPC characterisation, investigating the inter-metastatic heterogeneity in order to better understand the phenotypic plasticity of prostate cancer, including the neuroendocrine transdifferentiation that occurs during mCRPC progression. Based on 68 Ga-PSMA-617 or 68 Ga-DOTATATE PET positivity, the potential eligibility of patients for PSMA and DOTATATE-based RLT will be assessed. Non-invasive whole-body determination of mCRPC heterogeneity and transdifferentiation is highly innovative and might establish the basis for new therapeutic strategies. Comparison of molecular imaging findings with biopsies will also link metastasis biology to radiomic features. CONCLUSION: This study will add novel, biologically relevant dimensions to molecular imaging: the non-invasive detection of inter-metastatic heterogeneity and transdifferentiation to neuroendocrine prostate cancer by using a multi-tracer PET/CT strategy to further personalise the care of patients with mCRPC.


Subject(s)
Positron Emission Tomography Computed Tomography , Prostatic Neoplasms, Castration-Resistant , Canada , Fluorodeoxyglucose F18 , Gallium Radioisotopes/therapeutic use , Humans , Ligands , Male , Multicenter Studies as Topic , Observational Studies as Topic , Positron Emission Tomography Computed Tomography/methods , Positron-Emission Tomography , Prospective Studies , Prostatic Neoplasms, Castration-Resistant/drug therapy , Radionuclide Imaging , Radiopharmaceuticals/therapeutic use
11.
Anim Genet ; 53(5): 709-712, 2022 Oct.
Article in English | MEDLINE | ID: mdl-35864734

ABSTRACT

Hereditary ataxias are common among canine breeds with various molecular etiology. We identified a hereditary ataxia in young-adult Australian Shepherd dogs characterized by uncoordinated movements and spasticity, worsening progressively and leading to inability to walk. Pedigree analysis suggested an autosomal recessive transmission. By whole genome sequencing and variant filtering of an affected dog we identified a PNPLA8:c.1169_1170dupTT variant. This variant, located in PNPLA8 (Patatin Like Phospholipase Domain Containing 8), was predicted to induce a PNPLA8:p.(His391PhefsTer394) frameshift, leading to a premature stop codon in the protein. The truncated protein was predicted to lack the functional patatin catalytic domain of PNPLA8, a calcium-independent phospholipase. PNPLA8 is known to be essential for maintaining mitochondrial energy production through tailoring mitochondrial membrane lipid metabolism and composition. The Australian Shepherd ataxia shares molecular and clinical features with Weaver syndrome in cattle and the mitochondrial-related neurodegeneration associated with PNPLA8 loss-of-function variants in humans. By genotyping a cohort of 85 control Australian Shepherd dogs sampled in France, we found a 4.7% carrier frequency. The PNPLA8:c.[1169_1170dupTT] allele is easily detectable with a genetic test to avoid at-risk matings.


Subject(s)
Cattle Diseases , Dog Diseases , Spinocerebellar Degenerations , Animals , Australia , Cattle , Cattle Diseases/genetics , Dog Diseases/genetics , Dogs , Frameshift Mutation , Humans , Pedigree , Phospholipases/genetics
12.
Methods ; 176: 4-13, 2020 04 01.
Article in English | MEDLINE | ID: mdl-31128237

ABSTRACT

3'-end poly(A)+ sequencing is an efficient and economical method for global measurement of mRNA levels and alternative poly(A) site usage. A common method involves oligo(dT)19V reverse-transcription (RT)-based library preparation and high-throughput sequencing with a custom primer ending in (dT)19. While the majority of library products have the first sequenced nucleotide reflect the bona fide poly(A) site (pA), a substantial fraction of sequencing reads arise from various mis-priming events. These can result in incorrect pA site calls anywhere from several nucleotides downstream to several kilobases upstream from the bona fide pA site. While these mis-priming events can be mitigated by increasing annealing stringency (e.g. increasing temperature from 37 °C to 42 °C), they still persist at an appreciable level (∼10%) and computational methods must be used to prevent artifactual calls. Here we present a bioinformatics workflow for precise mapping of poly(A)+ 3' ends and handling of artifacts due to oligo(dT) mis-priming and sample polymorphisms. We test pA site calling with three different read mapping programs (STAR, BWA, and BBMap), and show that the way in which each handles terminal mismatches and soft clipping has a substantial impact on identifying correct pA sites, with BWA requiring the least post-processing to correct artifacts. We demonstrate the use of this pipeline for mapping pA sites in the model eukaryote S. cerevisiae, and further apply this technology to non-polyadenylated transcripts by employing in vitro polyadenylation prior to library prep (IVP-seq). As proof of principle, we show that a fraction of tRNAs harbor CCU 3' tails instead of the canonical CCA tail, and globally identify 3' ends of splicing intermediates arising from inefficiently spliced transcripts.


Subject(s)
Molecular Sequence Annotation/methods , RNA-Seq/methods , 3' Untranslated Regions/genetics , Computational Biology/methods , Nucleotides/genetics , Poly A/genetics , Polyadenylation/genetics , RNA Splicing , RNA, Fungal/genetics , Saccharomyces cerevisiae/genetics
13.
Mol Cell ; 51(1): 105-15, 2013 Jul 11.
Article in English | MEDLINE | ID: mdl-23747013

ABSTRACT

Zinc is an essential cofactor of all major eukaryotic RNA polymerases. How the activity of these enzymes is coordinated or regulated according to cellular zinc levels is largely unknown. Here we show that the stability of RNA polymerase I (RNAPI) is tightly coupled to zinc availability in vivo. In zinc deficiency, RNAPI is specifically degraded by proteolysis in the vacuole in a pathway dependent on the export in Xpo1p and deubiquitination of the RNAPI large subunit Rpa190p by Ubp2p and Ubp4p. RNAPII is unaffected, which allows for the expression of genes required in zinc deficiency. RNAPI export to the vacuole is required for survival during zinc starvation, suggesting that degradation of zinc-binding subunits might provide a last resort zinc reservoir. These results reveal a hierarchy of cellular transcriptional activities during zinc starvation and show that degradation of the most active cellular transcriptional machinery couples cellular growth and proliferation to zinc availability.


Subject(s)
RNA Polymerase I/physiology , Saccharomyces cerevisiae/growth & development , Zinc/metabolism , Down-Regulation , Endopeptidases/metabolism , Endopeptidases/physiology , Enzyme Stability , RNA Polymerase I/metabolism , RNA, Ribosomal/biosynthesis , Saccharomyces cerevisiae/cytology , Saccharomyces cerevisiae/metabolism , Ubiquitination , Vacuoles/metabolism
14.
Biochemistry ; 58(49): 4997-5010, 2019 12 10.
Article in English | MEDLINE | ID: mdl-31738538

ABSTRACT

To date, 12 protein lysine methyltransferases that modify translational elongation factors and ribosomal proteins (Efm1-7 and Rkm 1-5) have been identified in the yeast Saccharomyces cerevisiae. Of these 12, five (Efm1 and Efm4-7) appear to be specific to elongation factor 1A (EF1A), the protein responsible for bringing aminoacyl-tRNAs to the ribosome. In S. cerevisiae, the functional implications of lysine methylation in translation are mostly unknown. In this work, we assessed the physiological impact of disrupting EF1A methylation in a strain where four of the most conserved methylated lysine sites are mutated to arginine residues and in strains lacking either four or five of the Efm lysine methyltransferases specific to EF1A. We found that loss of EF1A methylation was not lethal but resulted in reduced growth rates, particularly under caffeine and rapamycin stress conditions, suggesting EF1A interacts with the TORC1 pathway, as well as altered sensitivities to ribosomal inhibitors. We also detected reduced cellular levels of the EF1A protein, which surprisingly was not reflected in its stability in vivo. We present evidence that these Efm methyltransferases appear to be largely devoted to the modification of EF1A, finding no evidence of the methylation of other substrates in the yeast cell. This work starts to illuminate why one protein can need five different methyltransferases for its functions and highlights the resilience of yeast to alterations in their posttranslational modifications.


Subject(s)
Lysine/metabolism , Peptide Elongation Factor 1/chemistry , Peptide Elongation Factor 1/metabolism , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/enzymology , Amino Acid Motifs , Methylation , Methyltransferases/genetics , Methyltransferases/metabolism , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/genetics
15.
Genome Res ; 26(10): 1363-1375, 2016 10.
Article in English | MEDLINE | ID: mdl-27540088

ABSTRACT

RNA polymerase II (Pol II) transcription termination by the Nrd1p-Nab3p-Sen1p (NNS) pathway is critical for the production of stable noncoding RNAs and the control of pervasive transcription in Saccharomyces cerevisiae To uncover determinants of NNS termination, we mapped the 3'-ends of NNS-terminated transcripts genome-wide. We found that nucleosomes and specific DNA-binding proteins, including the general regulatory factors (GRFs) Reb1p, Rap1p, and Abf1p, and Pol III transcription factors enhance the efficiency of NNS termination by physically blocking Pol II progression. The same DNA-bound factors that promote NNS termination were shown previously to define the 3'-ends of Okazaki fragments synthesized by Pol δ during DNA replication. Reduced binding of these factors results in defective NNS termination and Pol II readthrough. Furthermore, inactivating NNS enables Pol II elongation through these roadblocks, demonstrating that effective Pol II termination depends on a synergy between the NNS machinery and obstacles in chromatin. Consistent with this finding, loci exhibiting Pol II readthrough at GRF binding sites are depleted for upstream NNS signals. Overall, these results underscore how RNA termination signals influence the behavior of Pol II at chromatin obstacles, and establish that common genomic elements define boundaries for both DNA and RNA synthesis machineries.


Subject(s)
DNA Replication , Genome, Fungal , RNA, Untranslated/genetics , Transcription Elongation, Genetic , Transcription Termination, Genetic , DNA/genetics , DNA Helicases/genetics , DNA Helicases/metabolism , DNA Polymerase II/genetics , DNA Polymerase II/metabolism , DNA Polymerase III/genetics , DNA Polymerase III/metabolism , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Nuclear Proteins/genetics , Nuclear Proteins/metabolism , RNA Helicases/genetics , RNA Helicases/metabolism , RNA-Binding Proteins/genetics , RNA-Binding Proteins/metabolism , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism , Shelterin Complex , Telomere-Binding Proteins/genetics , Telomere-Binding Proteins/metabolism , Transcription Factors/genetics , Transcription Factors/metabolism
16.
RNA ; 23(4): 466-472, 2017 04.
Article in English | MEDLINE | ID: mdl-28053271

ABSTRACT

The RNA exosome is a conserved multiprotein complex that achieves a large number of processive and degradative functions in eukaryotic cells. Recently, mutations have been mapped to the gene encoding one of the subunits of the exosome, EXOSC3 (yeast Rrp40p), which results in pontocerebellar hypoplasia with motor neuron degeneration in human patients. However, the molecular impact of these mutations in the pathology of these diseases is not well understood. To investigate the molecular consequences of mutations in EXOSC3 that lead to neurological diseases, we analyzed the effect of three of the mutations that affect conserved residues of EXOSC3/Rrp40p (G31A, G191C, and W238R; G8A, G148C, and W195R, respectively, in human and yeast) in S. cerevisiae We show that the severity of the phenotypes of these mutations in yeast correlate with that of the disease in human patients, with the W195R mutant showing the strongest growth and RNA processing phenotypes. Furthermore, we show that these mutations affect more severely pre-ribosomal RNA processing functions of the exosome rather than other nuclear processing or surveillance functions. These results suggest that delayed or defective pre-rRNA processing might be the primary defect responsible for the pathologies detected in patients with mutations affecting EXOSC3 function in residues conserved throughout eukaryotes.


Subject(s)
Exosome Multienzyme Ribonuclease Complex/genetics , Mutation , RNA Precursors/genetics , RNA Processing, Post-Transcriptional , RNA, Fungal/genetics , RNA, Ribosomal/genetics , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae/genetics , Amino Acid Sequence , Amino Acid Substitution , Binding Sites , Conserved Sequence , Exosome Multienzyme Ribonuclease Complex/metabolism , Gene Expression Regulation, Fungal , Humans , Olivopontocerebellar Atrophies/genetics , Olivopontocerebellar Atrophies/metabolism , Olivopontocerebellar Atrophies/pathology , Protein Binding , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Protein Interaction Domains and Motifs , RNA Precursors/metabolism , RNA, Fungal/metabolism , RNA, Ribosomal/metabolism , RNA-Binding Proteins/genetics , RNA-Binding Proteins/metabolism , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Sequence Alignment , Sequence Homology, Amino Acid
17.
Am J Respir Cell Mol Biol ; 59(5): 601-613, 2018 11.
Article in English | MEDLINE | ID: mdl-29944393

ABSTRACT

RGS2 is a key modulator of stress in human airway epithelial cells, especially of hyperresponsiveness and mucin hypersecretion, both of which are features of cystic fibrosis (CF). Because its expression can be modulated through the DNA methylation pathway, we hypothesize that RGS2 is downregulated by DNA hypermethylation in CF airway epithelial cells. This downregulation would then lead to an enhanced inflammatory response. We demonstrated RGS2 transcript and protein downregulation in cultured airway epithelial cells from patients with CF and validated our findings in two CF epithelial cell lines. A methylated DNA immunoprecipitation array showed the presence of methylated cytosine on 13 gene promoters in CF. Among these genes, we confirmed that the RGS2 promoter was hypermethylated by using bisulfite conversion coupled with a methylation-specific PCR assay. Finally, we showed that downregulation of RGS2 in non-CF cells increased the expression of S100A12, a proinflammatory marker. These results highlight the importance of epigenetic regulation in gene expression in CF and show that RGS2 might modulate the inflammatory response in CF through DNA methylation control.


Subject(s)
Cystic Fibrosis/metabolism , DNA Methylation , Epithelial Cells/metabolism , Gene Expression Regulation , RGS Proteins/metabolism , Respiratory System/metabolism , S100A12 Protein/metabolism , Cells, Cultured , Cystic Fibrosis/genetics , Cystic Fibrosis/pathology , Epigenesis, Genetic , Epithelial Cells/cytology , Humans , Oligonucleotide Array Sequence Analysis , Promoter Regions, Genetic , RGS Proteins/genetics , Respiratory System/cytology , S100A12 Protein/genetics
18.
Phys Rev Lett ; 120(24): 245501, 2018 Jun 15.
Article in English | MEDLINE | ID: mdl-29956947

ABSTRACT

The total energy of acoustic emission (AE) events in externally stressed materials diverges when approaching macroscopic failure. Numerical and conceptual models explain this accelerated seismic release (ASR) as the approach to a critical point that coincides with ultimate failure. Here, we report ASR during soft uniaxial compression of three silica-based (SiO_{2}) nanoporous materials. Instead of a singular critical point, the distribution of AE energies is stationary, and variations in the activity rate are sufficient to explain the presence of multiple periods of ASR leading to distinct brittle failure events. We propose that critical failure is suppressed in the AE statistics by mechanisms of transient hardening. Some of the critical exponents estimated from the experiments are compatible with mean field models, while others are still open to interpretation in terms of the solution of frictional and fracture avalanche models.

19.
J Environ Manage ; 209: 426-439, 2018 Mar 01.
Article in English | MEDLINE | ID: mdl-29309966

ABSTRACT

Recife Metropolitan Region (RMR, NE Brazil) lies over a multi-layered aquifer system located in an estuarial area. The region has experienced fast population growth and repeated droughts in the last three decades, which led to unprecedented anthropogenic pressure on groundwater resources because of intense water pumping. Accordingly, scientific and stakeholder communities have been challenged to ensure the maintenance of sustainable groundwater resource by managing all water cycle. Because controlling pumping rates is difficult due to the large number of illegal wells, the Managed Aquifer Recharge (MAR) strategies are now under consideration. The RMR presents a tropical climate and an annual average rainfall rate of approximately 2450 mm year-1, providing great potential volumes of water to be used for piezometric level recovery. However, MAR implementation requires a detailed and in-depth knowledge of the human-impact on the hydrogeological behavior of the resource over the long-term, in order to find out the most appropriate recharge strategy. Therefore, the present study illustrates how routine data monitoring, i.e., piezometric level and electrical conductivity (EC), in combination with the geological knowledge, may allow proposing further MAR strategies. Two contrasted behaviors were observed in RMR: (i) groundwater level decrease and stable EC in the North and Southernmost areas of Recife; and (ii) stable groundwater level and high/varying EC values next to the estuarial zone. Although aquifers are undergoing over-abstraction, this spatiotemporal heterogeneity suggests that a recharge is possibly locally favored next to the estuarial area of the RMR thanks to hydraulic connections between surface and deep aquifers throughout extended paleo-channels. Thus, based on this typology, MAR implementation through controlled infiltration close to the estuarial area seems to be more appropriated, whereas the direct deep injection appears to be more relevant in more distant zones.


Subject(s)
Environmental Monitoring , Estuaries , Groundwater , Brazil , Electric Conductivity , Geology , Humans
20.
Article in English | MEDLINE | ID: mdl-28652242

ABSTRACT

Although respiratory syncytial virus (RSV) is the most common cause of lower respiratory tract infection in infants and young children, attempts to develop an effective therapy have so far proved unsuccessful. Here we report the preclinical profiles of PC786, a potent nonnucleoside RSV L protein polymerase inhibitor, designed for inhalation treatment of RSV infection. PC786 demonstrated a potent and selective antiviral activity against laboratory-adapted or clinical isolates of RSV-A (50% inhibitory concentration [IC50], <0.09 to 0.71 nM) and RSV-B (IC50, 1.3 to 50.6 nM), which were determined by inhibition of cytopathic effects in HEp-2 cells without causing detectable cytotoxicity. The underlying inhibition of virus replication was confirmed by PCR analysis. The effects of PC786 were largely unaffected by the multiplicity of infection (MOI) and were retained in the face of established RSV replication in a time-of-addition study. Persistent anti-RSV effects of PC786 were also demonstrated in human bronchial epithelial cells. In vivo intranasal once daily dosing with PC786 was able to reduce the virus load to undetectable levels in lung homogenates from RSV-infected mice and cotton rats. Treatment with escalating concentrations identified a dominant mutation in the L protein (Y1631H) in vitro In addition, PC786 potently inhibited RSV RNA-dependent RNA polymerase (RdRp) activity in a cell-free enzyme assay and minigenome assay in HEp-2 cells (IC50, 2.1 and 0.5 nM, respectively). Thus, PC786 was shown to be a potent anti-RSV agent via inhibition of RdRp activity, making topical treatment with this compound a novel potential therapy for the treatment of human RSV infections.


Subject(s)
Antiviral Agents/pharmacology , RNA-Dependent RNA Polymerase/antagonists & inhibitors , Respiratory Syncytial Virus Infections/drug therapy , Respiratory Syncytial Virus, Human/drug effects , Respiratory Tract Infections/drug therapy , Spiro Compounds/pharmacology , Virus Replication/drug effects , Animals , Benzamides , Benzazepines , Cell Line , Epithelial Cells/virology , Humans , Mice , Rats , Respiratory Mucosa/virology , Respiratory Tract Infections/virology , Viral Load/drug effects , Viral Proteins/biosynthesis
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