Biology subjects

Paturel, A.

Publications and source records attributed to Paturel, A..

2 recordsLinked to original sources

bioRxiv2024

Bolero: a dedicated workflow to decipher Hepatitis B virus transcriptome from long-reads sequencing method coupled to 5RACE amplification of transcripts

Hepatitis B virus (HBV) represents a major health burden, as it affects close to 290 million people worldwide. Although prophylactic vaccines are available, current therapeutic compounds do not usually achieve HBV eradication due to the persistence of the covalently closed circular (ccc)DNA that serves as viral reservoir. Thus, novel biomarkers that reliably reflect intrahepatic cccDNA transcriptional activity would be highly relevant for the monitoring of infected individuals, as well as the evaluation of new treatments targeting HBV. In this context, the development of 5 rapid amplification of complementary DNA ends (5RACE) as a strategy to capture and amplify full-length HBV RNAs, coupled with long-read and full-length sequencing approaches (e.g., Oxford Nanopore Technology), has recently enabled the detailed characterization of these molecules. The analysis of such data requires a dedicated bioinformatics pipeline due to the highly condensed nature of the HBV genome, which is characterized by the production of multiple transcripts and spliced variants that overlap each other. Here, we present Bolero, a computational method and built-in workflow designed to handle HBV sequencing data and evaluate the relative expression of viral RNAs and their spliced variants. The analysis of HBV-infected cell lines demonstrates that our bioinformatics pipeline is efficient for the identification and quantification of individual HBV mRNAs. Thus, Bolero represents a useful tool to study cccDNA transcriptional activity and the heterogeneity of HBV RNA spliced variants. Author summaryTranscriptomic analyses have brought comprehensive insights in the mechanisms controlling gene expression. Moreover, with the recent advances in sequencing technologies and computational methods, researchers can nowadays not only quantify gene expression, but also study alternative splicing, polyadenylation, transcription initiation, and even rare phenomena such as distant gene fusions. However, conventional analysis tools still rely heavily on the assumption of linear genomes with minimal overlap between open reading frames, rendering them insufficient for studying complex viruses such as hepatitis B virus (HBV). Unlike typical linear genomes, HBV genome consists in a circular DNA molecule, which results in an extensive sequence overlap between its transcripts. To tackle these challenges, we developed an innovative approach coupling 5 rapid amplification of complementary DNA ends (5RACE) and long-read sequencing to comprehensively explore the HBV transcriptome. Furthermore, we developed Bolero, a computational method designed to handle the peculiarities of HBV sequencing data, which allows a detailed characterization of the HBV transcriptome.

bioinformatics↗

bioRxiv2017

The Smc5/6 complex belongs to a novel class of evolutionary-constrained restriction factors and is antagonized by all mammalian hepatitis B virus X proteins

Infection with Hepatitis B virus (HBV) is a major cause of liver disease and cancer in humans. HBVs (family Hepadnaviridae) have been associated with mammals for millions of years. Recently, the Smc5/6 complex, known for its essential housekeeping functions in genome maintenance, was identified as an antiviral restriction factor of human HBV. The virus has however developed a counteraction mechanism by degrading the complex via its regulatory HBx protein. Whether the antiviral activity of the Smc5/6 complex against hepadnaviruses is an important and evolutionary-conserved function is unknown. Here, we used a combined evolutionary and functional approach to address this question. We first performed phylogenetic and positive selection analyses of the six Smc5/6 complex subunits and found that they have been highly conserved in primates and mammals. Yet, the Smc6 subunit showed marks of adaptive evolution, potentially reminiscent of virus-host \"arms-race\" We then functionally tested the HBx from six very divergent hepadnaviruses now naturally infecting primates, rodents, and bats. Despite little sequence homology, we demonstrate that these HBx efficiently degraded mammalian Smc5/6 complexes, independently of the host species and of the sites under positive selection. Importantly, all also rescued the replication of an HBx-deficient HBV in primary human hepatocytes. These findings point to an evolutionary-conserved requirement for Smc5/6 inactivation by HBx, showing that the Smc5/6 antiviral activity has been an important defense mechanism against hepadnaviruses in mammals. Interestingly, Smc5/6 may further be a restriction factor of other yet unidentified viruses that have driven some of its adaptation.\n\nImportanceInfection with hepatitis B virus (HBV) led to 887000 human deaths in 2015. HBV has been co-evolving with mammals for millions of years. Recently, the Smc5/6 complex, known for its essential housekeeping functions, was identified as a restriction factor of human HBV antagonized by the regulatory HBx protein. Here, we address whether the antiviral activity of Smc5/6 is an important evolutionary-conserved function. We found that all six subunits of Smc5/6 have been conserved in primates with only Smc6 showing signatures of \"evolutionary arms-race\" Using evolutionary-guided functional assays that include infections of primary human hepatocytes, we demonstrate that HBx from very divergent mammalian HBVs could all efficiently antagonize Smc5/6, independently of the host species and sites under positive selection. These findings show that the Smc5/6 antiviral activity against HBV is an important function in mammals. It also raises the intriguing possibility that Smc5/6 restricts other, yet unidentified viruses.

microbiology↗