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  • 1
    Publication Date: 2012-11-28
    Description: The human cytomegalovirus (HCMV) genome was sequenced 20 years ago. However, like those of other complex viruses, our understanding of its protein coding potential is far from complete. We used ribosome profiling and transcript analysis to experimentally define the HCMV translation products and follow their temporal expression. We identified hundreds of previously unidentified open reading frames and confirmed a fraction by means of mass spectrometry. We found that regulated use of alternative transcript start sites plays a broad role in enabling tight temporal control of HCMV protein expression and allowing multiple distinct polypeptides to be generated from a single genomic locus. Our results reveal an unanticipated complexity to the HCMV coding capacity and illustrate the role of regulated changes in transcript start sites in generating this complexity.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3817102/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3817102/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stern-Ginossar, Noam -- Weisburd, Ben -- Michalski, Annette -- Le, Vu Thuy Khanh -- Hein, Marco Y -- Huang, Sheng-Xiong -- Ma, Ming -- Shen, Ben -- Qian, Shu-Bing -- Hengel, Hartmut -- Mann, Matthias -- Ingolia, Nicholas T -- Weissman, Jonathan S -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Nov 23;338(6110):1088-93. doi: 10.1126/science.1227919.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisico, CA 94158, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23180859" target="_blank"〉PubMed〈/a〉
    Keywords: Alternative Splicing ; Cytomegalovirus/*genetics ; Cytomegalovirus Infections/*virology ; Genetic Variation ; *Genome, Viral ; Humans ; *Open Reading Frames ; Protein Biosynthesis/genetics ; Proteome/genetics ; Sequence Analysis, DNA ; Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2015-05-02
    Description: DNA interstrand cross-links (ICLs) block replication fork progression by inhibiting DNA strand separation. Repair of ICLs requires sequential incisions, translesion DNA synthesis, and homologous recombination, but the full set of factors involved in these transactions remains unknown. We devised a technique called chromatin mass spectrometry (CHROMASS) to study protein recruitment dynamics during perturbed DNA replication in Xenopus egg extracts. Using CHROMASS, we systematically monitored protein assembly and disassembly on ICL-containing chromatin. Among numerous prospective DNA repair factors, we identified SLF1 and SLF2, which form a complex with RAD18 and together define a pathway that suppresses genome instability by recruiting the SMC5/6 cohesion complex to DNA lesions. Our study provides a global analysis of an entire DNA repair pathway and reveals the mechanism of SMC5/6 relocalization to damaged DNA in vertebrate cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Raschle, Markus -- Smeenk, Godelieve -- Hansen, Rebecca K -- Temu, Tikira -- Oka, Yasuyoshi -- Hein, Marco Y -- Nagaraj, Nagarjuna -- Long, David T -- Walter, Johannes C -- Hofmann, Kay -- Storchova, Zuzana -- Cox, Jurgen -- Bekker-Jensen, Simon -- Mailand, Niels -- Mann, Matthias -- HL098316/HL/NHLBI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2015 May 1;348(6234):1253671. doi: 10.1126/science.1253671. Epub 2015 Apr 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany. ; Ubiquitin Signaling Group, Department of Disease Biology, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark. ; Howard Hughes Medical Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA. ; Institute of Genetics, University of Cologne, 50674 Cologne, Germany. ; Maintenance of Genome Stability Group, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany. ; Ubiquitin Signaling Group, Department of Disease Biology, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark. simon.bekker-jensen@cpr.ku.dk niels.mailand@cpr.ku.dk mmann@biochem.mpg.de. ; Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany. Novo Nordisk Foundation Center for Protein Research, Proteomics Program, University of Copenhagen, DK-2200 Copenhagen, Denmark. simon.bekker-jensen@cpr.ku.dk niels.mailand@cpr.ku.dk mmann@biochem.mpg.de.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25931565" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Chromatin/chemistry/metabolism ; *DNA Damage ; *DNA Repair ; DNA Repair Enzymes/*metabolism ; *DNA Replication ; DNA-Binding Proteins/metabolism ; Mass Spectrometry/methods ; Proteomics/methods ; RNA-Binding Proteins/metabolism ; Xenopus
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2016-08-31
    Description: Highly pathogenic severe acute respiratory syndrome coronavirus (SARS-CoV) has developed strategies to inhibit host immune recognition. We identify cellular E3 ubiquitin ligase ring-finger and CHY zinc-finger domain-containing 1 (RCHY1) as an interacting partner of the viral SARS-unique domain (SUD) and papain-like protease (PLpro), and, as a consequence, the involvement of...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 4
    Publication Date: 2012-11-22
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 2020-04-01
    Description: Mutualisms play a critical role in ecological communities; however, the importance and prevalence of mutualistic associations can be modified by external stressors. On coral reefs, elevated sediment deposition can be a major stressor reducing the health of corals and reef resilience. Here, we investigated the influence of severe sedimentation on the mutualistic relationship between small damselfishes ( Pomacentrus moluccensis and Dascyllus aruanus ) and their coral host ( Pocillopora damicornis ). In an aquarium experiment, corals were exposed to sedimentation rates of approximately 100 mg cm −2 d −1 , with and without fishes present, to test whether: (i) fishes influence the accumulation of sediments on coral hosts, and (ii) fishes moderate partial colony mortality and/or coral tissue condition. Colonies with fishes accumulated much less sediment compared with colonies without fishes, and this effect was strongest for colonies with D. aruanus (fivefold less sediment than controls) as opposed to P. moluccensis (twofold less sediment than controls). Colonies with symbiont fishes also had up to 10-fold less sediment-induced partial mortality, as well as higher chlorophyll and protein concentrations. These results demonstrate that fish mutualisms vary in the strength of their benefits, and indicate that some mutualistic or facilitative interactions might become more important for species health and resilience at high-stress levels.
    Electronic ISSN: 2054-5703
    Topics: Natural Sciences in General
    Published by The Royal Society
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