Mots-Clés

Transcriptomics Splicing Hepatitis B Virus Nanopore

Description

Title: Exploration and Description of HBV spliced-variants from Nanopore long-read sequencing.

Background:

The Hepatitis B Virus has a circular DNA genome expressing 8 major viral RNAs (preC, pgRNA, preS1, preS2, S, L-HBx, HBx and S-HBx) and 22 splice variants (20 deriving from pgRNA, 2 from preS1). The organization of the HBV genome is highly condensed and all transcripts are to various degrees subsets of each other. Indeed, all HBV transcripts share the same 3’ end and, thus, the HBx sequence constitutes the 3’ end of every viral transcript. Moreover, preC and pgRNA are longer than the viral DNA genome and thus are characterized by a 100bp redundancy at their 3’ ends identical to their 5’end. Due to these constraints, HBV RNAs are indistinguishable by classic approaches like quantitative real time PCR.

We recently published Bolero, a bioinformatics pipeline, taking advantage of 5’RACE specific amplification of HBV RNAs coupled to Nanopore sequencing, to decipher HBV transcriptome (Stadelmayer et al. 2020, Grand et al., 2024). Unlike other tools designed for HBV transcriptome analysis, Bolero's key advantage is its precise detection and sequencing of HBV spliced-variants (SP), describing the entire sequence and splice junctions of all known and potentially new SP.

Objective:
The goal of this project is to explore results produced by Bolero to cure detected known SP and describe, quantify and cure potentially new SP to guide their validation using molecular biology techniques.

Required skills :

Proficiency in Biology, with a strong focus on gene expression biology.

Desired but not mandatory skills in R and/or Python programming languages.

Proficiency in Excel or OpenOffice Calc, or a strong aptitude for handling and exploring flat data tables.

Languages : French (greatly appreciated but not mandatory if English-speaking).

Duration: 8 weeks max.

References:

Stadelmayer et al. 2020, Full-length 5’RACE identifies all major HBV transcripts in HBV-infected hepatocytes and patient serum. JHEP.

Grand et al. 2024, Bolero: a dedicated workflow to decipher Hepatitis B virus transcriptome from long-reads sequencing method coupled to 5’RACE amplification of transcripts. BioRXiv.