Depledge lab

Research summary

Research in my lab focuses on several broad themes including:

(1) Characterizing the roles of diverse base modifications (including m6A) on host and viral RNAs during productive infections

(2) Investigating the functions of herpesviral latency-associated transcripts and other non-coding RNAs (including miRNAs) during both lytic and latent infections

(3) Characterizing the transcriptional complexity of diverse viruses (herpesviruses, adenoviruses, coronaviruses) in distinct cell types, such as epithelial cells and neurons.

This is achieved through the integration of computational biology with a variety of high-throughput molecular techniques to study multiple aspects of virus-host interactions on a genome-wide scale. Specific targets of interest are subsequently followed up using classical molecular biology approaches.

Group members

Prof. D. Depledge/MHH

Team leader

  • Prof. Dr. Daniel P. Depledge

Medizinische Hochschule Hannover (Hannover Medical School)
Institute of Virology, OE5230
Carl-Neuberg-Str. 1
30625 Hannover

Phone +49 (0) 511 532 4310
Departmental Secretary +49 (0) 511 532 6736
Laboratory +49 (0) 511 532 4327 | FAX +49 (0) 511 532 8736
Email Depledge.Daniel [at] MH-Hannover.de

Dan obtained a BSc in Biological Sciences and an MSc in Bioinformatics at the University of Exeter. He completed his PhD on the comparative genomics of Leishmania in 2009 at the University of York. For his first postdoc, he switched fields to develop new approaches for the targeted capture and sequencing of viruses from clinical samples in the lab of Prof. Judy Breuer at University College London. He then obtained an Medical Research Foundation New Investigator Award that allowed him to pursue his long-standing interest in herpesvirus latency and that led to the discovery of the VZV latency transcript. In 2017, he joined the lab of Prof. Ian Mohr at NYU to work on viral latency and the role of RNA modifications in viral infections. In 2019 he became an Assistant Professor at NYU before joining the Institute of Virology at the Hannover Medical School (MHH) in 2021 as a DZIF Associate Professor.

 

Alumni of the Group

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Team

Dr. Ruth Verstraten

Dr. Ruth Verstraten

  • Postdoctoral scientist
    • Tel.: +49 511 532 -4310
Email
Dr. Carolin Vogt

Dr. Carolin Vogt

  • Postdoctoral scientist
    • Tel.: +49 511 532 -4307
Email
Elene Loliashvili

Elene Loliashvili

  • PhD student
    • Tel.: +49 511 532 -4310
Email

Niclas Ritter

  • PhD student

Pierina Cetraro

  • PhD student

Selected articles, reviews, and book chapters:

  1. Depledge DP, Breuer J. Varicella-Zoster Virus-Genetics, Molecular Evolution and Recombination. Curr Top Microbiol Immunol. 2021. https://doi.org/10.1007/82_2021_238
  2. Srinivas KP, Depledge DP, Abebe JS, Rice SA, Mohr I, Wilson AC. Widespread remodeling of the m6A RNA-modification landscape by a viral regulator of RNA processing and export. PNAS. 2021 https://doi.org/10.1073/pnas.2104805118
  3. Burgess HM, Depledge DP, Thompson L, Srinivas KP, Grande RC, Vink EI, Abebe JS, Blackaby WP, Hendrick A, Albertella MR, Kouzarides T, Stapleford KA, Wilson AC, Mohr I. Targeting the m6A RNA modification pathway blocks SARS-CoV-2 and HCoV-OC43 replication. Genes & Dev. 2021 https://doi.org/10.1101/gad.348320.121
  4. Ouwendijk WJD*, Depledge DP*, Rajbhandari  L, Lenac-Rovis T, Jonjic S, Breuer J, Venkatesan A, Verjans GMGM, Sadaoka T. Expression of varicella-zoster virus VLT-ORF63 fusion transcript induces broad viral gene expression during reactivation from neuronal latency. Nature Comms. 2020. https://doi.org/10.1038/s41467-020-20031-4. *joint first authors
  5. Price AM, Hayer EK, McIntyre ABR, Gokhale NS, Abebe JS, Della Fera AN, Mason CE, Horner SM, Wilson AC, Depledge DP, Weitzman MD. Direct RNA sequencing reveals m6A modifications on adenovirus RNA are necessary for efficient splicing. Nature Comms. 2020. https://doi.org/10.1038/s41467-020-19787-6
  6. Braspenning SE, Sadaoka T, Breuer J, Verjans GMGM, Ouwendijk WJD, Depledge DP. Decoding the architecture of the varicella-zoster virus transcriptome. mBio. 2020. https://doi.org/10.1128/mbio.01568-20
  7. Hu M*, Depledge DP*, Flores Cortes E, Breuer J, Schang LM. Chromatin dynamics and the transcriptional competence of HSV-1 genomes during lytic infections. PLoS Path. 2019. https://doi.org/10.1371/journal.ppat.1008076 *joint first authors
  8. Depledge DP, Puthankalam SP, Sadaoaka T, Beady D, Mori Y, Placantonakis D, Mohr I, Wilson AC. Native RNA sequencing on nanopore arrays redefines the transcriptional complexity of a viral pathogen. Nature Comms. 2019. https://doi.org/10.1038/s41467-019-08734-9
  9. Depledge DP, Sadaoka T, Ouwendijk WJD. Molecular aspects of Varicella-Zoster Virus latency. Viruses. 2018. https://doi.org/10.3390/v10070349 [Invited Review]
  10. Depledge DP, Mohr I, Wilson AC. Going the distance - optimising RNA-Seq strategies for transcriptomic analysis of complex viral genomes. J. Virol. 2018. https://doi.org/10.1128/JVI.01342-18 [Invited Review]
  11. Rubio RM, Depledge DP, Bianco C, Thompson L, Mohr I. RNA m6A modification enzymes shape innate responses to DNA by regulating interferon β. Genes & Dev. 2018. https://doi.org/10.1101/gad.319475.118  
  12. Depledge DP*, Ouwendijk WJD*, Sadaoka T*, Braspenning S, Mori Y, Cohrs R, Verjans GMGM# & Breuer J#. A varicella-zoster virus latency transcript represses viral regulatory gene 61 expression. Nature Communications. 2018. https://doi.org/10.1038/s41467-018-03569-2 *joint first authors #joint senior author
  13. Depledge DP, Brown J, Macanovic J, Underhill G, Breuer J. Viral genome sequencing proves nosocomial transmission of fatal varicella. J Infect Dis. 2016. https://doi.org/10.1093/infdis/jiw398 [Article featured in Infectious Disease Archives]
  14. Depledge DP, Yamanishi K, Gomi Y, Gershon A, Breuer J. Deep-sequencing of distinct preparations of the live-attenuated VZV vaccine reveals a conserved core of attenuating SNPs. J Virol. 2016. https://doi.org/10.1128/JVI.00998-16 [Article of significant interest selected by JVI Editors]
  15. Lassalle F*, Depledge DP*, Reeves MB, Brown AC, Christiansen MT, Tutill HJ, Williams RJ, Einer-Jensen K, Holdstock J, Atkinson C, Brown JR, van Loenen FB, Clark DA, Griffiths PD, Verjans GMGM, Schutten M, Milne RSB, Balloux F, Breuer J. Islands of linkage in an ocean of pervasive recombination reveals two-speed evolution of human cytomegalovirus genomes. Virus Evol. 2016. https://doi.org/10.1093/ve/vew017 * joint first authors
  16. Sadaoka T, Depledge DP, Rajbhandari L, Venkatesan A, Breuer J, Cohen JI. In vitro system using human neurons demonstrates that varicella-zoster vaccine virus is impaired for reactivation, but not latency. Proc Natl Acad Sci USA. 2016. https://doi.org/10.1073/pnas.1522575113 
  17. Weinert LA, Depledge DP, Kundu S, Gershon AA, Nichols RA, Balloux F, Welch JJ, Breuer J. Rates of vaccine evolution show strong effects of latency: implications for varicella zoster virus epidemiology. Mol Biol Evol. 2015. https://doi.org/10.1093/molbev/msu406
  18. Depledge DP*, Gray ER*, Kundu S, Cooray S, Poulsen A, Aaby P, Breuer J. Evolution of cocirculating varicella-zoster virus genotypes during a chickenpox outbreak in Guinea-Bissau. J Virol. 2014. http://dx.doi.org/10.1128/JVI.02337-14 *joint first authors
  19. Depledge DP, Kundu S, Jensen NJ, Gray ER, Jones M, Steinberg S, Gershon A, Kinchington PR, Schmid DS, Balloux F, Nichols RA, Breuer J. Deep sequencing of viral genomes provides insight into the evolution and pathogenesis of varicella zoster virus and its vaccine in humans. Mol Biol Evol. 2014. https://doi.org/10.1093/molbev/mst210
  20. Depledge DP, Palser AL, Watson SJ, Lai IY, Gray ER, Grant P, Kanda RK, Leproust E, Kellam P, Breuer J. Specific capture and whole-genome sequencing of viruses from clinical samples. PLoS One. 2011. https://doi.org/10.1371/journal.pone.0027805.t001

Current funding