A comprehensive analysis of 3' end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogeneous ribonucleoprotein C on cleavage and polyadenylation

Alternative polyadenylation (APA) is a general mechanism of transcript diversification in mammals, which has been recently linked to proliferative states and cancer. Different 3' untranslated region (3' UTR) isoforms interact with different RNA-binding proteins (RBPs), which modify the stability, translation, and subcellular localization of the corresponding transcripts. Although the heterogeneity of pre-mRNA 3' end processing has been established with high-throughput approaches, the mechanisms that underlie systematic changes in 3' UTR lengths remain to be characterized. Through a uniform analysis of a large number of 3' end sequencing data sets, we have uncovered 18 signals, six of which are novel, whose positioning with respect to pre-mRNA cleavage sites indicates a role in pre-mRNA 3' end processing in both mouse and human. With 3' end sequencing we have demonstrated that the heterogeneous ribonucleoprotein C (HNRNPC), which binds the poly(U) motif whose frequency also peaks in the vicinity of polyadenylation (poly(A)) sites, has a genome-wide effect on poly(A) site usage. HNRNPC-regulated 3' UTRs are enriched in ELAV-like RBP 1 (ELAVL1) binding sites and include those of the CD47 gene, which participate in the recently discovered mechanism of 3' UTR-dependent protein localization (UDPL). Our study thus establishes an up-to-date, high-confidence catalog of 3' end processing sites and poly(A) signals, and it uncovers an important role of HNRNPC in regulating 3' end processing. It further suggests that U-rich elements mediate interactions with multiple RBPs that regulate different stages in a transcript's life cycle

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

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

Primary structure and evolutionary relationship between the adult alpha-globin genes and their 5'-flanking regions of Xenopus laevis and Xenopus tropicalis

To investigate the evolution of globin genes in the genus Xenopus, we have determined the primary structure of the related adult alpha I- and alpha II-globin genes of X. laevis and of the adult alpha-globin gene of X. tropicalis, including their 5'-flanking regions. All three genes are comprised of three exons and two introns at homologous positions. The exons are highly conserved and code for 141 amino acids. By contrast, the corresponding introns vary in length and show considerable divergence. Comparison of 900 bp of the 5'-flanking region revealed that the X. tropicalis gene contains a conserved proximal 310-bp promoter sequence, comprised of the canonical TATA and CCAAT motifs at homologous positions, and five conserved elements in the same order and at similar positions as previously shown for the corresponding genes of X. laevis. We therefore conclude that these conserved upstream elements may represent regulatory sequences for cell-specific regulation of the adult Xenopus globin genes

Load Distribution in the Lumbar Spine During Modeled Compression Depends on Lordosis

Excessive or incorrect loading of lumbar spinal structures is commonly assumed as one of the factors to accelerate degenerative processes, which may lead to lower back pain. Accordingly, the mechanics of the spine under medical conditions, such as scoliosis or spondylolisthesis, is well-investigated. Treatments via both conventional therapy and surgical methods alike aim at restoring a “healthy” (or at least pain-free) load distribution. Yet, surprisingly little is known about the inter-subject variability of load bearings within a “healthy” lumbar spine. Hence, we utilized computer tomography data from 28 trauma-room patients, whose lumbar spines showed no visible sign of degeneration, to construct simplified multi-body simulation models. The subject-specific geometries, measured by the corresponding lumbar lordosis (LL) between the endplates of vertebra L1 and the sacrum, served as ceteris paribus condition in a standardized forward dynamic compression procedure. Further, the influence of stimulating muscles from the M. multifidus group was assessed. For the range of available LL from 28 to 66°, changes in compressive and shear forces, bending moments, as well as facet joint forces between adjacent vertebrae were calculated. While compressive forces tended to decrease with increasing LL, facet forces were tendentiously increasing. Shear forces decreased between more cranial vertebrae and increased between more caudal ones, while bending moments remained constant. Our results suggest that there exist significant, LL-dependent variations in the loading of “healthy” spinal structures, which should be considered when striving for individually appropriate therapeutic measures

Ongoing transients in carbonate compensation

Uptake of anthropogenic CO2 is acidifying the oceans. Over the next 2000 years, this will modify the dissolution and preservation of sedimentary carbonate. By coupling new formulas for the positions of the calcite saturation horizon, zsat, the compensation depth, zcc, and the snowline, zsnow, to a biogeochemical model of the oceanic carbonate system, we evaluate how these horizons will change with ongoing ocean acidification. Our model is an extended Havardton-Bear-type box model, which includes novel kinetic descriptions for carbonate dissolution above, between, and below these critical depths. In the preindustrial ocean, zsat and zcc are at 3939 and 4750 m, respectively. When forced with the IS92a CO2 emission scenario, the model forecasts (1) that zsat will rise rapidly (“runaway” conditions) so that all deep water becomes undersaturated, (2) that zcc will also rise and over 1000 years will pass before it will be stabilized by the dissolution of previously deposited CaCO3, and (3) that zsnow will respond slowly to acidification, rising by ∼1150 m during a 2000 year timeframe. A further simplified model that equates the compensation and saturation depths produces quantitatively different results. Finally, additional feedbacks due to acidification on calcification and increased atmospheric CO2 on organic matter productivity strongly affect the positions of the compensation horizons and their dynamics.

The Fermi GBM Gamma-Ray Burst Spectral Catalog: Four Years Of Data

In this catalog we present the updated set of spectral analyses of GRBs detected by the Fermi Gamma-Ray Burst Monitor (GBM) during its first four years of operation. It contains two types of spectra, time-integrated spectral fits and spectral fits at the brightest time bin, from 943 triggered GRBs. Four different spectral models were fitted to the data, resulting in a compendium of more than 7500 spectra. The analysis was performed similarly, but not identically to Goldstein et al. 2012. All 487 GRBs from the first two years have been re-fitted using the same methodology as that of the 456 GRBs in years three and four. We describe, in detail, our procedure and criteria for the analysis, and present the results in the form of parameter distributions both for the observer-frame and rest-frame quantities. The data files containing the complete results are available from the High-Energy Astrophysics Science Archive Research Center (HEASARC).Comment: Accepted for publication in ApJ