31 research outputs found
Storytelling, women's authority and the 'Old-Wife's Tale': 'The Story of the Bottle of Medicine'
No full textThe focus of this article is a single personal narrative – a Shetland woman’s telling of a story about two girls on a journey to fetch a cure for a sick relative from a wise woman. The story is treated as a cultural document which offers the historian a conduit to a past that is respectful of indigenous woman-centred interpretations of how that past was experienced and understood. The ‘story of the bottle of medicine’ is more than a skilful telling of a local tale; it is a memory practice that provides a path to a deeper and more nuanced understanding of a culture. Applying perspectives from anthropology, oral history and narrative analysis, three sets of questions are addressed: the issue of authenticity; the significance of the narrative structure and storytelling strategies employed; and the nature of the female performance. Ultimately the article asks what this story can tell us about women’s interpretation of their own history
PTBP1 and PTBP2 Repress Nonconserved Cryptic Exons
No full textSummaryThe fidelity of RNA splicing is maintained by a network of factors, but the molecular mechanisms that govern this process have yet to be fully elucidated. We previously found that TDP-43, an RNA-binding protein implicated in neurodegenerative disease, utilizes UG microsatellites to repress nonconserved cryptic exons and prevent their incorporation into mRNA. Here, we report that two well-characterized splicing factors, polypyrimidine tract-binding protein 1 (PTBP1) and polypyrimidine tract-binding protein 2 (PTBP2), are also nonconserved cryptic exon repressors. In contrast to TDP-43, PTBP1 and PTBP2 utilize CU microsatellites to repress both conserved tissue-specific exons and nonconserved cryptic exons. Analysis of these conserved splicing events suggests that PTBP1 and PTBP2 repression is titrated to generate the transcriptome diversity required for neuronal differentiation. We establish that PTBP1 and PTBP2 are members of a family of cryptic exon repressors
Genome-wide mapping of yeast RNA polymerase II termination.
No full textYeast RNA polymerase II (Pol II) terminates transcription of coding transcripts through the polyadenylation (pA) pathway and non-coding transcripts through the non-polyadenylation (non-pA) pathway. We have used PAR-CLIP to map the position of Pol II genome-wide in living yeast cells after depletion of components of either the pA or non-pA termination complexes. We show here that Ysh1, responsible for cleavage at the pA site, is required for efficient removal of Pol II from the template. Depletion of Ysh1 from the nucleus does not, however, lead to readthrough transcription. In contrast, depletion of the termination factor Nrd1 leads to widespread runaway elongation of non-pA transcripts. Depletion of Sen1 also leads to readthrough at non-pA terminators, but in contrast to Nrd1, this readthrough is less processive, or more susceptible to pausing. The data presented here provide delineation of in vivo Pol II termination regions and highlight differences in the sequences that signal termination of different classes of non-pA transcripts
Nrd1 increases the stability of the readthrough transcripts.
No full text<p><b>A.</b> Northern blot and qPCR at different times after addition of rap using the amplicon highlighted in red. <b>B.</b> Histograms representing normalized reads with Nrd1 (grey) and without Nrd1 (black) at the given genomic locations. The Y-axis has been changed to emphasize the differences between treatment with (black) and without rap (grey) for the <i>SNR13-TRS31</i> locus. <b>C.</b> Similar to A but Schultz et. al. <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004632#pgen.1004632-Schulz1" target="_blank">[65]</a> 4tU-seq data is also represented in as a histogram below each graph for the same region of the genome with Nrd1 (grey) and without Nrd1 (black).</p
Mapping Nrd1-dependent terminators.
No full text<p><b>A.</b> Histograms representing of normalized reads for <i>NRD1-FRB</i> with Nrd1 (grey) and without Nrd1 (black) at the given genomic locations. The difference between WT and Nrd1-depleted at every nucleotide is represented as a histogram below each graph. <b>B.</b> Mean reads every 10 bp for 49 snoRNA termination sites showing the highest level of readthrough and 144 CUT termination sites with Nrd1 (dotted) and without Nrd1 (solid). <b>C.</b> Most abundant Nrd1 motif and the most abundant Nab3 motif in the 150 nt 5′ of the snoRNA and CUT terminators, respectively. MEME input parameters were any number of motifs of length 4–15 nt. Results are presented using WebLogo <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004632#pgen.1004632-Crooks1" target="_blank">[92]</a>.</p
New Zealand breakfast cereals: are there sufficient low-sugar, low-sodium options?
No full textWe wish to respond to a letter by Gina Levy of Kellogg (Australia) Pty Ltd – Research and Technology, Australia entitled ‘The New Zealand breakfast cereal category is dynamic and responsive to consumer preferences’, published in Public Health Nutrition⁽¹⁾ in response to our published article ‘The nutritional quality of New Zealand breakfast cereals: an update’⁽²⁾. We thank the author for her interest in our publication and will respond to several of her comment
Ysh1 depletion causes readthrough at pA sites.
No full text<p><b>A.</b> Mean reads every 10 bp for the 500 most frequently used pA sites with (dotted) and without (solid) Ysh1. <b>B.</b> Plot showing percent readthrough of each of 500 pA terminators as a fraction of the total 500 pA terminators. <b>C and D.</b> Histograms representing normalized reads with Ysh1 (grey) and without Ysh1 (black) at the given genomic locations. The TSS with the direction of transcription is indicated by an arrow. Genes and pA sites are represented below each graph and the length of the genome depicted is given in the lower right hand corner.</p
Schematic representation of Pol II termination after removal of non-pA and pA termination factors.
No full text<p>Elongating Pol II (green) terminates pA transcripts (A) after an allosteric change (red) that reduces processivity. (B) Depletion of Ysh1 leads to minimally extended readthrough transcripts but does not block the allosteric change in Pol II. (C) Nrd1 and Nab3 binding recruit Sen1 for termination of non-pA transcripts. (D) Pol II elongation complex lacking Nrd1 does not recognize termination sequences in the nascent transcript and thus does not facilitate the allosteric transition in Pol II. This leads to processive readthrough. (E) Nrd1 and Nab3 recognize terminator sequences allowing the allosteric change in Pol II but depletion of Sen1 blocks removal of Pol II from the template.</p
SNR13 termination region.
No full text<p>NET-Seq data from Churchman and Weissman <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004632#pgen.1004632-Churchman1" target="_blank">[53]</a> are shown above PAR-CLIP data from the <i>SNR13-TRS31</i> locus. The number of NET-seq reads from peaks of Pol II are shown above the lines. The asterisk indicates reads derived from mature snR13 RNA that contaminates the NET-seq library. The calculated <i>SNR13</i> termination region has been expanded to show U-rich sequences (red) surrounding the termination point. The sequences of several antisense CUT termination regions are shown below the SNR13 sequence.</p
