NCL Data2026 · dataset
<p>RDME–ODE simulation trajectory (60 min, with ER, chromosome, and ribosome competition).</p><p>RDME–ODE simulation trajectory (60 min, with ER, chromosome, and ribosome competition).</p>
NCL Data2026 · dataset
<p>Fold change in total GAL protein abundance at 111 mM galactose (2% [w/v]). Values show the ratio of induced (111 mM galactose) to basal (raffinose) protein levels from Paulo et al. [37], Ramsey et al. [18], and our simplified ODE simulations. Bold values indicate the model result closest to the experimental data.</p><p>Fold change in total GAL protein abundance at 111 mM galactose (2% [w/v]). Values show the ratio of induced (111 mM galactose) to basal (raffinose) protein levels from Paulo et al. [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1014811#pcbi.1014811.ref037" target="_blank">37</a>], Ramsey et al. [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.p
NCL Data2026 · dataset
<p>Cryo-ET movie of wild-type <i>S. cerevisiae</i> showing 3D annotations of peripheral ER (pmaER) and cytosolic ribosomes, highlighting ribosomes with peptide exit tunnels within 8 nm of the ER.</p><p>Cryo-ET movie of wild-type <i>S. cerevisiae</i> showing 3D annotations of peripheral ER (pmaER) and cytosolic ribosomes, highlighting ribosomes with peptide exit tunnels within 8 nm of the ER.</p>
NCL Data2026 · dataset
<p>Fold change in GAL protein abundance at 11.1 mM galactose (0.2% [w/v]) across modeling frameworks. The fold change closest to Ramsey’s ODE result is highlighted in bold for each species. In Ramsey’s work, they only experimentally measured GAL1-GFP fluorescence level, all other fold changes came from his ODE model.</p><p>Fold change in GAL protein abundance at 11.1 mM galactose (0.2% [w/v]) across modeling frameworks. The fold change closest to Ramsey’s ODE result is highlighted in bold for each species. In Ramsey’s work, they only experimentally measured GAL1-GFP fluorescence level, all other fold changes came from his ODE model.</p>
NCL Data2026 · dataset
<p>Cryo-ET movie of wild-type <i>S. cerevisiae</i> showing the nucleus with the nuclear envelope and central cisternal ER (cecER) continuous with the nuclear envelope, and cytosol densely populated with ribosomes.</p><p>Cryo-ET movie of wild-type <i>S. cerevisiae</i> showing the nucleus with the nuclear envelope and central cisternal ER (cecER) continuous with the nuclear envelope, and cytosol densely populated with ribosomes.</p>
NCL Data2026 · dataset
<p>RDME–ODE simulation trajectory (60 min, with ER and chromosome).</p><p>RDME–ODE simulation trajectory (60 min, with ER and chromosome).</p>
NCL Data2026 · dataset
<p>RDME–ODE simulation trajectory (60 min, without chromosome and ER).</p><p>RDME–ODE simulation trajectory (60 min, without chromosome and ER).</p>
NCL Data2026 · dataset
<p>Cryo-ET movie of wild-type <i>S. cerevisiae</i> showing cytosol with ribosomes and peripheral ER subdomains, including plasma membrane–associated ER (pmaER) and tubular ER (tubER).</p><p>Cryo-ET movie of wild-type <i>S. cerevisiae</i> showing cytosol with ribosomes and peripheral ER subdomains, including plasma membrane–associated ER (pmaER) and tubular ER (tubER).</p>
NCL Data2026 · dataset
<p>Comparison of ribosome surface densities on ER regions as calculated in previous literature and in the present study. (Units: ribosomes/).</p><p>Comparison of ribosome surface densities on ER regions as calculated in previous literature and in the present study. (Units: ribosomes/).</p>
NCL Data2026 · dataset
<p>Final yeast geometry with ER organelle used in the simulation.</p><p>Final yeast geometry with ER organelle used in the simulation.</p>
ZivaHub + Deakin Research Online + DMU Figshare + UCL Research Data Repository + HKU DataHub + Swinburne Figshare + DaYta Ya Rona + SUNScholarData + figshare + Loughborough Research Repository + GRANTS Data + UP Research Data Repository2026 · Astronomical catalogue
<p>Strains used in this study.</p><div><p>Ribosomal proteins, because of their RNA-binding capacity, may engage various cellular RNAs and fulfill non-ribosomal roles. Previously, we and others described the intergenic regulation mediated by splicing of <i>RPL22</i> paralogs in <i>Saccharomyces cerevisiae</i>. Here, we prepared a panel of <i>RPL22A/B</i> intronic mutants with respect to their RNAfold-predicted features and analyzed
ZivaHub + Deakin Research Online + DMU Figshare + UCL Research Data Repository2026 · dataset
<p>Raw images of gels and blots.</p><div><p>Ribosomal proteins, because of their RNA-binding capacity, may engage various cellular RNAs and fulfill non-ribosomal roles. Previously, we and others described the intergenic regulation mediated by splicing of <i>RPL22</i> paralogs in <i>Saccharomyces cerevisiae</i>. Here, we prepared a panel of <i>RPL22A/B</i> intronic mutants with respect to their RNAfold-predicted features and analyzed
ZivaHub + Deakin Research Online + DMU Figshare + UCL Research Data Repository2026 · dataset
<p>Splicing-inhibitory mutations block <i>RPL22</i> intron reporter splicing <i>in vivo</i> irrespective of the presence of the Rpl22 protein.</p><p>(A) Mutants stabilizing the inhibitory conformation of <i>RPL22B</i>i inhibited splicing irrespective of the presence of the Rpl22 protein <i>in vivo.</i> The splicing efficiency of <i>RPL22B-CUP1</i> reporters was tested in <i>rpl22a</i>Δ <i>rpl22b</i>Δ strain harboring the plasmid pVTU260/RPL22A for overexpression of Rpl22A and in the same strain transformed with empty vector. Semi-quantitati
ZivaHub + Deakin Research Online + DMU Figshare + UCL Research Data Repository2026 · dataset
<p>Rpl22 homologs complemented the extra ribosomal function of Rpl22A in <i>S. cerevisiae.</i></p><p>(A) Projection of invariant amino acids on the surface of Rpl22A of <i>S. cerevisiae.</i> The structure of Rpl22 and 25S rRNA was extracted from the ribosome structure (PDB: 4V88) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0359197#pone.0359197.ref064" target="_blank">64</a>] using the ChimeraX program (<a href="https://www.rbvi.ucsf.edu/chimerax" target="_blank">http
ZivaHub + Deakin Research Online + DMU Figshare + UCL Research Data Repository2026 · dataset
<p>Secondary structure prediction of the <i>RPL22B</i> intron by RNAfold is supported by DMS reactivity data published previously.</p><p>Secondary structure prediction of the <i>RPL22B</i> intron by RNAfold is supported by DMS reactivity data published previously.</p>
ZivaHub + Deakin Research Online + DMU Figshare + UCL Research Data Repository + HKU DataHub + Swinburne Figshare + DaYta Ya Rona + SUNScholarData + figshare + Loughborough Research Repository + GRANTS Data + UP Research Data Repository2026 · Astronomical catalogue
<p>Primers used in this study.</p><div><p>Ribosomal proteins, because of their RNA-binding capacity, may engage various cellular RNAs and fulfill non-ribosomal roles. Previously, we and others described the intergenic regulation mediated by splicing of <i>RPL22</i> paralogs in <i>Saccharomyces cerevisiae</i>. Here, we prepared a panel of <i>RPL22A/B</i> intronic mutants with respect to their RNAfold-predicted features and analyzed
ZivaHub + Deakin Research Online + DMU Figshare + UCL Research Data Repository2026 · dataset
<p>RNAfold predicted structures of introns and their mutants tested in Fig 4.</p><p>RNAfold predicted structures of introns and their mutants tested in Fig 4.</p>
ZivaHub + Deakin Research Online + DMU Figshare + UCL Research Data Repository2026 · dataset
<p>Levels of heterologous Rpl22 proteins in the experiments of Fig 7.</p><p>Levels of heterologous Rpl22 proteins in the experiments of Fig 7.</p>
ZivaHub + Deakin Research Online + DMU Figshare + UCL Research Data Repository2026 · dataset
<p>RNAfold predicted structures of introns and their mutants tested in Fig 5.</p><p>RNAfold predicted structures of introns and their mutants tested in Fig 5.</p>
ZivaHub + Deakin Research Online + DMU Figshare + UCL Research Data Repository2026 · dataset
<p>Splicing-permissive mutations did not block <i>RPL22B</i>i splicing <i>in vivo</i> irrespective of the presence of the Rpl22 protein.</p><p>The experiment was done and the figure was formatted as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0359197#pone.0359197.g002" target="_blank">Fig 2</a>. (A) Mutants disrupting the inhibitory conformation of <i>RPL22B</i>i were splicing permissive. See the legend of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0359197#pone.0359197.g002" targ
ZivaHub + Deakin Research Online + DMU Figshare + UCL Research Data Repository2026 · dataset
<p>RNAfold predicted structures of introns and their mutants tested in Fig 3.</p><p>RNAfold predicted structures of introns and their mutants tested in Fig 3.</p>
ZivaHub + Deakin Research Online + DMU Figshare + UCL Research Data Repository + HKU DataHub + Swinburne Figshare + DaYta Ya Rona + SUNScholarData + figshare + Loughborough Research Repository + GRANTS Data + UP Research Data Repository2026 · Astronomical catalogue
<p>List of intronic manipulations tested.</p><div><p>Ribosomal proteins, because of their RNA-binding capacity, may engage various cellular RNAs and fulfill non-ribosomal roles. Previously, we and others described the intergenic regulation mediated by splicing of <i>RPL22</i> paralogs in <i>Saccharomyces cerevisiae</i>. Here, we prepared a panel of <i>RPL22A/B</i> intronic mutants with respect to their RNAfold-predicted features and analyzed
ZivaHub + Deakin Research Online + DMU Figshare + UCL Research Data Repository2026 · dataset
<p>The main stem loop of the inhibitory structure of <i>RPL22B</i>i was necessary but not sufficient for splicing inhibition.</p><p>The experiment was done and the figure was formatted as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0359197#pone.0359197.g002" target="_blank">Fig 2</a>. (A) The inhibitory mechanism required that specific structural details of the I structure remain intact. In the mutants analyzed in this set, the main stem loop is predicted to form. Melting of Loop2 of the I struc
ZivaHub + Deakin Research Online + DMU Figshare + UCL Research Data Repository2026 · dataset
<p>The reporter constructs used to analyze RPL22B splicing <i>in vivo.</i></p><p>The reporter constructs used to analyze RPL22B splicing <i>in vivo.</i></p>
ZivaHub + Deakin Research Online + DMU Figshare + UCL Research Data Repository2026 · dataset
<p>I ⇋ P interconversion of the intronic RNA would require an extensive change of base pairs.</p><p>I ⇋ P interconversion of the intronic RNA would require an extensive change of base pairs.</p>