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  • 1
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    Identification of the m6Am Methyltransferase PCIF1 Reveals the Location and Functions of m6Am in the Transcriptome (2019)
    Elsevier
    Details
    Publikationsdatum: 2019
    Beschreibung: 〈p〉Publication date: Available online 3 July 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Molecular Cell〈/p〉 〈p〉Author(s): Konstantinos Boulias, Diana Toczydłowska-Socha, Ben R. Hawley, Noa Liberman, Ken Takashima, Sara Zaccara, Théo Guez, Jean-Jacques Vasseur, Françoise Debart, L. Aravind, Samie R. Jaffrey, Eric Lieberman Greer〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉mRNAs are regulated by nucleotide modifications that influence their cellular fate. Two of the most abundant modified nucleotides are 〈em〉N〈/em〉〈sup〉6〈/sup〉-methyladenosine (m〈sup〉6〈/sup〉A), found within mRNAs, and 〈em〉N〈/em〉〈sup〉6〈/sup〉,2′-〈em〉O〈/em〉-dimethyladenosine (m〈sup〉6〈/sup〉Am), which is found at the first transcribed nucleotide. Distinguishing these modifications in mapping studies has been difficult. Here, we identify and biochemically characterize PCIF1, the methyltransferase that generates m〈sup〉6〈/sup〉Am. We find that PCIF1 binds and is dependent on the m〈sup〉7〈/sup〉G cap. By depleting PCIF1, we generated transcriptome-wide maps that distinguish m〈sup〉6〈/sup〉Am and m〈sup〉6〈/sup〉A. We find that m〈sup〉6〈/sup〉A and m〈sup〉6〈/sup〉Am misannotations arise from mRNA isoforms with alternative transcription start sites (TSSs). These isoforms contain m〈sup〉6〈/sup〉Am that maps to “internal” sites, increasing the likelihood of misannotation. We find that depleting PCIF1 does not substantially affect mRNA translation but is associated with reduced stability of a subset of m〈sup〉6〈/sup〉Am-annotated mRNAs. The discovery of PCIF1 and our accurate mapping technique will facilitate future studies to characterize m〈sup〉6〈/sup〉Am’s function.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S1097276519304393-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉
    Print ISSN: 1097-2765
    Digitale ISSN: 1097-4164
    Thema: Biologie , Medizin
    Publiziert von Elsevier im Namen von Cell Press.
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  • 2
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    PCIF1 Catalyzes m6Am mRNA Methylation to Regulate Gene Expression (2019)
    Elsevier
    Details
    Publikationsdatum: 2019
    Beschreibung: 〈p〉Publication date: Available online 3 July 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Molecular Cell〈/p〉 〈p〉Author(s): Erdem Sendinc, David Valle-Garcia, Abhinav Dhall, Hao Chen, Telmo Henriques, Jose Navarrete-Perea, Wanqiang Sheng, Steven P. Gygi, Karen Adelman, Yang Shi〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉mRNA modifications play important roles in regulating gene expression. One of the most abundant mRNA modifications is N6,2-O-dimethyladenosine (m6Am). Here, we demonstrate that m6Am is an evolutionarily conserved mRNA modification mediated by the Phosphorylated CTD Interacting Factor 1 (PCIF1), which catalyzes m6A methylation on 2-O-methylated adenine located at the 5′ ends of mRNAs. Furthermore, PCIF1 catalyzes only 5′ m6Am methylation of capped mRNAs but not internal m6A methylation 〈em〉in vitro〈/em〉 and 〈em〉in vivo〈/em〉. To study the biological role of m6Am, we developed a robust methodology (m6Am-Exo-Seq) to map its transcriptome-wide distribution, which revealed no global crosstalk between m6Am and m6A under assayed conditions, suggesting that m6Am is functionally distinct from m6A. Importantly, we find that m6Am does not alter mRNA transcription or stability but negatively impacts cap-dependent translation of methylated mRNAs. Together, we identify the only human mRNA m6Am methyltransferase and demonstrate a mechanism of gene expression regulation through PCIF1-mediated m6Am mRNA methylation.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S1097276519304022-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉
    Print ISSN: 1097-2765
    Digitale ISSN: 1097-4164
    Thema: Biologie , Medizin
    Publiziert von Elsevier im Namen von Cell Press.
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  • 3
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    Disease-Causing Mutations in SF3B1 Alter Splicing by Disrupting Interaction with SUGP1 (2019)
    Elsevier
    Details
    Publikationsdatum: 2019
    Beschreibung: 〈p〉Publication date: Available online 29 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Molecular Cell〈/p〉 〈p〉Author(s): Jian Zhang, Abdullah M. Ali, Yen K. Lieu, Zhaoqi Liu, Jianchao Gao, Raul Rabadan, Azra Raza, Siddhartha Mukherjee, James L. Manley〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉〈em〉SF3B1〈/em〉, which encodes an essential spliceosomal protein, is frequently mutated in myelodysplastic syndromes (MDS) and many cancers. However, the defect of mutant SF3B1 is unknown. Here, we analyzed RNA sequencing data from MDS patients and confirmed that SF3B1 mutants use aberrant 3′ splice sites. To elucidate the underlying mechanism, we purified complexes containing either wild-type or the hotspot K700E mutant SF3B1 and found that levels of a poorly studied spliceosomal protein, SUGP1, were reduced in mutant spliceosomes. Strikingly, SUGP1 knockdown completely recapitulated the splicing errors, whereas SUGP1 overexpression drove the protein, which our data suggest plays an important role in branchsite recognition, into the mutant spliceosome and partially rescued splicing. Other hotspot SF3B1 mutants showed similar altered splicing and diminished interaction with SUGP1. Our study demonstrates that SUGP1 loss is a common defect of spliceosomes with disease-causing 〈em〉SF3B1〈/em〉 mutations and, because this defect can be rescued, suggests possibilities for therapeutic intervention.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S1097276519305477-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉
    Print ISSN: 1097-2765
    Digitale ISSN: 1097-4164
    Thema: Biologie , Medizin
    Publiziert von Elsevier im Namen von Cell Press.
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  • 4
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    Regulation of Co-transcriptional Pre-mRNA Splicing by m6A through the Low-Complexity Protein hnRNPG (2019)
    Elsevier
    Details
    Publikationsdatum: 2019
    Beschreibung: 〈p〉Publication date: Available online 21 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Molecular Cell〈/p〉 〈p〉Author(s): Katherine I. Zhou, Hailing Shi, Ruitu Lyu, Adam C. Wylder, Żaneta Matuszek, Jessica N. Pan, Chuan He, Marc Parisien, Tao Pan〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉〈em〉N〈/em〉〈sup〉6〈/sup〉-methyladenosine (m〈sup〉6〈/sup〉A) modification occurs co-transcriptionally and impacts pre-mRNA processing; however, the mechanism of co-transcriptional m〈sup〉6〈/sup〉A-dependent alternative splicing regulation is still poorly understood. Heterogeneous nuclear ribonucleoprotein G (hnRNPG) is an m〈sup〉6〈/sup〉A reader protein that binds RNA through RRM and Arg-Gly-Gly (RGG) motifs. Here, we show that hnRNPG directly binds to the phosphorylated carboxy-terminal domain (CTD) of RNA polymerase II (RNAPII) using RGG motifs in its low-complexity region. Through interactions with the phosphorylated CTD and nascent RNA, hnRNPG associates co-transcriptionally with RNAPII and regulates alternative splicing transcriptome-wide. m〈sup〉6〈/sup〉A near splice sites in nascent pre-mRNA modulates hnRNPG binding, which influences RNAPII occupancy patterns and promotes exon inclusion. Our results reveal an integrated mechanism of co-transcriptional m〈sup〉6〈/sup〉A-mediated splicing regulation, in which an m〈sup〉6〈/sup〉A reader protein uses RGG motifs to co-transcriptionally interact with both RNAPII and m〈sup〉6〈/sup〉A-modified nascent pre-mRNA to modulate RNAPII occupancy and alternative splicing.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S1097276519305350-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉
    Print ISSN: 1097-2765
    Digitale ISSN: 1097-4164
    Thema: Biologie , Medizin
    Publiziert von Elsevier im Namen von Cell Press.
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  • 5
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    Msp1 Clears Mistargeted Proteins by Facilitating Their Transfer from Mitochondria to the ER (2019)
    Elsevier
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    Publikationsdatum: 2019
    Beschreibung: 〈p〉Publication date: Available online 21 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Molecular Cell〈/p〉 〈p〉Author(s): Shunsuke Matsumoto, Kunio Nakatsukasa, Chika Kakuta, Yasushi Tamura, Masatoshi Esaki, Toshiya Endo〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉Normal mitochondrial functions rely on optimized composition of their resident proteins, and proteins mistargeted to mitochondria need to be efficiently removed. Msp1, an AAA-ATPase in the mitochondrial outer membrane (OM), facilitates degradation of tail-anchored (TA) proteins mistargeted to the OM, yet how Msp1 cooperates with other factors to conduct this process was unclear. Here, we show that Msp1 recognizes substrate TA proteins and facilitates their transfer to the endoplasmic reticulum (ER). Doa10 in the ER membrane then ubiquitinates them with Ubc6 and Ubc7. Ubiquitinated substrates are extracted from the ER membrane by another AAA-ATPase in the cytosol, Cdc48, with Ufd1 and Npl4 for proteasomal degradation in the cytosol. Thus, Msp1 functions as an extractase that mediates clearance of mistargeted TA proteins by facilitating their transfer to the ER for protein quality control.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S1097276519305362-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉
    Print ISSN: 1097-2765
    Digitale ISSN: 1097-4164
    Thema: Biologie , Medizin
    Publiziert von Elsevier im Namen von Cell Press.
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  • 6
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    Proteomics Links Ubiquitin Chain Topology Change to Transcription Factor Activation (2019)
    Elsevier
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    Publikationsdatum: 2019
    Beschreibung: 〈p〉Publication date: Available online 20 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Molecular Cell〈/p〉 〈p〉Author(s): Yanchang Li, Eric B. Dammer, Yuan Gao, Qiuyan Lan, Mark A. Villamil, Duc M. Duong, Chengpu Zhang, Lingyan Ping, Linda Lauinger, Karin Flick, Zhongwei Xu, Wei Wei, Xiaohua Xing, Lei Chang, Jianping Jin, Xuechuan Hong, Yunping Zhu, Junzhu Wu, Zixin Deng, Fuchu He〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉A surprising complexity of ubiquitin signaling has emerged with identification of different ubiquitin chain topologies. However, mechanisms of how the diverse ubiquitin codes control biological processes remain poorly understood. Here, we use quantitative whole-proteome mass spectrometry to identify yeast proteins that are regulated by lysine 11 (K11)-linked ubiquitin chains. The entire Met4 pathway, which links cell proliferation with sulfur amino acid metabolism, was significantly affected by K11 chains and selected for mechanistic studies. Previously, we demonstrated that a K48-linked ubiquitin chain represses the transcription factor Met4. Here, we show that efficient Met4 activation requires a K11-linked topology. Mechanistically, our results propose that the K48 chain binds to a topology-selective tandem ubiquitin binding region in Met4 and competes with binding of the basal transcription machinery to the same region. The change to K11-enriched chain architecture releases this competition and permits binding of the basal transcription complex to activate transcription.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S1097276519305040-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉
    Print ISSN: 1097-2765
    Digitale ISSN: 1097-4164
    Thema: Biologie , Medizin
    Publiziert von Elsevier im Namen von Cell Press.
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  • 7
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    Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase (2019)
    Elsevier
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    Publikationsdatum: 2019
    Beschreibung: 〈p〉Publication date: Available online 20 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Molecular Cell〈/p〉 〈p〉Author(s): Jinjun Wu, Nadine L. Samara, Isao Kuraoka, Wei Yang〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉Endonuclease V (EndoV) cleaves the second phosphodiester bond 3′ to a deaminated adenosine (inosine). Although highly conserved, EndoV homologs change substrate preference from DNA in bacteria to RNA in eukaryotes. We have characterized EndoV from six different species and determined crystal structures of human EndoV and three EndoV homologs from bacteria to mouse in complex with inosine-containing DNA/RNA hybrid or double-stranded RNA (dsRNA). Inosine recognition is conserved, but changes in several connecting loops in eukaryotic EndoV confer recognition of 3 ribonucleotides upstream and 7 or 8 bp of dsRNA downstream of the cleavage site, and bacterial EndoV binds only 2 or 3 nt flanking the scissile phosphate. In addition to the two canonical metal ions in the active site, a third Mn〈sup〉2+〈/sup〉 that coordinates the nucleophilic water appears necessary for product formation. Comparison of EndoV with its homologs RNase H1 and Argonaute reveals the principles by which these enzymes recognize RNA versus DNA.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S1097276519305039-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉
    Print ISSN: 1097-2765
    Digitale ISSN: 1097-4164
    Thema: Biologie , Medizin
    Publiziert von Elsevier im Namen von Cell Press.
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  • 8
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    Conserved Pseudoknots in lncRNA MEG3 Are Essential for Stimulation of the p53 Pathway (2019)
    Elsevier
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    Publikationsdatum: 2019
    Beschreibung: 〈p〉Publication date: Available online 20 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Molecular Cell〈/p〉 〈p〉Author(s): Tina Uroda, Eleni Anastasakou, Annalisa Rossi, Jean-Marie Teulon, Jean-Luc Pellequer, Paolo Annibale, Ombeline Pessey, Alberto Inga, Isabel Chillón, Marco Marcia〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉Long non-coding RNAs (lncRNAs) are key regulatory molecules, but unlike with other RNAs, the direct link between their tertiary structure motifs and their function has proven elusive. Here we report structural and functional studies of human maternally expressed gene 3 (MEG3), a tumor suppressor lncRNA that modulates the p53 response. We found that, in an evolutionary conserved region of MEG3, two distal motifs interact by base complementarity to form alternative, mutually exclusive pseudoknot structures (“kissing loops”). Mutations that disrupt these interactions impair MEG3-dependent p53 stimulation 〈em〉in vivo〈/em〉 and disrupt MEG3 folding 〈em〉in vitro〈/em〉. These findings provide mechanistic insights into regulation of the p53 pathway by MEG3 and reveal how conserved motifs of tertiary structure can regulate lncRNA biological function.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S1097276519305635-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉
    Print ISSN: 1097-2765
    Digitale ISSN: 1097-4164
    Thema: Biologie , Medizin
    Publiziert von Elsevier im Namen von Cell Press.
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  • 9
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    Naa10p Inhibits Beige Adipocyte-Mediated Thermogenesis through N-α-acetylation of Pgc1α (2019)
    Elsevier
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    Publikationsdatum: 2019
    Beschreibung: 〈p〉Publication date: Available online 15 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Molecular Cell〈/p〉 〈p〉Author(s): Chen-Cheng Lee, Yi-Chun Shih, Ming-Lun Kang, Yi-Cheng Chang, Lee-Ming Chuang, Ramanan Devaraj, Li-Jung Juan〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉Diet-induced obesity can be caused by impaired thermogenesis of beige adipocytes, the brown-like adipocytes in white adipose tissue (WAT). Promoting brown-like features in WAT has been an attractive therapeutic approach for obesity. However, the mechanism underlying beige adipocyte formation is largely unknown. N-α-acetyltransferase 10 protein (Naa10p) catalyzes N-α-acetylation of nascent proteins, and overexpression of human Naa10p is linked to cancer development. Here, we report that both conventional and adipose-specific Naa10p deletions in mice result in increased energy expenditure, thermogenesis, and beige adipocyte differentiation. Mechanistically, Naa10p acetylates the N terminus of Pgc1α, which prevents Pgc1α from interacting with Pparγ to activate key genes, such as 〈em〉Ucp1〈/em〉, involved in beige adipocyte function. Consistently, fat tissues of obese human individuals show higher 〈em〉NAA10〈/em〉 expression. Thus, Naa10p-mediated N-terminal acetylation of Pgc1α downregulates thermogenic gene expression, making inhibition of Naa10p enzymatic activity a potential strategy for treating obesity.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S1097276519305647-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉
    Print ISSN: 1097-2765
    Digitale ISSN: 1097-4164
    Thema: Biologie , Medizin
    Publiziert von Elsevier im Namen von Cell Press.
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  • 10
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    One-Carbon Metabolism Supports S-Adenosylmethionine and Histone Methylation to Drive Inflammatory Macrophages (2019)
    Elsevier
    Details
    Publikationsdatum: 2019
    Beschreibung: 〈p〉Publication date: Available online 13 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Molecular Cell〈/p〉 〈p〉Author(s): Weiwei Yu, Zhen Wang, Kailian Zhang, Zhexu Chi, Ting Xu, Danlu Jiang, Sheng Chen, Wenxin Li, Xuyan Yang, Xue Zhang, Yingliang Wu, Di Wang〈/p〉 〈h5〉Summary〈/h5〉 〈div〉〈p〉Activated macrophages adapt their metabolic pathways to drive the pro-inflammatory phenotype, but little is known about the biochemical underpinnings of this process. Here, we find that lipopolysaccharide (LPS) activates the pentose phosphate pathway, the serine synthesis pathway, and one-carbon metabolism, the synergism of which drives epigenetic reprogramming for interleukin-1β (IL-1β) expression. Glucose-derived ribose and one-carbon units fed by both glucose and serine metabolism are synergistically integrated into the methionine cycle through 〈em〉de novo〈/em〉 ATP synthesis and fuel the generation of S-adenosylmethionine (SAM) during LPS-induced inflammation. Impairment of these metabolic pathways that feed SAM generation lead to anti-inflammatory outcomes, implicating SAM as an essential metabolite for inflammatory macrophages. Mechanistically, SAM generation maintains a relatively high SAM:S-adenosylhomocysteine ratio to support histone H3 lysine 36 trimethylation for IL-1β production. We therefore identify a synergistic effect of glucose and amino acid metabolism on orchestrating SAM availability that is intimately linked to the chromatin state for inflammation.〈/p〉〈/div〉 〈h5〉Graphical Abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S1097276519304964-fx1.jpg" width="375" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉
    Print ISSN: 1097-2765
    Digitale ISSN: 1097-4164
    Thema: Biologie , Medizin
    Publiziert von Elsevier im Namen von Cell Press.
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