Alternative polyadenylation: Less than meets the eye

Abstract With the advances in deep-sequencing techniques over the last decade, the study of alternative cleavage and polyadenylation (APA) has shifted from individual gene to whole transcriptome analysis. Findings from such global studies have elevated APA to its currently accepted status as a major player in the regulation of eukaryotic gene expression. Although ∼70 % of human genes have been shown to contain multiple cleavage and polyadenylation sites, the extent of the consequences of APA and its role in regulating physiological processes are still largely unknown. The present review aims to summarize the experimental evidence that supports a physiological role of APA and highlights some of the shortcomings that need addressing to substantiate the widely proposed claim that APA is a key player in global gene regulation

AEROSOL MEASUREMENTS IN THE RHINE VALLEY DURING FOEHN – ANOTHER FORM PERSPECTIVE

While the main focus of the MAP subproject FORM (Foehn in the Rhine Valley during MAP) was on atmospheric dynamics, numerous measurements of chemical constituents of the atmosphere have been performed with various instruments on different platforms. Aerosol measurements have been obtained with routinely operated conventional surface stations, in-situ airborne particle counters and a backscatter lidar. For the MAP SOP it was found that near-surface aerosol concentrations are reduced by the foehn, i.e. they are lowest at the day after the foehn event, especially in the late fall when the valley inversion becomes stronger. A case study for 2 Oct 1999 (IOP 5) reveals considerable spatial variability in aerosol concentrations and shows interactions of the aerosols with the humidity field

Analysis of C. elegans intestinal gene expression and polyadenylation by fluorescence-activated nuclei sorting and 3′-end-seq

Despite the many advantages of Caenorhabditis elegans, biochemical approaches to study tissue-specific gene expression in post-embryonic stages are challenging. Here, we report a novel experimental approach for efficient determination of tissue-specific transcriptomes involving the rapid release and purification of nuclei from major tissues of post-embryonic animals by fluorescence-activated nuclei sorting (FANS), followed by deep sequencing of linearly amplified 3′-end regions of transcripts (3′-end-seq). We employed these approaches to compile the transcriptome of the developed C. elegans intestine and used this to analyse tissue-specific cleavage and polyadenylation. In agreement with intestinal-specific gene expression, highly expressed genes have enriched GATA-elements in their promoter regions and their functional properties are associated with processes that are characteristic for the intestine. We systematically mapped pre-mRNA cleavage and polyadenylation sites, or polyA sites, including more than 3000 sites that have previously not been identified. The detailed analysis of the 3′-ends of the nuclear mRNA revealed widespread alternative polyA site use (APA) in intestinally expressed genes. Importantly, we found that intestinal polyA sites that undergo APA tend to have U-rich and/or A-rich upstream auxiliary elements that may contribute to the regulation of 3′-end formation in the intestin

Quantitative sampling and analysis of trace elements in atmospheric aerosols: impactor characterization and Synchrotron-XRF mass calibration.

he presented work is partly funded by theSwiss Federal Roads Office (ASTRA), the Swiss Federal Office forthe Environment (BAFU) and a post-doc contract sponsored by theSpanish Ministry of Science and Innovation (MICINN). Parts ofthe work were performed at the Swiss Light Source, Paul ScherrerInstitut, Villigen, Switzerland.We thank Andreas Jaggi fortechnical support at the beamline X05DA. Portions of this researchwere carried out at the light source facility DORIS III at HASY-LAB/DESY. DESY is a member of the Helmholtz Association(HGF)

Source apportionment of size and time resolved trace elements and organic aerosols from an urban courtyard site in Switzerland

Time and size resolved data of trace elements were obtained from measurements with a rotating drum impactor (RDI) and subsequent X-ray fluorescence spectrometry. Trace elements can act as indicators for the identification of sources of particulate matter <10 μm (PM10) in ambient air. Receptor modeling was performed with positive matrix factorization (PMF) for trace element data from an urban background site in Zürich, Switzerland. Eight different sources were identified for the three examined size ranges (PM1-0.1, PM2.5-1 and PM 10-2.5): secondary sulfate, wood combustion, fire works, road traffic, mineral dust, de-icing salt, industrial and local anthropogenic activities. The major component was secondary sulfate for the smallest size range; the road traffic factor was found in all three size ranges. This trace element analysis is complemented with data from an Aerodyne high-resolution time-of-flight aerosol mass spectrometer (AMS), assessing the PM1 fraction of organic aerosols. A separate PMF analysis revealed three factors related to three of the sources found with the RDI: oxygenated organic aerosol (OOA, related to inorganic secondary sulfate), hydrocarbon-like organic aerosol (HOA, related to road traffic) and biomass burning organic aerosol (BBOA), explaining 60 %, 22 % and 17 % of total measured organics, respectively. Since different compounds are used for the source classification, a higher percentage of the ambient PM10 mass concentration can be apportioned to sources by the combination of both methods. © 2011 Author(s)

Regulation of transcription termination in the nematode Caenorhabditis elegans

The current predicted mechanisms that describe RNA polymerase II (pol II) transcription termination downstream of protein expressing genes fail to adequately explain, how premature termination is prevented in eukaryotes that possess operon-like structures. Here we address this issue by analysing transcription termination at the end of single protein expressing genes and genes located within operons in the nematode Caenorhabditis elegans. By using a combination of RT-PCR and ChIP analysis we found that pol II generally transcribes up to 1 kb past the poly(A) sites into the 3′ flanking regions of the nematode genes before it terminates. We also show that pol II does not terminate after transcription of internal poly(A) sites in operons. We provide experimental evidence that five randomly chosen C. elegans operons are transcribed as polycistronic pre-mRNAs. Furthermore, we show that cis-splicing of the first intron located in downstream positioned genes in these polycistronic pre-mRNAs is critical for their expression and may play a role in preventing premature pol II transcription termination

α-MSH regulates intergenic splicing of MC1R and TUBB3 in human melanocytes

Alternative splicing enables higher eukaryotes to increase their repertoire of proteins derived from a restricted number of genes. However, the possibility that functional diversity may also be augmented by splicing between adjacent genes has been largely neglected. Here, we show that the human melanocortin 1 receptor (MC1R) gene, a critical component of the facultative skin pigmentation system, has a highly complex and inefficient poly(A) site which is instrumental in allowing intergenic splicing between this locus and its immediate downstream neighbour tubulin-β-III (TUBB3). These transcripts, which produce two distinct protein isoforms localizing to the plasma membrane and the endoplasmic reticulum, seem to be restricted to humans as no detectable chimeric mRNA could be found in MC1R expressing mouse melanocytes. Significantly, treatment with the MC1R agonist α-MSH or activation of the stress response kinase p38-MAPK, both key molecules associated with ultraviolet radiation dermal insult and subsequent skin tanning, result in a shift in expression from MC1R in favour of chimeric MC1R-TUBB3 isoforms in cultured melanocytes. We propose that these chimeric proteins serve to equip melanocytes with novel cellular phenotypes required as part of the pigmentation response

Changes of daily surface ozone maxima in Switzerland in all seasons from 1992 to 2002 and discussion of summer 2003

International audienceAn Analysis of Covariance (ANCOVA) was used to derive the influence of the meteorological variability on the daily maximum ozone concentrations at 12 low-elevation sites north of the Alps in Switzerland during the four seasons in the 1992?2002 period. The afternoon temperature and the morning global radiation were the variables that accounted for most of the meteorological variability in summer and spring, while other variables that can be related to vertical mixing and dilution of primary pollutants (afternoon global radiation, wind speed, stability or day of the week) were more significant in winter. In addition, the number of days after a frontal passage was important to account for ozone build-up in summer and ozone destruction in winter. The statistical model proved to be a robust tool for reducing the impact of the meteorological variability on the ozone concentrations. The explained variance of the model, averaged over all stations, ranged from 60.2% in winter to 71.9% in autumn. The year-to-year variability of the seasonal medians of daily ozone maxima was reduced by 85% in winter, 60% in summer, and 50% in autumn and spring after the meteorological adjustment. For most stations, no significantly negative trends (at the 95% confidence level) of the summer medians of daily O3 or Ox (O3+NO2) maxima were found despite the significant reduction in the precursor emissions in Central Europe. However, significant downward trends in the summer 90th percentiles of daily Ox maxima were observed at 6 sites in the region around Zürich (on average ?0.73 ppb yr-1 for those sites). The lower effect of the titration by NO as a consequence of the reduced emissions could partially explain the significantly positive O3 trends in the cold seasons (on average 0.69 ppb yr-1 in winter and 0.58 ppb yr-1 in autumn). The increase of Ox found for most stations in autumn (on average 0.23 ppb yr-1) and winter (on average 0.39 ppb yr-1) could be due to increasing European background ozone levels, in agreement with other studies. The statistical model was also able to explain the very high ozone concentrations in summer 2003, the warmest summer in Switzerland for at least ~150 years. On average, the measured daily ozone maximum was 15 ppb (nearly 29%) higher than in the reference period summer 1992?2002, corresponding to an excess of 5 standard deviations of the summer means of daily ozone maxima in that period

Elemental composition of ambient aerosols measured with high temporal resolution using an online XRF spectrometer

The Xact 625 Ambient Metals Monitor was tested during a 3-week field campaign at the rural, traffic-influenced site Härkingen in Switzerland during the summer of 2015. The field campaign encompassed the Swiss National Day fireworks event, providing increased concentrations and unique chemical signatures compared to non-fireworks (or background) periods. The objective was to evaluate the data quality by intercomparison with other independent measurements and test its applicability for aerosol source quantification. The Xact was configured to measure 24 elements in PM10 with 1g h time resolution. Data quality was evaluated for 10 24g h averages of Xact data by intercomparison with 24g h PM10 filter data analysed with ICP-OES for major elements, ICP-MS for trace elements, and gold amalgamation atomic absorption spectrometry for Hg. Ten elements (S, K, Ca, Ti, Mn, Fe, Cu, Zn, Ba, Pb) showed excellent correlation between the compared methods, with r2 values ≥ g 0.95. However, the slopes of the regressions between Xact 625 and ICP data varied from 0.97 to 1.8 (average 1.28) and thus indicated generally higher Xact elemental concentrations than ICP for these elements. Possible reasons for these differences are discussed, but further investigations are needed. For the remaining elements no conclusions could be drawn about their quantification for various reasons, mainly detection limit issues. An indirect intercomparison of hourly values was performed for the fireworks peak, which brought good agreement of total masses when the Xact data were corrected with the regressions from the 24g h value intercomparison. The results demonstrate that multi-metal characterization at high-time-resolution capability of Xact is a valuable and practical tool for ambient monitoring. © Author(s) 2017.This study has been partly funded by the Swiss Federal Office for the Environment (FOEN). M. C. Minguillón acknowledges the Ramón y Cajal Fellowship awarded by the Spanish Ministry of Economy, Industry and Competitiveness. We thank René Richter and Roland Scheidegger of PSI for their support during the field campaign. We are grateful to Chris Koch and John Cooper of Cooper Environmental Services for instructions on instrument operation and numerous discussions on the results. Andrés Alastuey, Xavier Querol, and laboratory personnel from IDAEA-CSIC are also acknowledged. We also thank Julie Swift and Randy Mercurio of ERG for the ICP-MS analyses.Peer reviewe