3'-UTR SIRF: A database for identifying clusters of whort interspersed repeats in 3' untranslated regions

<p>Abstract</p> <p>Background</p> <p>Short (~5 nucleotides) interspersed repeats regulate several aspects of post-transcriptional gene expression. Previously we developed an algorithm (REPFIND) that assigns P-values to all repeated motifs in a given nucleic acid sequence and reliably identifies clusters of short CAC-containing motifs required for mRNA localization in <it>Xenopus </it>oocytes.</p> <p>Description</p> <p>In order to facilitate the identification of genes possessing clusters of repeats that regulate post-transcriptional aspects of gene expression in mammalian genes, we used REPFIND to create a database of all repeated motifs in the 3' untranslated regions (UTR) of genes from the Mammalian Gene Collection (MGC). The MGC database includes seven vertebrate species: human, cow, rat, mouse and three non-mammalian vertebrate species. A web-based application was developed to search this database of repeated motifs to generate species-specific lists of genes containing specific classes of repeats in their 3'-UTRs. This computational tool is called 3'-UTR SIRF (<b>S</b>hort <b>I</b>nterspersed <b>R</b>epeat <b>F</b>inder), and it reveals that hundreds of human genes contain an abundance of short CAC-rich and CAG-rich repeats in their 3'-UTRs that are similar to those found in mRNAs localized to the neurites of neurons. We tested four candidate mRNAs for localization in rat hippocampal neurons by <it>in situ </it>hybridization. Our results show that two candidate CAC-rich (<it>Syntaxin 1B </it>and <it>Tubulin β4</it>) and two candidate CAG-rich (<it>Sec61α </it>and <it>Syntaxin 1A</it>) mRNAs are localized to distal neurites, whereas two control mRNAs lacking repeated motifs in their 3'-UTR remain primarily in the cell body.</p> <p>Conclusion</p> <p>Computational data generated with 3'-UTR SIRF indicate that hundreds of mammalian genes have an abundance of short CA-containing motifs that may direct mRNA localization in neurons. <it>In situ </it>hybridization shows that four candidate mRNAs are localized to distal neurites of cultured hippocampal neurons. These data suggest that short CA-containing motifs may be part of a widely utilized genetic code that regulates mRNA localization in vertebrate cells. The use of 3'-UTR SIRF to search for new classes of motifs that regulate other aspects of gene expression should yield important information in future studies addressing <it>cis</it>-regulatory information located in 3'-UTRs.</p

Localisation of RNAs into the germ plasm of vitellogenic xenopus oocytes

We have studied the localisation of mRNAs in full-grown Xenopus laevis oocytes by injecting fluorescent RNAs, followed by confocal microscopy of the oocyte cortex. Concentrating on RNA encoding the Xenopus Nanos homologue, nanos1 (formerly Xcat2), we find that it consistently localised into aggregated germ plasm ribonucleoprotein (RNP) particles, independently of cytoskeletal integrity. This implies that a diffusion/entrapment-mediated mechanism is active, as previously reported for previtellogenic oocytes. Sometimes this was accompanied by localisation into scattered particles of the “late”, Vg1/VegT pathway; occasionally only late pathway localisation was seen. The Xpat RNA behaved in an identical fashion and for neither RNA was the localisation changed by any culture conditions tested. The identity of the labelled RNP aggregates as definitive germ plasm was confirmed by their inclusion of abundant mitochondria and co-localisation with the germ plasm protein Hermes. Further, the nanos1/Hermes RNP particles are interspersed with those containing the germ plasm protein Xpat. These aggregates may be followed into the germ plasm of unfertilized eggs, but with a notable reduction in its quantity, both in terms of injected molecules and endogenous structures. Our results conflict with previous reports that there is no RNA localisation in large oocytes, and that during mid-oogenesis even germ plasm RNAs localise exclusively by the late pathway. We find that in mid oogenesis nanos1 RNA also localises to germ plasm but also by the late pathway. Late pathway RNAs, Vg1 and VegT, also may localise into germ plasm. Our results support the view that mechanistically the two modes of localisation are extremely similar, and that in an injection experiment RNAs might utilise either pathway, the distinction in fates being very subtle and subject to variation. We discuss these results in relation to their biological significance and the results of others

Discrimination of common and unique RNA-binding activities among Fragile X mental retardation protein paralogs

Fragile X mental retardation is caused by loss-of-function of a single gene encoding FMRP, an RNA-binding protein that harbors three canonical RNA-binding domains, two KH-type and one RGG box. Two autosomal paralogs of FMRP, FXR1P and FXR2P, are similar to FMRP in their overall structure, including the presence of putative RNA-binding domains, but to what extent they provide functional redundancy with FMRP is unclear. Although FMRP has been characterized as a polyribosome-associated regulator of translation, less is known about the functions of FXR1P and FXR2P. For example, FMRP binds intramolecular G-quadruplex and kissing complex RNA (kcRNA) ligands via the RGG box and KH2 domain, respectively, although the RNA ligands of FXR1P and FXR2P are unknown. Here we demonstrate that FXR1P and FXR2P KH2 domains bind kcRNA ligands with the same affinity as the FMRP KH2 domain although other KH domains do not. RNA ligand recognition by this family is highly conserved, as the KH2 domain of the single Drosophila ortholog, dFMRP, also binds kcRNA. kcRNA was able to displace FXR1P and FXR2P from polyribosomes as it does for FMRP, and this displacement was FMRP-independent. This suggests that all three family members recognize the same binding site on RNA mediating their polyribosome association, and that they may be functionally redundant with regard to this aspect of translational control. In contrast, FMRP is unique in its ability to recognize G-quadruplexes, suggesting the FMRP RGG domain may play a non-redundant role in the pathophysiology of the disease

Sources of increase in lowermost stratospheric sulphurous and carbonaceous aerosol background concentrations during 1999–2008 derived from CARIBIC flights

This study focuses on sulphurous and carbonaceous aerosol, the major constituents of particulate matter in the lowermost stratosphere (LMS), based on in situ measurements from 1999 to 2008. Aerosol particles in the size range of 0.08–2 µm were collected monthly during intercontinental flights with the CARIBIC passenger aircraft, presenting the first long-term study on carbonaceous aerosol in the LMS. Elemental concentrations were derived via subsequent laboratory-based ion beam analysis. The stoichiometry indicates that the sulphurous fraction is sulphate, while an O/C ratio of 0.2 indicates that the carbonaceous aerosol is organic. The concentration of the carbonaceous component corresponded on average to approximately 25% of that of the sulphurous, and could not be explained by forest fires or biomass burning, since the average mass ratio of Fe to K was 16 times higher than typical ratios in effluents from biomass burning. The data reveal increasing concentrations of particulate sulphur and carbon with a doubling of particulate sulphur from 1999 to 2008 in the northern hemisphere LMS. Periods of elevated concentrations of particulate sulphur in the LMS are linked to downward transport of aerosol from higher altitudes, using ozone as a tracer for stratospheric air. Tropical volcanic eruptions penetrating the tropical tropopause are identified as the likely cause of the particulate sulphur and carbon increase in the LMS, where entrainment of lower tropospheric air into volcanic jets and plumes could be the cause of the carbon increase

Total volcanic stratospheric aerosol optical depths and implications for global climate change

Understanding the cooling effect of recent volcanoes is of particular interest in the context of the post-2000 slowing of the rate of global warming. Satellite observations of aerosol optical depth above 15 km have demonstrated that small-magnitude volcanic eruptions substantially perturb incoming solar radiation. Here we use lidar, Aerosol Robotic Network, and balloon-borne observations to provide evidence that currently available satellite databases neglect substantial amounts of volcanic aerosol between the tropopause and 15 km at middle to high latitudes and therefore underestimate total radiative forcing resulting from the recent eruptions. Incorporating these estimates into a simple climate model, we determine the global volcanic aerosol forcing since 2000 to be −0.19 ± 0.09 Wm−2. This translates into an estimated global cooling of 0.05 to 0.12°C. We conclude that recent volcanic events are responsible for more post-2000 cooling than is implied by satellite databases that neglect volcanic aerosol effects below 15 km

Observations of the Antarctic ozone hole from 2003-2010

Póster presentado en: EGU General Assembly 2011 celebrada del 3 al 8 de abril en Viena, Austria.The Global Atmosphere Watch of WMO includes several stations in Antarctica that keep a close eye on the ozone layer during the ozone hole season. Observations made during the ozone holes from 2003 to 2010 will be compared to each other and interpreted in light of the meteorological conditions. Satellite observations will be used to get a more general picture of the size and depth of the ozone hole and will also be used to calculate various metrics for ozone hole severity. In 2003, 2005 and 2006, the ozone hole was relatively large with more ozone loss than normal. This is in particular the case for 2006, which by most ozone hole metrics was the most severe ozone holeon record. On the other hand, the ozone holes of 2004, 2007 and 2010 were less severe than normal, and only the very special ozone hole of 2002 had less ozone depletion when one regards the ozone holes of the last decade. The interannual variability will be discussed with the help of meteorological data, such as temperature conditions, possibility for polar stratospheric clouds, vortex shape and vortex longevity. Observations will also be compared to 3-D chemical transport model calculations

Approaches to link RNA secondary structures with splicing regulation

In higher eukaryotes, alternative splicing is usually regulated by protein factors, which bind to the pre-mRNA and affect the recognition of splicing signals. There is recent evidence that the secondary structure of the pre-mRNA may also play an important role in this process, either by facilitating or by hindering the interaction with factors and small nuclear ribonucleoproteins (snRNPs) that regulate splicing. Moreover, the secondary structure could play a fundamental role in the splicing of yeast species, which lack many of the regulatory splicing factors present in metazoans. This review describes the steps in the analysis of the secondary structure of the pre-mRNA and its possible relation to splicing. As a working example, we use the case of yeast and the problem of the recognition of the 3-prime splice site.Comment: 21 pages, 7 figure

An introduction to the SCOUT-AMMA stratospheric aircraft, balloons and sondes campaign in West Africa, August 2006: rationale and roadmap

A multi-platform field measurement campaign involving aircraft and balloons took place over West Africa between 26 July and 25 August 2006, in the frame of the concomitant AMMA Special Observing Period and SCOUT-O3 African tropical activities. Specifically aiming at sampling the upper troposphere and lower stratosphere, the high-altitude research aircraft M55 Geophysica was deployed in Ouagadougou (12.3° N, 1.7° W), Burkina Faso, in conjunction with the German D-20 Falcon, while a series of stratospheric balloon and sonde flights were conducted from Niamey (13.5° N, 2.0° E), Niger. The stratospheric aircraft and balloon flights intended to gather experimental evidence for a better understanding of large scale transport, assessing the effect of lightning on NOx production, and studying the impact of intense mesoscale convective systems on water, aerosol, dust and chemical species in the upper troposphere and lower stratosphere. The M55 Geophysica carried out five local and four transfer flights between southern Europe and the Sahel and back, while eight stratospheric balloons and twenty-nine sondes were flown from Niamey. These experiments allowed a characterization of the tropopause and lower stratosphere of the region. We provide here an overview of the campaign activities together with a description of the general meteorological situation during the flights and a summary of the observations accomplished