The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes

Long non-coding (lnc) RNAs are numerous and found throughout the mammalian genome, and many are thought to be involved in the regulation of gene expression. However, the majority remain relatively uncharacterised and of uncertain function making the use of model systems to uncover their mode of action valuable. Imprinted lncRNAs target and recruit epigenetic silencing factors to a cluster of imprinted genes on the same chromosome, making them one of the best characterized lncRNAs for silencing distant genes in cis. In this study we examined silencing of the distant imprinted gene Slc22a3 by the lncRNA Airn in the Igf2r imprinted cluster in mouse. Previously we proposed that imprinted lncRNAs may silence distant imprinted genes by disrupting promoter-enhancer interactions by being transcribed through the enhancer, which we called the enhancer interference hypothesis. Here we tested this hypothesis by first using allele-specific chromosome conformation capture (3C) to detect interactions between the Slc22a3 promoter and the locus of the Airn lncRNA that silences it on the paternal chromosome. In agreement with the model, we found interactions enriched on the maternal allele across the entire Airn gene consistent with multiple enhancer-promoter interactions. Therefore, to test the enhancer interference hypothesis we devised an approach to delete the entire Airn gene. However, the deletion showed that there are no essential enhancers for Slc22a2, Pde10a and Slc22a3 within the Airn gene, strongly indicating that the Airn RNA rather than its transcription is responsible for silencing distant imprinted genes. Furthermore, we found that silent imprinted genes were covered with large blocks of H3K27me3 on the repressed paternal allele. Therefore we propose an alternative hypothesis whereby the chromosome interactions may initially guide the lncRNA to target imprinted promoters and recruit repressive chromatin, and that these interactions are lost once silencing is established

Correction: The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes.

[This corrects the article DOI: 10.1371/journal.pgen.1008268.]

Controlling the mitochondrial antisense – role of the SUV3-PNPase complex and its co-factor GRSF1 in mitochondrial RNA surveillance

Transcription of the human mitochondrial genome produces a vast amount of non-coding antisense RNAs. These RNA species can form G-quadraplexes (G4), which affect their decay. We found that the mitochondrial degradosome, a complex of RNA helicase SUPV3L1 (best known as SUV3) and the ribonuclease PNPT1 (also known as PNPase), together with G4-melting protein GRSF1, is a key player in restricting antisense mtRNAs

Virtue ethics and social psychology

Virtue ethics has emerged as an alternative to deontological and utilitarian theory in recent moral philosophy. The basic notion of virtue ethics is to reassert the importance of virtuous character in ethical judgement in contrast to the emphasis on principles and consequences. Since questions of virtue have been largely neglected in modern moral theory, there has been a return to Aristotle’s account of virtue as character. This in turn has been questioned as the basis of virtue ethics and there has been a search for alternative accounts of moral agency. One aspect of this critical reflection on virtue ethics is an engagement with social psychology as a source of criticism of the Aristotelian conception of character and as a more plausible alternative foundation for a theory of moral character with contemporary relevance. This paper aims to introduce this area of moral theory to a psychological audience and reflect on the interpretation of social psychological theory and evidence in criticisms of virtuous character, focusing on the use of Milgram’s (1974) experiments on obedience to authority as an argument for situationism. A number of questions emerge concerning the interpretation and use of social psychological theory and evidence in debates within moral philosophy

Comparison of gene expression inducers.

<p>(A-D) Cells were treated with different concentrations of tetracycline or doxycycline and gene expression was monitored by western blot (A: anti-EGFP, B: anti-THOC5 antibodies, Ponceau S staining of the membrane was performed as a loading control) or flow cytometry (C, D: EGFP fluorescence). (D) Quantitative representation of data shown in panel C. Data are represented as mean ± SD (n = 3). (E) Analysis of the kinetics of expression of the indicated transgenes. Cells were treated with tetracycline, collected after indicated time and analyzed by flow cytometry. Mean fluorescent intensity of EGFP positive cells is shown (mean ± SD, n = 3).</p

Involvement of XRN2 in transcription termination.

<p>(A) Flow cytometry measurement of transgenes expression after 24 hours of induction (EGFP tags XRN2, mCherry is a reporter of miRNA expression). (B) Confocal live cell imaging of EGFP tagged XRN2 and Hoechst 33342 stained nuclei. (C) Western blot analysis of XRN2 protein with anti-XRN2 antibodies. Parental 293 cells and their derivatives analyzed in panel A and B were treated with tetracycline for 72 hours and subjected to western blot. Ponceau S staining of the membrane was performed as a loading control. (D) Meta-gene analysis of transcriptional read-through in wild-type and mutant XRN2 cells. Strand-specific read densities were averaged across 250-bp genomic windows placed directly downstream of 3' ends of highly expressed (TPM > 10), spliced transcripts. The signal is normalized to the average expression detected in the last 250 nt of the analyzed transcripts (250-bp windows upstream to the expected termination site). The shaded part of the graph marks transcripts downstream of transcription termination site (products of transcriptional read-through). It is important to note that lines representing RNA steady-state levels overlay in the part of the graph which correspond to RNAs originating from the transcription upstream of the transcription termination site. This is in contrast to the part of the graph which represent RNA resulting from the unsuccessful transcription termination (shaded part of the graph).</p

SLIC-based DNA cloning strategy.

<p>See main text for detailed description. RE–restriction enzymes used for vector linearization. These are BshTI and NheI in our protocol for universal SLIC. EGFP is an example of tag that can be used. A detailed protocol for the SLIC procedure can be found in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0194887#pone.0194887.s007" target="_blank">S2 Supporting Information</a>.</p