Browsing by Subject "rRNA"

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  • Ford, Brittany; Wei, Ting; Liu, Hester; Scull, Catherine E.; Najmi, Saman M.; Pitts, Stephanie; Fan, Wenjun; Schneider, David A.; Laiho, Marikki (2023)
  • Evsyukov, Valentin; Domanskyi, Andrii; Bierhoff, Holger; Gispert, Suzana; Mustafa, Rasem; Schlaudraff, Falk; Liss, Birgit; Parlato, Rosanna (2017)
    Genetic mutations underlying neurodegenerative disorders impair ribosomal DNA (rDNA) transcription suggesting that nucleolar dysfunction could be a novel pathomechanism in polyglutamine diseases and in certain forms of amyotrophic lateral sclerosis/frontotemporal dementia. Here, we investigated nucleolar activity in pre-symptomatic digenic models of Parkinson's disease (PD) that model the multifactorial aetiology of this disease. To this end, we analysed a novel mouse model mildly overexpressing mutant human alpha-synuclein (hA53T-SNCA) in a PTEN-induced kinase 1 (PINK1/ PARK6) knockout background and mutant mice lacking both DJ-1 (also known as PARK7) and PINK1. We showed that overexpressed hA53T-SNCA localizes to the nucleolus. Moreover, these mutants show a progressive reduction of rDNA transcription linked to a reduced mouse lifespan. By contrast, rDNA transcription is preserved in DJ-1/PINK1 double knockout (DKO) mice. mRNA levels of the nucleolar transcription initiation factor 1A (TIF-IA, also known as RRN3) decrease in the substantia nigra of individuals with PD. Because loss of TIF-IA, as a tool to mimic nucleolar stress, increases oxidative stress and because DJ-1 and PINK1 mutations result in higher vulnerability to oxidative stress, we further explored the synergism between these PD-associated genes and impaired nucleolar function. By the conditional ablation of TIF-IA, we blocked ribosomal RNA (rRNA) synthesis in adult dopaminergic neurons in a DJ-1/PINK1 DKO background. However, the early phenotype of these triple knockout mice was similar to those mice exclusively lacking TIF-IA. These data sustain a model in which loss of DJ-1 and PINK1 does not impair nucleolar activity in a pre-symptomatic stage. This is the first study to analyse nucleolar function in digenic PD models. We can conclude that, at least in these models, the nucleolus is not as severely disrupted as previously shown in DA neurons from PD patients and neurotoxin-based PD mouse models. The results also show that the early increase in rDNA transcription and nucleolar integrity may represent specific homeostatic responses in these digenic pre-symptomatic PD models.
  • Mengual, Ximo; Ståhls, Gunilla; Skevington, Jeffrey H. (2020)
    Phylogenetic relationships of theSphaerophorialineage (SphaerophoriaLe Peletier & Audinet-Serville and related genera) were inferred based on molecular characters, with the specific aim to infer the phylogenetic placement of the AfrotropicalSphaerophoriaspecies andLoveridgeana beattieivan Doesburg & van Doesburg. Three molecular markers were used, i.e., the mitochondrial protein-coding gene cytochrome c oxidase subunit I (COI) and the nuclear 28S and 18S ribosomal RNA genes. TheSphaerophorialineage generaExallandraVockeroth andLoveridgeanawere resolved within the genusSphaerophoria, and the IndomalayanEosphaerophoriaFrey was placed sister toCitrogrammaVockeroth, both related to a large species radiation from the New World.FaziaShannon andAllograptaOsten Sacken were recovered as non-monophyletic. Our results recovered two differentFaziaclades with dissimilar natural history resulted from our analyses, andAllograptaspecies were resolved into two clades, one with Nearctic and Neotropical species and a second clade with species from Oceanian, Indomalayan and Afrotropical Regions.Exallandrais considered a subgenus ofSphaerophoria,S. (Exallandra)stat. rev.,andSphaerophoria cinctifacies(Speiser)n. comb.a member of this subgenus together withS. loewiiZetterstedt. A newSphaerophoriasubgenus is designatedS.(Loveridgeana)stat. includeS. beattiein. comb.and the South African species, i.e.,S. quadrituberculataBezzi,S. retrocurvaHull, andS. aff.retrocurva. Based on their phylogenetic distinctiveness, functional traits, and ecological relevance we do recommend further ecological study and protection efforts for this Afrotropical group of pollinators.
  • Wei, Ting; Najmi, Saman M.; Liu, Hester; Peltonen, Karita; Kucerova, Alena; Schneider, David A.; Laiho, Marikki (2018)
    Summary Inhibition of RNA polymerase I (Pol I) is a promising strategy for modern cancer therapy. BMH-21 is a first-in-class small molecule that inhibits Pol I transcription and induces degradation of the enzyme, but how this exceptional response is enforced is not known. Here, we define key elements requisite for the response. We show that Pol I preinitiation factors and polymerase subunits (e.g., RPA135) are required for BMH-21-mediated degradation of RPA194. We further find that Pol I inhibition and induced degradation by BMH-21 are conserved in yeast. Genetic analyses demonstrate that mutations that induce transcription elongation defects in Pol I result in hypersensitivity to BMH-21. Using a fully reconstituted Pol I transcription assay, we show that BMH-21 directly impairs transcription elongation by Pol I, resulting in long-lived polymerase pausing. These studies define a conserved regulatory checkpoint that monitors Pol I transcription and is activated by therapeutic intervention.
  • Fan, Wenjun; Eklund, Eetu; Sherman, Rachel M.; Liu, Hester; Pitts, Stephanie; Ford, Brittany; Rajeshkumar, N.; Laiho, Marikki (2022)
    Polymorphism drives survival under stress and provides adaptability. Genetic polymorphism of ribosomal RNA (rRNA) genes derives from internal repeat variation of this multicopy gene, and from interindividual variation. A considerable amount of rRNA sequence heterogeneity has been proposed but has been challenging to estimate given the scarcity of accurate reference sequences. We identified four rDNA copies on chromosome 21 (GRCh38) with 99% similarity to recently introduced reference sequence KY962518.1. We customized a GATK bioinformatics pipeline using the four rDNA loci, spanning a total 145 kb, for variant calling and used high-coverage whole-genome sequencing (WGS) data from the 1000 Genomes Project to analyze variants in 2504 individuals from 26 populations. We identified a total of 3791 variant positions. The variants positioned nonrandomly on the rRNA gene. Invariant regions included the promoter, early 5 ' ETS, most of 18S, 5.8S, ITS1, and large areas of the intragenic spacer. A total of 470 variant positions were observed on 28S rRNA. The majority of the 28S rRNA variants were located on highly flexible human-expanded rRNA helical folds ES7L and ES27L, suggesting that these represent positions of diversity and are potentially under continuous evolution. Several variants were validated based on RNA-seq analyses. Population analyses showed remarkable ancestry-linked genetic variance and the presence of both high penetrance and frequent variants in the 5 ' ETS, ITS2, and 28S regions segregating according to the continental populations. These findings provide a genetic view of rRNA gene array heterogeneity and raise the need to functionally assess how the 28S rRNA variants affect ribosome functions.