Central resource facility for virus genomics and host transcriptomics

Research area: Molecular Virology

Complete viral genome analyses and transcriptomics studies of virus-infected host cells have become key technologies in the field of RNA virus research. Recent advances in next-generation sequencing (NGS) and microarray technologies resulted in higher throughput, improved accuracy and lower costs. The technical improvements and the wealth of information obtained from these technologies make them extremely valuable tools for studying RNA viruses and virus-host interactions in vitro and in vivo.
The microarray facility of Z02 will provide the infrastructure to plan and perform whole transcriptome analyses using the Agilent microarray platform. The available microarrays encompass all known protein-coding genes and more than 30,000 unique long non-coding RNAs (lncRNA), the latter being suggested to play important roles in virus replication. Also, expression profiles obtained in these analyses will be linked to information on viral and cellular non-coding RNA-associated interactions provided by recently developed databases such as ViRBase.
The NGS infrastructure of Z02 project will perform (i) whole transcriptome analyses using RNA-seq (ii) targeted resequencing (including amplicon sequencing), (iii) tRNA-seq and (iv) RNA virus genome sequencing for all members of the CRC. Furthermore (v), viral RNA genome quasispecies will be analyzed using  recently established protocols suitable to generate “PCR and sequencing error bias free” NGS datasets and study true genetic variants of RNA virus genomes by circle sequencing (Cir-seq).
NGS via RNA-seq of host cells will be used to (vi) analyze samples for which appropriate DNA microarrays are not (yet) available or (vii) obtain parallel sequence information for both host cell and virus (Dual-seq) including single-cell RNA sequencing (scRNA-seq) of virus-infected/mock-infected cells.
The Z02 project will provide biostatistical support in the planning of microarray and NGS experiments, generate genome sequencing and expression profiling data and apply bioinformatics methods, such as over-representation and gene-set enrichment analyses, to identify specific signalling pathways and regulatory networks relevant to specific RNA virus infections. Together with other CRC1021 researchers, we will provide additional training (sample preparation, bioinformatics) to PhD students and postdocs using these technologies in their projects. Also, we will contribute to developing hypotheses and writing manuscripts arising from data generated in the Z02 project.

Project-related publications of the investigators:

  • Vazquez-Armendariz AI, Heiner M, El Agha E, Salwig I, Hoek A, Hessler MC, Shalashova I, Shrestha A, Carraro G, Mengel JP, Gunther A, Morty RE, Vadasz I, Schwemmle M, Kummer W, Hain T, Goesmann A, Bellusci S, Seeger W, Braun T, Herold S. 2020. Multilineage murine stem cells generate complex organoids to model distal lung development and disease. EMBO J 39:e103476.
  • Shaban MS, Müller C, Mayr-Buro C, Weiser H, Albert B, Weber A, Linne U, Hain T, Babayev I, Karl N, Hofmann N, Becker S, Herold S, Lienhard Schmitz M, Ziebuhr J, Kracht M. 2020. Inhibiting coronavirus replication in cultured cells by chemical ER stress. bioRxiv doi:10.1101/ 2020.08.26.266304.
  • Schwengers O, Hoek A, Fritzenwanker M, Falgenhauer L, Hain T, Chakraborty T, Goesmann A. 2020. ASA3P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates. PLoS Comput Biol 16:e1007134.
  • Schwengers O, Hain T, Chakraborty T, Goesmann A. 2020. ReferenceSeeker: rapid determination of appropriate reference genomes. Journal of Open Source Software 5:1994.
  • Shrestha A, Carraro G, Nottet N, Vazquez-Armendariz AI, Herold S, Cordero J, Singh I, Wilhelm J, Barreto G, Morty R, El Agha E, Mari B, Chen C, Zhang JS, Chao CM, Bellusci S. 2019. A critical role for miR-142 in alveolar epithelial lineage formation in mouse lung development. Cell Mol Life Sci 76:2817-2832.
  • Hu P, Wilhelm J, Gerresheim GK, Shalamova LA, Niepmann M. 2019. Lnc-ITM2C-1 and GPR55 Are Proviral Host Factors for Hepatitis C Virus. Viruses 11.
  • Whitmer SLM, Strecker T, Cadar D, Dienes HP, Faber K, Patel K, Brown SM, Davis WG, Klena JD, Rollin PE, Schmidt-Chanasit J, Fichet-Calvet E, Noack B, Emmerich P, Rieger T, Wolff S, Fehling SK, Eickmann M, Mengel JP, Schultze T, Hain T, Ampofo W, Bonney K, Aryeequaye JND, Ribner B, Varkey JB, Mehta AK, Lyon GM, 3rd, Kann G, De Leuw P, Schuettfort G, Stephan C, Wieland U, Fries JWU, Kochanek M, Kraft CS, Wolf T, Nichol ST, Becker S, Stroher U, Gunther S. 2018. New Lineage of Lassa Virus, Togo, 2016. Emerg Infect Dis 24:599-602.
  • Ehmann R, Kristen-Burmann C, Bank-Wolf B, Konig M, Herden C, Hain T, Thiel HJ, Ziebuhr J, Tekes G. 2018. Reverse Genetics for Type I Feline Coronavirus Field Isolate To Study the Molecular Pathogenesis of Feline Infectious Peritonitis. mBio 9.
  • Rodriguez-Gil A, Ritter O, Saul VV, Wilhelm J, Yang CY, Grosschedl R, Imai Y, Kuba K, Kracht M, Schmitz ML. 2017. The CCR4-NOT complex contributes to repression of Major Histocompatibility Complex class II transcription. Sci Rep 7:3547.
  • Poppe M, Wittig S, Jurida L, Bartkuhn M, Wilhelm J, Muller H, Beuerlein K, Karl N, Bhuju S, Ziebuhr J, Schmitz ML, Kracht M. 2017. The NF-kappaB-dependent and -independent transcriptome and chromatin landscapes of human coronavirus 229E-infected cells. PLoS Pathog 13:e1006286.