Project 12

Deregulated transcriptome 3’ end diversification affecting thrombo-inflammation.

Home institution

Center for Thrombosis and Hemostasis, CTH (Mainz, Germany)

Supervisory team

primary: Prof. Dr. Sven Danckwardt (CTH), secondary: Dr. Elisabetta Castoldi (CARIM)

Project locations

CTH (Mainz, Germany), CARIM (Maastricht, Netherlands)

Joint PhD Degree

Universities of Mainz and Maastricht

Project details

The diversification of the transcriptome evolved as a global and evolutionarily conserved layer of gene regulation. In this project, we want to illuminate the pathology of thrombo-inflammation by exploring how transcriptome 3’ end diversification (TREND) affects components of blood coagulation and thereby causes perturbances of the hemostatic system. In a proof-of-concept study, we want to explore whether TREND of blood coagulation components can be exploited therapeutically to correct deregulated blood coagulation.

By applying high-throughput TRENDseq based sequencing, ESR12 will screen which blood coagulation factor mRNAs are regulated by TREND in cell cultures and murine and human blood cells. In cell cultures, specific properties of TREND-affected coagulation factors will be examined. A recently established miRNA target interaction atlas will serve as the source for identification of bona fide miRNAs. ESR12 will analyze how TREND of relevant coagulation factor RNAs is associated with a procoagulant phenotype in mice. To this end, the mouse phenotype will be compared with respective TREND isoforms expressed under inflammatory conditions. This work will be performed in connection with ESR2 and ESR7, who are using the same mice. A similar comparison will be made with mouse strains that have recently been generated to manipulate TREND signatures. At the second host CARIM, ESR12 will study how main TREND-regulated mRNAs encoding coagulation proteins can be used as future therapeutic targets. This work involves specific silencing of regulated TREND sites, by using morpholino-based antisense RNA therapies, which have already successfully been applied to correct aberrant splicing in factor V deficiency. In connection to ESR11, the fibrinogen gamma-chain gene, which produces two alternatively spliced mRNAs with different 3’-ends, each regulated by inflammatory stimuli, will serve as a prototype. Additionally, ESR12 will make several short visits to Bayer for bioinformatics training.


  • Processing and transcriptome expansion at the mRNA 3' end in health and disease: finding the right end. Ogorodnikov A, Kargapolova Y, Danckwardt S. Pflugers Arch. 2016
  • Large-scale identification of functional microRNA targeting reveals cooperative regulation of the hemostatic system. Nourse J, Braun J, Lackner K, Hüttelmaier S, Danckwardt S. J Thromb Haemost. 2018
  • p38 MAPK controls prothrombin expression by regulated RNA 3' end processing. Danckwardt S, Gantzert AS, Macher-Goeppinger S, Probst HC, Gentzel M, Wilm M, Gröne HJ, Schirmacher P, Hentze MW, Kulozik AE. Mol Cell. 2011
  • Transcriptome 3’end organization by PCF11 links alternative polyadenylation to formation and spontaneous regression of neuroblastoma. Ogorodnikov A, Levin M, Tattikota S, Tokalov S, Hoque M, Scherzinger D, Marini F, Poetsch A, Binder H, Macher-Goeppinger S, Probst HC, Tian B, Schaefer M, Lackner K, Westermann F, Danckwardt S. Nat Commun. 2018 Dec 14;9(1):5331. doi: 10.1038/s41467-018-07580-5.

Desirable student skills

  • Strong background and interest for gene regulatory mechanisms
  • Profound knowledge of the hemostatic system
  • Wet-lab expertise in the following field(s): molecular biology, cell culture work, animal work
Prof. Dr. Sven Danckwardt

Prof. Dr. Sven Danckwardt


Dr. Elisabetta Castoldi

Dr. Elisabetta Castoldi