Pervasive isoform-specific translational regulation via alternative transcription start sites in mammals

Transcription initiated at alternative sites can produce mRNA isoforms with different 5'UTRs, which are potentially subjected to differential translational regulation. However, the prevalence of such isoform-specific translational control across mammalian genomes is currently unknown. By combining polysome profiling with high-throughput mRNA 5' end sequencing, we directly measured the translational status of mRNA isoforms with distinct start sites. Among 9,951 genes expressed in mouse fibroblasts, we identified 4,153 showed significant initiation at multiple sites, of which 745 genes exhibited significant isoform-divergent translation. Systematic analyses of the isoform-specific translation revealed that isoforms with longer 5'UTRs tended to translate less efficiently. Further investigation of cis-elements within 5'UTRs not only provided novel insights into the regulation by known sequence features, but also led to the discovery of novel regulatory sequence motifs. Quantitative models integrating all these features explained over half of the variance in the observed isoform-divergent translation. Overall, our study demonstrated the extensive translational regulation by usage of alternative transcription start sites and offered comprehensive understanding of translational regulation by diverse sequence features embedded in 5'UTRs

Long-term monitoring of black carbon across Germany

Lately, black carbon (BC) has received significant attention due to its climate-warming properties and adverse health effects. Nevertheless, long-term observations in urban areas are scarce, most likely because BC monitoring is not required by environmental legislation. This, however, handicaps the evaluation of air quality models which can be used to assess the effectiveness of policy measures which aim to reduce BC concentrations. Here, we present a new dataset of atmospheric BC measurements from Germany constructed from over six million measurements at over 170 stations. Data covering the period between 1994 and 2014 were collected from twelve German Federal States and the Federal Environment Agency, quality checked and harmonized into a database with comprehensive metadata. The final data in original time resolution are available for download (https://doi.org/10.1594/PANGAEA.881173). Though assembled in a consistent way, the dataset is characterized by differences in (a) measurement methodologies for determining evolved carbon and optical absorption, (b) covered time periods, and (c) temporal resolutions that ranged from half hourly to measurements every 6th day. Usage and interpretation of this dataset thus requires a careful consideration of these differences. Our analysis focuses on 2009, the year with the largest data coverage with one single methodology, as well as on the relative changes in long-term trends over ten years. For 2009, we find that BC concentrations at traffic sites were at least twice as high as at urban background, industrial and rural sites. Weekly cycles are most prominent at traffic stations, however, the presence of differences in concentrations during the week and on weekends at other station types suggests that traffic plays an important role throughout the full network. Generally higher concentrations and weaker weekly cycles during the winter months point towards the influence of other sources such as domestic heating. Regarding the long-term trends, advanced statistical techniques allow us to account for instrumentation changes and to separate seasonal and long-term changes in our dataset. Analysis shows a downward trend in BC at nearly all locations and in all conditions, with a high level of confidence for the period of 2005–2014. In depth analysis indicates that background BC is decreasing slowly, while the occurrences of high concentrations are decreasing more rapidly. In summary, legislation – both in Europe and locally – to reduce particulate emissions and indirectly BC appear to be working, based on this analysis. Adverse human health and climate impacts are likely to be diminished because of the improvements in air quality

DNA sonication inverse PCR for genome scale analysis of uncharacterized flanking sequences

1. There are few available tools to comprehensively and economically identify uncharacterized flanking regions that are not extremely labour intensive and which exploit the advantages of emerging long‐read sequencing platforms. 2. We describe SIP; a sonication‐based inverse PCR high‐throughput sequencing strategy to investigate uncharacterized flanking region sequences, including those flanking mobile DNA. SIP combines unbiased fragmentation by sonication and target enrichment by coupling outward facing PCR priming with long‐read sequencing technologies. 3. We demonstrate the effectiveness of SIP by determining retroviral integrations which are high copy and challenging to characterize. We further describe SIP's workflow, examine retroviral (proviral) enrichment and characterize viral structural variants identified. When SIP was coupled with long‐read sequencing using the PacBio RS II platform, proviral integration was extensively characterized at high sequence depth per integration. By interrogating the sequence data, we were also able to test several intrinsic factors including SIP's propensity to form chimeric sequences and adapter ligation efficiencies. 4. SIP is an adaption of a traditional molecular biology technique that can be used to characterize any unknown genomic flanking sequence or to extend any sequence for which only minimal sequence information is available. SIP can be applied broadly to study complex biological systems such as mobile genetic elements with high throughput

Full-length transcriptome reconstruction reveals a large diversity of RNA and protein isoforms in rat hippocampus

Gene annotation is a critical resource in genomics research. Many computational approaches have been developed to assemble transcriptomes based on high-throughput short-read sequencing, however, only with limited accuracy. Here, we combine next-generation and third-generation sequencing to reconstruct a full-length transcriptome in the rat hippocampus, which is further validated using independent 5´ and 3´-end profiling approaches. In total, we detect 28,268 full-length transcripts (FLTs), covering 6,380 RefSeq genes and 849 unannotated loci. Based on these FLTs, we discover co-occurring alternative RNA processing events. Integrating with polysome profiling and ribosome footprinting data, we predict isoform-specific translational status and reconstruct an open reading frame (ORF)-eome. Notably, a high proportion of the predicted ORFs are validated by mass spectrometry-based proteomics. Moreover, we identify isoforms with subcellular localization pattern in neurons. Collectively, our data advance our knowledge of RNA and protein isoform diversity in the rat brain and provide a rich resource for functional studies

De novo whole genome assembly of the Roborovski dwarf hamster (Phodopus roborovskii) genome, an animal model for severe/critical COVID-19

The Roborovski dwarf hamster Phodopus roborovskii belongs to the Phodopus genus, one of seven within Cricetinae subfamily. Like other rodents such as mice, rats or ferrets, hamsters can be important animal models for a range of diseases. Whereas the Syrian hamster from the genus Mesocricetus is now widely used as a model for mild to moderate COVID-19, Roborovski dwarf hamster show a severe to lethal course of disease upon infection with the novel human coronavirus SARS-CoV-2

BAERLIN2014 -The influence of land surface types on and the horizontal heterogeneity of air pollutant levels in Berlin

Urban air quality and human health are among the key aspects of future urban planning. In order to address pollutants such as ozone and particulate matter, efforts need to be made to quantify and reduce their concentrations. One important aspect in understanding urban air quality is the influence of urban vegetation which may act as both emitter and sink for trace gases and aerosol particles. In this context, the "Berlin Air quality and Ecosystem Research: Local and long-range Impact of anthropogenic and Natural hydrocarbons 2014" (BAERLIN2014) campaign was conducted between 2 June and 29 August in the metropolitan area of Berlin and Brandenburg, Germany. The predominant goals of the campaign were (1) the characterization of urban gaseous and particulate pollution and its attribution to anthropogenic and natural sources in the region of interest, especially considering the connection between biogenic volatile organic compounds and particulates and ozone; (2) the quantification of the impact of urban vegetation on organic trace gas levels and the presence of oxidants such as ozone; and (3) to explain the local heterogeneity of pollutants by defining the distribution of sources and sinks relevant for the interpretation of model simulations. In order to do so, the campaign included stationary measurements at urban background station and mobile observations carried out from bicycle, van and airborne platforms. This paper provides an overview of the mobile measurements (Mobile BAERLIN2014) and general conclusions drawn from the analysis. Bicycle measurements showed micro-scale variations of temperature and particulate matter, displaying a substantial reduction of mean temperatures and particulate levels in the proximity of vegetated areas compared to typical urban residential area (background) measurements. Van measurements extended the area covered by bicycle observations and included continuous measurements of O3, NOx, CO, CO2 and point-wise measurement of volatile organic compounds (VOCs) at representative sites for traffic- and vegetation-affected sites. The quantification displayed notable horizontal heterogeneity of the short-lived gases and particle number concentrations. For example, baseline concentrations of the traffic-related chemical species CO and NO varied on average by up to ±22.2 and ±63.5 %, respectively, on the scale of 100 m around any measurement location. Airborne observations revealed the dominant source of elevated urban particulate number and mass concentrations being local, i.e., not being caused by long-range transport. Surface-based observations related these two parameters predominantly to traffic sources. Vegetated areas lowered the pollutant concentrations substantially with ozone being reduced most by coniferous forests, which is most likely caused by their reactive biogenic VOC emissions. With respect to the overall potential to reduce air pollutant levels, forests were found to result in the largest decrease, followed by parks and facilities for sports and leisure. Surface temperature was generally 0.6–2.1 °C lower in vegetated regions, which in turn will have an impact on tropospheric chemical processes. Based on our findings, effective future mitigation activities to provide a more sustainable and healthier urban environment should focus predominantly on reducing fossil-fuel emissions from traffic as well as on increasing vegetated areas

BAERLIN2014-stationary measurements and source apportionment at an urban background station in Berlin, Germany

The "Berlin Air quality and Ecosystem Research: Local and long-range Impact of anthropogenic and Natural hydrocarbons" (BAERLIN2014) campaign was conducted during the 3 summer months (June-August) of 2014. During this measurement campaign, both stationary and mobile measurements were undertaken to address complementary aims. This paper provides an overview of the stationary measurements and results that were focused on characterization of gaseous and particulate pollution, including source attribution, in the Berlin-Potsdam area, and quantification of the role of natural sources in determining levels of ozone and related gaseous pollutants. Results show that biogenic contributions to ozone and particulate matter are substantial. One indicator for ozone formation, the OH reactivity, showed a 31% (0.82 +/- 0.44 s(-1) and 75% (3.7 +/- 0.90 s(-1) contribution from biogenic non-methane volatile organic com-pounds (NMVOCs) for urban background (2.6 +/- 0.68 s(-1) and urban park (4.9 +/- 1.0 s(-1) location, respectively, emphasizing the importance of such locations as sources of biogenic NMVOCs in urban areas. A comparison to NMVOC measurements made in Berlin approximately 20 years earlier generally show lower levels today for anthropogenic NMVOCs. A substantial contribution of secondary organic and inorganic aerosol to PM10 concentrations was quantified. In addition to secondary aerosols, source apportionment analysis of the organic carbon fraction identified the contribution of biogenic (plant-based) particulate matter, as well as primary contributions from vehicles, with a larger contribution from diesel compared to gasoline vehicles, as well as a relatively small contribution from wood burning, linked to measured levoglucosan

Male carriers of HLA-C*04:01 have increased risk of cardiac injury in COVID-19

Identification of factors that lead to the severe clinical course of COVID-19 is crucial for timely allocation of resources. The purpose of this study was to evaluate possible sex differences in cardiac injury associated with HLA-C*04:01. High sensitivity troponin T on admission (hs-TnTa) and maximum high sensitivity troponin T (hs-TnTmax) were used to assess for cardiac injury in patients with COVID-19 (n = 435). We tested for the association of elevated hs-TnT with HLA-C* 04:01 and evaluated for potential sex-specific differences. An association between hs-TnTa and the severity of clinical course was identified. In addition, our study revealed that hs-TnTmax was higher in men who were carriers of HLA-C*04:01 compared to men without the risk allele. Male carriers of HLA-C*04:01 with COVID-19 developed higher hs-TnTmax, suggesting a larger extent of cardiac injury. This association suggests the presence of different pathomechanisms in COVID-19 based on sex

Increased risk of severe clinical course of COVID-19 in carriers of HLA-C*04:01

Background: Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic, there has been increasing urgency to identify pathophysiological characteristics leading to severe clinical course in patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Human leukocyte antigen alleles (HLA) have been suggested as potential genetic host factors that affect individual immune response to SARS-CoV-2. We sought to evaluate this hypothesis by conducting a multicenter study using HLA sequencing. Methods: We analyzed the association between COVID-19 severity and HLAs in 435 individuals from Germany (n = 135), Spain (n = 133), Switzerland (n = 20) and the United States (n = 147), who had been enrolled from March 2020 to August 2020. This study included patients older than 18 years, diagnosed with COVID19 and representing the full spectrum of the disease. Finally, we tested our results by meta-analysing data from prior genome-wide association studies (GWAS). Findings: We describe a potential association of HLA-C*04:01 with severe clinical course of COVID-19. Carriers of HLA-C*04:01 had twice the risk of intubation when infected with SARS-CoV-2 (risk ratio 1.5 [95% CI 1.1-2.1], odds ratio 3.5 [95% CI 1.9-6.6], adjusted p-value = 0.0074). These findings are based on data from four countries and corroborated by independent results from GWAS. Our findings are biologically plausible, as HLA-C*04:01 has fewer predicted bindings sites for relevant SARS-CoV-2 peptides compared to other HLA alleles. Interpretation: HLA-C*04:01 carrier state is associated with severe clinical course in SARS-CoV-2. Our findings suggest that HLA class I alleles have a relevant role in immune defense against SARS-CoV-2. Funding: Funded by Roche Sequencing Solutions, Inc

Increased risk of severe clinical course of COVID-19 in carriers of HLA-C*04:01

BACKGROUND: Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic, there has been increasing urgency to identify pathophysiological characteristics leading to severe clinical course in patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Human leukocyte antigen alleles (HLA) have been suggested as potential genetic host factors that affect individual immune response to SARS-CoV-2. We sought to evaluate this hypothesis by conducting a multicenter study using HLA sequencing. METHODS: We analyzed the association between COVID-19 severity and HLAs in 435 individuals from Germany ((n) = 135), Spain ((n) = 133), Switzerland ((n) = 20) and the United States ((n) = 147), who had been enrolled from March 2020 to August 2020. This study included patients older than 18 years, diagnosed with COVID-19 and representing the full spectrum of the disease. Finally, we tested our results by meta-analysing data from prior genome-wide association studies (GWAS). FINDINGS: We describe a potential association of HLA-C*04:01 with severe clinical course of COVID-19. Carriers of HLA-C*04:01 had twice the risk of intubation when infected with SARS-CoV-2 (risk ratio 1.5 [95% CI 1.1-2.1], odds ratio 3.5 [95% CI 1.9-6.6], adjusted (p)-value = 0.0074). These findings are based on data from four countries and corroborated by independent results from GWAS. Our findings are biologically plausible, as HLA-C*04:01 has fewer predicted bindings sites for relevant SARS-CoV-2 peptides compared to other HLA alleles. INTERPRETATION: HLA-C*04:01 carrier state is associated with severe clinical course in SARS-CoV-2. Our findings suggest that HLA class I alleles have a relevant role in immune defense against SARS-CoV-2