Reannotation of the CELO genome characterizes a set of previously unassigned open reading frames and points to novel modes of host interaction in avian adenoviruses

BACKGROUND: The genome of the avian adenovirus Chicken Embryo Lethal Orphan (CELO) has two terminal regions without detectable homology in mammalian adenoviruses that are left without annotation in the initial analysis. Since adenoviruses have been a rich source of new insights into molecular cell biology and practical applications of CELO as gene a delivery vector are being considered, this genome appeared worth revisiting. We conducted a systematic reannotation and in-depth sequence analysis of the CELO genome. RESULTS: We describe a strongly diverged paralogous cluster including ORF-2, ORF-12, ORF-13, and ORF-14 with an ATPase/helicase domain most likely acquired from adeno-associated parvoviruses. None of these ORFs appear to have retained ATPase/helicase function and alternative functions (e.g. modulation of gene expression during the early life-cycle) must be considered in an adenoviral context. Further, we identified a cluster of three putative type-1-transmembrane glycoproteins with IG-like domains (ORF-9, ORF-10, ORF-11) which are good candidates to substitute for the missing immunomodulatory functions of mammalian adenoviruses. ORF-16 (located directly adjacent) displays distant homology to vertebrate mono-ADP-ribosyltransferases. Members of this family are known to be involved in immuno-regulation and similiar functions during CELO life cycle can be considered for this ORF. Finally, we describe a putative triglyceride lipase (merged ORF-18/19) with additional domains, which can be expected to have specific roles during the infection of birds, since they are unique to avian adenoviruses and Marek's disease-like viruses, a group of pathogenic avian herpesviruses. CONCLUSIONS: We could characterize most of the previously unassigned ORFs pointing to functions in host-virus interaction. The results provide new directives for rationally designed experiments

Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals

Long intergenic noncoding RNAs (lincRNAs) play diverse regulatory roles in human development and disease, but little is known about their evolutionary history and constraint. Here, we characterize human lincRNA expression patterns in nine tissues across six mammalian species and multiple individuals. Of the 1898 human lincRNAs expressed in these tissues, we find orthologous transcripts for 80% in chimpanzee, 63% in rhesus, 39% in cow, 38% in mouse, and 35% in rat. Mammalian-expressed lincRNAs show remarkably strong conservation of tissue specificity, suggesting that it is selectively maintained. In contrast, abundant splice-site turnover suggests that exact splice sites are not critical. Relative to evolutionarily young lincRNAs, mammalian-expressed lincRNAs show higher primary sequence conservation in their promoters and exons, increased proximity to protein-coding genes enriched for tissue-specific functions, fewer repeat elements, and more frequent single-exon transcripts. Remarkably, we find that ∼20% of human lincRNAs are not expressed beyond chimpanzee and are undetectable even in rhesus. These hominid-specific lincRNAs are more tissue specific, enriched for testis, and faster evolving within the human lineage.National Institutes of Health (U.S.) (U54-HG004555)National Institutes of Health (U.S.) (R01-HG004037)National Science Foundation (U.S.) (CAREER 0644282

MAGNOLIA: multiple alignment of protein–coding and structural RNA sequences

MAGNOLIA is a new software for multiple alignment of nucleic acid sequences, which are recognized to be hard to align. The idea is that the multiple alignment process should be improved by taking into account the putative function of the sequences. In this perspective, MAGNOLIA is especially designed for sequences that are intended to be either protein-coding or structural RNAs. It extracts information from the similarities and differences in the data, and searches for a specific evolutionary pattern between sequences before aligning them. The alignment step then incorporates this information to achieve higher accuracy. The website is available at http://bioinfo.lifl.fr/magnolia

A benchmark of multiple sequence alignment programs upon structural RNAs

To date, few attempts have been made to benchmark the alignment algorithms upon nucleic acid sequences. Frequently, sophisticated PAM or BLOSUM like models are used to align proteins, yet equivalents are not considered for nucleic acids; instead, rather ad hoc models are generally favoured. Here, we systematically test the performance of existing alignment algorithms on structural RNAs. This work was aimed at achieving the following goals: (i) to determine conditions where it is appropriate to apply common sequence alignment methods to the structural RNA alignment problem. This indicates where and when researchers should consider augmenting the alignment process with auxiliary information, such as secondary structure and (ii) to determine which sequence alignment algorithms perform well under the broadest range of conditions. We find that sequence alignment alone, using the current algorithms, is generally inappropriate <50–60% sequence identity. Second, we note that the probabilistic method ProAlign and the aging Clustal algorithms generally outperform other sequence-based algorithms, under the broadest range of applications

Kapitalverbrechen und Medien-Hype. Lehren aus dem Inzestfall von Amstetten und dem Entführungsfall Kampusch

Aufsehen erregende Kapitalverbrechen, die im ersten Halbjahr 2008 in Österreich verübt oder - weil sie älteren Datums waren - durch äußere Einflüsse neu aufgerollt wurden, lösten eine ungewohnt intensive medienethische und medienrechtliche Debatte aus. Sie wurde in den meisten Medien, aber auch auf Justizebene und bis hinein ins Parlament geführt und bewirkte eine Sensibilisierung bezüglich Opferschutz und Schutz der Privatsphäre in der Berichterstattung. Sollte es im Herbst nach sechs Jahren peinlicher Pause zur Wiederbelebung eines „Presserates" in Österreich kommen, hätte auch daran die Medien- und Opferschutzdebatte einen wesentlichen Anteil. Es gibt inzwischen weit mehr Verständnis für die Komplexität der Materie, wenn auch nicht unbedingt eine größere Sicherheit in der Beurteilung medienethischer Grenzfälle. Soweit die positive Seite der Medaille. (...

Und bitte nicht mehr „Content“ sagen. Die Zeit ist reif, von der gedanklichen Trennung von Print und Online abzugehen

Die Rahmenbedingungen für Qualität sind besser, als sie beschrieben werden. Qualität ist bei führenden Journalisten gut aufgehoben. Wenn den Verlagsmanagern in wirtschaftlich angespannten Jahren die Lust vergeht, sich mit solchen Nebenfragen zu befassen, sind es Journalisten, die das Qualitätsanliegen hinüberretten. Über Boulevardisierung zu klagen, bringt wenig – sie ist sogar in der politischen Klasse Realität geworden und bedauerlich. Unbeirrt sollte die Mehrheit der Journalisten, egal ob in Print oder Online, einer praktischen Berufsethik im Kampf um das richtige Wort zum Durchbruch verhelfen. Abseits des Boulevards breitet sich nämlich selbst in besten Medien ein Mainstream journalistischer Gedankenlosigkeit aus, die einen sich selbst wiederholenden Unsinn erzeugt. Unter dem Modebegriff Content fällt sie als solche gar nicht auf. EnglishAnd Please Refrain from Saying „Content“. The time is Ripe to Leave the Notional Separation of Print and Online Behind.The general conditions regarding quality are better than they are being described. Quality is well looked-after among leading journalists. When, during economically tense years, publishing managers lose their inclination to occupy themselves with such “side issues”, it is the journalists themselves who forward the cause of quality. To complain about “Boulevardisation” doesn’t bring much – among the political class it has even become a reality and is most unfortunate. Undeterred, the majority of journalists, irrespective of from Print or Online, should help to bring about a breakthrough regarding practical professional ethics in the battle for the right word. Apart from the boulevard namely, even among the foremost media, a mainstream of journalistic mindlessness is spreading, which creates a self-repeating loop of nonsense. Falling under the vogue expression “Content”, it isn’t even being noticed as such.

The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures

Many non-coding RNA genes and cis-acting regulatory elements of mRNAs contain RNA secondary structures that are critical for their function. Such functional RNAs can be predicted on the basis of thermodynamic stability and evolutionary conservation. We present a web server that uses the RNAz algorithm to detect functional RNA structures in multiple alignments of nucleotide sequences. The server provides access to a complete and fully automatic analysis pipeline that allows not only to analyze single alignments in a variety of formats, but also to conduct complex screens of large genomic regions. Results are presented on a website that is illustrated by various structure representations and can be downloaded for local view. The web server is available at: rna.tbi.univie.ac.at/RNAz

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo

RNA has a dual role as an informational molecule and a direct effector of biological tasks. The latter function is enabled by RNA’s ability to adopt complex secondary and tertiary folds and thus has motivated extensive computational and experimental efforts for determining RNA structures. Existing approaches for evaluating RNA structure have been largely limited to in vitro systems, yet the thermodynamic forces which drive RNA folding in vitro may not be sufficient to predict stable RNA structures in vivo. Indeed, the presence of RNA-binding proteins and ATP-dependent helicases can influence which structures are present inside cells. Here we present an approach for globally monitoring RNA structure in native conditions in vivo with single-nucleotide precision. This method is based on in vivo modification with dimethyl sulphate (DMS), which reacts with unpaired adenine and cytosine residues, followed by deep sequencing to monitor modifications. Our data from yeast and mammalian cells are in excellent agreement with known messenger RNA structures and with the high-resolution crystal structure of the Saccharomyces cerevisiae ribosome. Comparison between in vivo and in vitro data reveals that in rapidly dividing cells there are vastly fewer structured mRNA regions in vivo than in vitro. Even thermostable RNA structures are often denatured in cells, highlighting the importance of cellular processes in regulating RNA structure. Indeed, analysis of mRNA structure under ATP-depleted conditions in yeast shows that energy-dependent processes strongly contribute to the predominantly unfolded state of mRNAs inside cells. Our studies broadly enable the functional analysis of physiological RNA structures and reveal that, in contrast to the Anfinsen view of protein folding whereby the structure formed is the most thermodynamically favourable, thermodynamics have an incomplete role in determining mRNA structure in vivo

Strategies for measuring evolutionary conservation of RNA secondary structures

<p>Abstract</p> <p>Background</p> <p>Evolutionary conservation of RNA secondary structure is a typical feature of many functional non-coding RNAs. Since almost all of the available methods used for prediction and annotation of non-coding RNA genes rely on this evolutionary signature, accurate measures for structural conservation are essential.</p> <p>Results</p> <p>We systematically assessed the ability of various measures to detect conserved RNA structures in multiple sequence alignments. We tested three existing and eight novel strategies that are based on metrics of folding energies, metrics of single optimal structure predictions, and metrics of structure ensembles. We find that the folding energy based SCI score used in the RNAz program and a simple base-pair distance metric are by far the most accurate. The use of more complex metrics like for example tree editing does not improve performance. A variant of the SCI performed particularly well on highly conserved alignments and is thus a viable alternative when only little evolutionary information is available. Surprisingly, ensemble based methods that, in principle, could benefit from the additional information contained in sub-optimal structures, perform particularly poorly. As a general trend, we observed that methods that include a consensus structure prediction outperformed equivalent methods that only consider pairwise comparisons.</p> <p>Conclusion</p> <p>Structural conservation can be measured accurately with relatively simple and intuitive metrics. They have the potential to form the basis of future RNA gene finders, that face new challenges like finding lineage specific structures or detecting mis-aligned sequences.</p