Analysis and impact of epitranscriptomic modifications on life cycle of retroviruses

UNIL main applicant

Dr Angela Ciuffi, Faculty of Biology and Medicine

ULB main applicant

Prof. Carine Van Lint, Faculty of Sciences




Joint research project


In the past few years, the field of epitranscriptomic collected promising data highlighting the important role of mRNAs modifications in modulating several molecular and biological processes such as stability, splicing, export and translation of mRNAs, underlying the versatile coding, structural and catalytic functions of RNA (Zhao et al., 2017). The term epitranscriptomic was coined in analogy to epigenetic regulation mediated by modifications of histones and DNA.

So far, over one hundred post-transcriptional modifications of RNA molecules have been described, occurring at almost every position of pyrimidine and purine rings, including methylation, hydroxylation, acylation, glycosylation, isomerization, sulfation and adjunction of amino acids or nucleotides, enriching for the nucleotide repertoire, and which vary between different species of RNA molecules (mRNA, tRNA, rRNA, lncRNA, sncRNA...), between cellular locations or organelles, and across different organisms of all domains of life (Machnicka et al., 2013). Despite this, the field of epitranscriptomics remained largely uncharted, mainly due to technical limitations and constraints. The development of novel biological tools and technologies, such as specific antibodies and next-generation sequencing (NGS), are helping to overcome some of these limitations.

m6A is currently the most investigated epitranscriptomic modification thanks to the availability of an antibody recognizing specifically this modification. m6A is commonly found in both eukaryotic mRNAs and viral RNAs, with unique distribution patterns along the molecule (Dominissini et al., 2012; Schwartz et al., 2014). Indeed, m6A is mostly abundant at translation start sites, stop codons and 3’UTRs, thereby affecting stability and translation efficiency (Dominissini et al., 2012; Schwartz et al., 2014). However, individual RNA molecules of the same primary sequence are not all modified equally, providing additional diversity and potentially diverse fates or biological functions.

m5C modification in RNA is more challenging to detect than its DNA counterpart, but uses a similar approach with bisulfite conversion. Recent studies suggest that the m5C/C ratio in mRNAs is extremely low, pointing to a more targeted modification of specific cytosines (Squires et al., 2012). Despite the under-representation of m5C in mRNAs, these modified bases are mostly located in untranslated regions (UTR), and rarely found in coding sequences (Schaefer, 2015). The impact of m5C on mRNA fate or function remains to be defined, but seems to be linked to RNA degradation and translation efficiency (Squires et al., 2012).

Therefore, our research project aims at characterizing in detail the major epitranscriptomic modifications of viral RNAs of different retroviruses, assessing their implication on viral replication, and comparing the epitranscriptomic strategies used among the different retroviral genera. A better understanding of viral epitranscriptomics will provide additional knowledge on retroviral life cycle and pathogenesis, as well as potentially identify novel therapeutic strategies. We will concentrate at first on m6A and m5C post-transcriptional modifications, and on three retroviral genera: lentiviruses (HIV and SIV, human and simian immunodeficiency viruses), the oncogenic deltaretroviruses (HTLV and BLV, human T-lymphotropic virus and bovine leukemia virus), and the oncogenic gammaretrovirus (MLV, mouse leukemia virus). In order to do this, we rely on the expertise of the main applicants, renowned in the field of HIV-1 research. The two laboratories implicated in the present proposal have a strong experience in different fields of retroviral biology and pathogenicity, as attested by their publications.

To summarize, the present research project aims in a multidisciplinary approach to decipher the post- transcriptional modifications of retroviral RNAs. As it has been demonstrated that mRNAs post-transcriptional modifications modulate expression of viral genes, it clearly appears that a better understanding of the epitranscriptomic mechanism implicated in viral life cycle is necessary to improve our knowledge of viral pathogenicity.


  • July 2018: organization of the first workshop in Lausanne in order to define precisely the schedule of the experiments to do and describe in detail the protocols to apply.
  • January 2019: organization of the second workshop in Belgium with both teams in order to analyze the first results, brainstorm all together and discuss the essential points required for the application to the Lead Agency Procedure 2019.


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