How New RNA Genes Are Born
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
A Co-Opted ISG15-USP18 Binding Mechanism Normally Reserved for Deisgylation Controls Type I IFN Signalling
bioRxiv preprint doi: https://doi.org/10.1101/2021.06.01.446527; this version posted June 3, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 A co-opted ISG15-USP18 binding mechanism normally reserved for deISGylation controls 2 type I IFN signalling 3 4 5 6 Andri Vasou1, Katie Nightingale2, Vladimíra Cetkovská 1, Connor G.G. Bamford3‡, Jelena 7 Andrejeva1, Richard E. Randall1, John McLauchlan3, Michael P. Weekes2, David J Hughes1* 8 9 10 11 1Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St 12 Andrews, United Kingdom. 2Cambridge Institute for Medical Research, Hills Road, Cambridge, 13 United Kingdom 3MRC-University of Glasgow Centre for Virus Research, Glasgow, United 14 Kingdom. 15 16 17 ‡ Present addresses: Wellcome-Wolfson Institute for Experimental Medicine, Queen’s 18 University, Belfast UK. 19 20 21 22 * Corresponding author: [email protected]; Tel: +44 1334 467197 23 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.06.01.446527; this version posted June 3, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 24 Abstract 25 Type I interferon (IFN) signalling induces the expression of several hundred IFN-stimulated 26 genes that provide an unfavourable environment for viral replication. -
Ancient Metaproteomics: a Novel Approach for Understanding Disease And
Ancient metaproteomics: a novel approach for understanding disease and diet in the archaeological record Jessica Hendy PhD University of York Archaeology August, 2015 ii Abstract Proteomics is increasingly being applied to archaeological samples following technological developments in mass spectrometry. This thesis explores how these developments may contribute to the characterisation of disease and diet in the archaeological record. This thesis has a three-fold aim; a) to evaluate the potential of shotgun proteomics as a method for characterising ancient disease, b) to develop the metaproteomic analysis of dental calculus as a tool for understanding both ancient oral health and patterns of individual food consumption and c) to apply these methodological developments to understanding individual lifeways of people enslaved during the 19th century transatlantic slave trade. This thesis demonstrates that ancient metaproteomics can be a powerful tool for identifying microorganisms in the archaeological record, characterising the functional profile of ancient proteomes and accessing individual patterns of food consumption with high taxonomic specificity. In particular, analysis of dental calculus may be an extremely valuable tool for understanding the aetiology of past oral diseases. Results of this study highlight the value of revisiting previous studies with more recent methodological approaches and demonstrate that biomolecular preservation can have a significant impact on the effectiveness of ancient proteins as an archaeological tool for this characterisation. Using the approaches developed in this study we have the opportunity to increase the visibility of past diseases and their aetiology, as well as develop a richer understanding of individual lifeways through the production of molecular life histories. iii iv List of Contents Abstract ............................................................................................................................... -
Type I IFN Signaling Infection by Up-Regulating Typhimurium
Enhanced Antibacterial Potential in UBP43-Deficient Mice against Salmonella typhimurium Infection by Up-Regulating Type I IFN Signaling This information is current as of September 24, 2021. Keun Il Kim, Oxana A. Malakhova, Kasper Hoebe, Ming Yan, Bruce Beutler and Dong-Er Zhang J Immunol 2005; 175:847-854; ; doi: 10.4049/jimmunol.175.2.847 http://www.jimmunol.org/content/175/2/847 Downloaded from References This article cites 45 articles, 21 of which you can access for free at: http://www.jimmunol.org/content/175/2/847.full#ref-list-1 http://www.jimmunol.org/ Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication by guest on September 24, 2021 *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2005 by The American Association of Immunologists All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology Enhanced Antibacterial Potential in UBP43-Deficient Mice against Salmonella typhimurium Infection by Up-Regulating Type I IFN Signaling1 Keun Il Kim,2* Oxana A. Malakhova,* Kasper Hoebe,† Ming Yan,* Bruce Beutler,† and Dong-Er Zhang3* ISG15 is an IFN-inducible ubiquitin-like protein and its expression and conjugation to target proteins are dramatically induced upon viral or bacterial infection. -
Decelerated Genome Evolution in Modern Vertebrates Revealed by Analysis of Multiple Lancelet Genomes
ARTICLE Received 20 May 2014 | Accepted 18 Nov 2014 | Published 19 Dec 2014 DOI: 10.1038/ncomms6896 OPEN Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes Shengfeng Huang1, Zelin Chen1, Xinyu Yan1, Ting Yu1, Guangrui Huang1, Qingyu Yan1, Pierre Antoine Pontarotti2, Hongchen Zhao1, Jie Li1, Ping Yang1, Ruihua Wang1, Rui Li1, Xin Tao1, Ting Deng1, Yiquan Wang3,4, Guang Li3,4, Qiujin Zhang5, Sisi Zhou1, Leiming You1, Shaochun Yuan1, Yonggui Fu1, Fenfang Wu1, Meiling Dong1, Shangwu Chen1 & Anlong Xu1,6 Vertebrates diverged from other chordates B500 Myr ago and experienced successful innovations and adaptations, but the genomic basis underlying vertebrate origins are not fully understood. Here we suggest, through comparison with multiple lancelet (amphioxus) genomes, that ancient vertebrates experienced high rates of protein evolution, genome rearrangement and domain shuffling and that these rates greatly slowed down after the divergence of jawed and jawless vertebrates. Compared with lancelets, modern vertebrates retain, at least relatively, less protein diversity, fewer nucleotide polymorphisms, domain combinations and conserved non-coding elements (CNE). Modern vertebrates also lost substantial transposable element (TE) diversity, whereas lancelets preserve high TE diversity that includes even the long-sought RAG transposon. Lancelets also exhibit rapid gene turnover, pervasive transcription, fastest exon shuffling in metazoans and substantial TE methylation not observed in other invertebrates. These new lancelet genome sequences provide new insights into the chordate ancestral state and the vertebrate evolution. 1 State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China. 2 Evolution Biologique et Mode´lisation UMR 7353 Aix Marseille Universite´/CNRS, 3 Place Victor Hugo, 13331 Marseille, France. -
Genesis of Non-Coding RNA Genes in Human Chromosome 22—A Sequence Connection with Protein Genes Separated by Evolutionary Time
non-coding RNA Perspective Genesis of Non-Coding RNA Genes in Human Chromosome 22—A Sequence Connection with Protein Genes Separated by Evolutionary Time Nicholas Delihas Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, NY 11794-5222, USA; [email protected] Received: 16 July 2020; Accepted: 1 September 2020; Published: 3 September 2020 Abstract: A small phylogenetically conserved sequence of 11,231 bp, termed FAM247, is repeated in human chromosome 22 by segmental duplications. This sequence forms part of diverse genes that span evolutionary time, the protein genes being the earliest as they are present in zebrafish and/or mice genomes, and the long noncoding RNA genes and pseudogenes the most recent as they appear to be present only in the human genome. We propose that the conserved sequence provides a nucleation site for new gene development at evolutionarily conserved chromosomal loci where the FAM247 sequences reside. The FAM247 sequence also carries information in its open reading frames that provides protein exon amino acid sequences; one exon plays an integral role in immune system regulation, specifically, the function of ubiquitin-specific protease (USP18) in the regulation of interferon. An analysis of this multifaceted sequence and the genesis of genes that contain it is presented. Keywords: de novo gene birth; gene evolution; protogene; long noncoding RNA genes; pseudogenes; USP18; GGT5; Alu sequences 1. Introduction The genesis of genes has been a major topic of interest for several decades [1,2]. One mechanism of gene formation is by duplication of existing genes [1,3]. -
USP18 Is a Key Regulator of the Interferon-Driven Gene Network Modulating Pancreatic Beta Cell Inflammation and Apoptosis
Citation: Cell Death and Disease (2012) 3, e419; doi:10.1038/cddis.2012.158 & 2012 Macmillan Publishers Limited All rights reserved 2041-4889/12 www.nature.com/cddis USP18 is a key regulator of the interferon-driven gene network modulating pancreatic beta cell inflammation and apoptosis I Santin*,1, F Moore1, FA Grieco1, P Marchetti2, C Brancolini3 and DL Eizirik1 Type 1 diabetes (T1D) is an autoimmune disease targeting pancreatic beta cells. Genome-wide association studies and gene expression analysis identified interferon (IFN)-driven gene networks as crucial pathways in the pathogenesis of T1D. IFNs are linked to the response to viral infections and might contribute to the initiation of the autoimmune process in T1D. We presently analyzed the role of ubiquitin-specific peptidase 18 (USP18), an interferon-stimulated gene 15-specific protease, on IFN-induced pancreatic beta cell inflammation and apoptosis. Our findings indicate that USP18 inhibition induces inflammation by increasing the STAT signaling and exacerbates IFN-induced beta cell apoptosis by the mitochondrial pathway of cell death. USP18 regulates activation of three BH3-only proteins, namely, DP5, Bim and PUMA in pancreatic beta cells, suggesting a direct link between regulators of the type I IFN signaling pathway and members of the BCL-2 family. USP18 depletion increases the expression of the T1D candidate gene MDA5, leading to an upregulation of double-stranded RNA-induced chemokine production. These data suggest a cross talk between the type I IFN signaling pathway and a candidate gene for T1D to increase pro-inflammatory responses in beta cells. The present study shows that USP18 is a key regulator of IFN signaling in beta cells and underlines the importance of this pathway in beta cell inflammation and death. -
Proteomic Strategies for Cultural Heritage: from Bones to Paintings☆
Microchemical Journal 126 (2016) 341–348 Contents lists available at ScienceDirect Microchemical Journal journal homepage: www.elsevier.com/locate/microc Proteomic strategies for cultural heritage: From bones to paintings☆ Roberto Vinciguerra a, Addolorata De Chiaro a, Piero Pucci a, Gennaro Marino b, Leila Birolo a,⁎ a Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario Monte S.Angelo, Via Cinthia, Napoli, Italy b Università degli Studi ‘Suor Orsola Benincasa’, 80132 Napoli, Italy article info abstract Article history: In recent years, proteomics procedures have become increasingly popular for the characterization of proteina- Received 30 July 2015 ceous materials in ancient samples of several cultural heritage objects. The knowledge of the materials used in Received in revised form 18 December 2015 a work of art is crucial, not only to give an insight in the historical context of objects and artists, but also to analyse Accepted 18 December 2015 degradation processes taking place in aged objects and to develop appropriate conservation and/or restoration Available online 29 December 2015 treatments. However, protocols routinely applied for typical modern samples still need to be fully adapted to Keywords: take into account the low amount of proteinaceous material, the heterogeneity and the unusual physical state Proteomics of the samples, as well as the high levels of damage found in ancient samples. This paper deals with some exam- Ancient proteins ples of the adaptation of classical proteomic strategies in the analysis of ancient samples to meet the different LC-MS/MS aims in the cultural heritage field. © 2015 Elsevier B.V. All rights reserved. -
Analysis of 5000 Year-Old Human Teeth Using Optimized Large-Scale And
Analysis of 5000 year-old human teeth using optimized large-scale and targeted proteomics approaches for detection of sex-specific peptides Carine Froment, Mathilde Hourset, Nancy Sáenz-Oyhéréguy, Emmanuelle Mouton-Barbosa, Claire Willmann, Clément Zanolli, Rémi Esclassan, Richard Donat, Catherine Thèves, Odile Burlet-Schiltz, et al. To cite this version: Carine Froment, Mathilde Hourset, Nancy Sáenz-Oyhéréguy, Emmanuelle Mouton-Barbosa, Claire Willmann, et al.. Analysis of 5000 year-old human teeth using optimized large-scale and targeted proteomics approaches for detection of sex-specific peptides. Journal of Proteomics, Elsevier, 2020, 211, pp.103548. 10.1016/j.jprot.2019.103548. hal-02322441 HAL Id: hal-02322441 https://hal.archives-ouvertes.fr/hal-02322441 Submitted on 18 Nov 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Journal Pre-proof Analysis of 5000year-old human teeth using optimized large- scale and targeted proteomics approaches for detection of sex- specific peptides Carine Froment, Mathilde Hourset, Nancy Sáenz-Oyhéréguy, Emmanuelle Mouton-Barbosa, Claire Willmann, Clément Zanolli, Rémi Esclassan, Richard Donat, Catherine Thèves, Odile Burlet- Schiltz, Catherine Mollereau PII: S1874-3919(19)30320-3 DOI: https://doi.org/10.1016/j.jprot.2019.103548 Reference: JPROT 103548 To appear in: Journal of Proteomics Received date: 24 January 2019 Revised date: 30 August 2019 Accepted date: 7 October 2019 Please cite this article as: C. -
STAT2 Is an Essential Adaptor in USP18-Mediated Suppression of Type I Interferon Signaling
ARTICLES STAT2 is an essential adaptor in USP18-mediated suppression of type I interferon signaling Kei-ichiro Arimoto1,8, Sara Löchte2,8, Samuel A Stoner1, Christoph Burkart1, Yue Zhang3, Sayuri Miyauchi1, Stephan Wilmes2, Jun-Bao Fan1, Jürgen J Heinisch2, Zhi Li4, Ming Yan1, Sandra Pellegrini4, Frédéric Colland5,7, Jacob Piehler2 & Dong-Er Zhang1,3,6 Type I interferons (IFNs) are multifunctional cytokines that regulate immune responses and cellular functions but also can have detrimental effects on human health. A tight regulatory network therefore controls IFN signaling, which in turn may interfere with medical interventions. The JAK–STAT signaling pathway transmits the IFN extracellular signal to the nucleus, thus resulting in alterations in gene expression. STAT2 is a well-known essential and specific positive effector of type I IFN signaling. Here, we report that STAT2 is also a previously unrecognized, crucial component of the USP18-mediated negative-feedback control in both human and mouse cells. We found that STAT2 recruits USP18 to the type I IFN receptor subunit IFNAR2 via its constitutive membrane-distal STAT2-binding site. This mechanistic coupling of effector and negative-feedback functions of STAT2 may provide novel strategies for treatment of IFN-signaling-related human diseases. Type I interferon (IFN) signaling has emerged as a highly complex thereby resulting in formation of the DNA-binding STAT1–STAT2– regulatory network coordinating the host’s defense against pathogens IRF9 ternary complex IFN-stimulated gene factor 3 (ISGF3). ISGF3 and cancer via expression of over 300 IFN-stimulated genes (ISGs)1,2. promotes expression of genes with an IFN-stimulated response ele- Proteins encoded by ISGs include cytokines and chemokines that mod- ment in their promoters12,13. -
SYSTEMS BIOLOGY Ancient Protein Complexes Revealed
RESEARCH HIGHLIGHTS SYSTEMS BIOLOGY Ancient protein complexes revealed A systematic analysis of protein-complex history, they applied the approach to eight some interesting conclusions. For example, composition across a billion years of evo- species—mouse, frog, fly, worm, sea urchin, despite the fact that the majority of human lution reveals a spectrum of conservation. sea anemone, amoeba and yeast—spanning proteins arose in animals, they found that by Comparative analyses of protein-protein a billion years of evolution. and large, most stable human protein com- interaction networks from Escherichia coli to With this massive set of experiments, the plexes were likely inherited from a unicellular humans have shown that such networks are researchers identified and quantified 13,386 ancestor. Membership in such ancient com- conserved and relatively slow-evolving. Yet protein orthologues. They developed a plexes was either conserved or mixed with open questions remain about whether physi- machine learning–classification method to animal-specific components, and these com- cal interactions are preserved between evolu- pull out interactions that were conserved plexes tended to be abundant, ubiquitously tionarily distinct species, what these protein between human proteins and their worm, expressed and functionally associated with complexes are and what they do. fly, mouse and sea urchin orthologues (the core cellular processes. The relatively rare These are some of the questions that data from the other four species were used complexes consisting solely of proteins that Andrew Emili of the University of Toronto, to benchmark the approach). Their final net- arose in animals, in contrast, tended to have Edward Marcotte of the University of Texas at work contained 16,655 human co-complex functions strongly linked to multicellularity. -
Type I IFN Is Siloed in Endosomes BRIEF REPORT Jennie B
Type I IFN is siloed in endosomes BRIEF REPORT Jennie B. Altmana, Justin Tafta, Tim Wedekingb, Conor N. Grubera, Michael Holtmannspötterb,c, Jacob Piehlerb,d, and Dusan Bogunovica,e,f,g,1 aDepartment of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029; bDivision of Biophysics, Department of Biology, Osnabrück University, 49076 Osnabrück, Germany; cIntegrated Bioimaging Facility, Osnabrück University, 49076 Osnabrück, Germany; dCenter for Cellular Nanoanalytics, Osnabrück University, 49076 Osnabrück, Germany; eDepartment of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029; fPrecision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029; and gMindich Child Heath and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 Edited by Tak W. Mak, University of Toronto, Toronto, ON, Canada, and approved June 16, 2020 (received for review December 6, 2019) Type I IFN (IFN-I) is thought to be rapidly internalized and degraded ISGs in ISG15- and USP18-deficient cells, but not control cells following binding to its receptor and initiation of signaling. How- (Fig. 1B). Thus, transcription occurs long after the elimination of ever, many studies report the persistent effects mediated by IFN-I IFN-I in ISG15- and USP18-deficient cells. for days or even weeks, both ex vivo and in vivo. These long- We investigated molecules acting farther upstream and de- lasting effects are attributed to downstream signaling molecules tected pSTAT1 and pSTAT2 (mediators of IFN-I proximal sig- or induced effectors having a long half-life, particularly in specific naling) (9) in ISG15- and USP18-deficient cells, but not control cell types. -
Ancient Protein Analysis in Archaeology
This is a repository copy of Ancient protein analysis in archaeology. White Rose Research Online URL for this paper: https://eprints.whiterose.ac.uk/171551/ Version: Published Version Article: Hendy, Jessica orcid.org/0000-0002-3718-1058 (2021) Ancient protein analysis in archaeology. Science Advances. eabb9314. ISSN 2375-2548 https://doi.org/10.1126/sciadv.abb9314 Reuse This article is distributed under the terms of the Creative Commons Attribution-NonCommercial (CC BY-NC) licence. This licence allows you to remix, tweak, and build upon this work non-commercially, and any new works must also acknowledge the authors and be non-commercial. You don’t have to license any derivative works on the same terms. More information and the full terms of the licence here: https://creativecommons.org/licenses/ Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request. [email protected] https://eprints.whiterose.ac.uk/ SCIENCE ADVANCES | REVIEW ANTHROPOLOGY Copyright © 2021 The Authors, some Ancient protein analysis in archaeology rights reserved; exclusive licensee Jessica Hendy1,2 American Association for the Advancement of Science. No claim to The analysis of ancient proteins from paleontological, archeological, and historic materials is revealing insights original U.S. Government into past subsistence practices, patterns of health and disease, evolution and phylogeny, and past environments. Works. Distributed This review tracks the development of this field, discusses some of the major methodological strategies used, and under a Creative synthesizes recent developments in archeological applications of ancient protein analysis.