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      Circadian control of hepatitis B virus replication

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          Abstract

          Chronic hepatitis B virus (HBV) infection is a major cause of liver disease and cancer worldwide for which there are no curative therapies. The major challenge in curing infection is eradicating or silencing the covalent closed circular DNA (cccDNA) form of the viral genome. The circadian factors BMAL1/CLOCK and REV-ERB are master regulators of the liver transcriptome and yet their role in HBV replication is unknown. We establish a circadian cycling liver cell-model and demonstrate that REV-ERB directly regulates NTCP-dependent hepatitis B and delta virus particle entry. Importantly, we show that pharmacological activation of REV-ERB inhibits HBV infection in vitro and in human liver chimeric mice. We uncover a role for BMAL1 to bind HBV genomes and increase viral promoter activity. Pharmacological inhibition of BMAL1 through REV-ERB ligands reduces pre-genomic RNA and de novo particle secretion. The presence of conserved E-box motifs among members of the Hepadnaviridae family highlight an evolutionarily conserved role for BMAL1 in regulating this family of small DNA viruses.

          Abstract

          The circadian factors BMAL1/CLOCK and REV-ERB are master regulators of the human liver transcriptome but their role in hepatitis B virus infection is largely unknown. Here, Zhuang et al. show that REV-ERB regulates hepatitis B virus entry and BMAL1 directly binds HBV DNA and activates viral genome transcription.

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          STAR: ultrafast universal RNA-seq aligner.

          Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively short read lengths and constantly increasing throughput of the sequencing technologies. Currently available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read length limitation and mapping biases. To align our large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, we experimentally validated 1960 novel intergenic splice junctions with an 80-90% success rate, corroborating the high precision of the STAR mapping strategy. STAR is implemented as a standalone C++ code. STAR is free open source software distributed under GPLv3 license and can be downloaded from http://code.google.com/p/rna-star/.
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            edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

            Summary: It is expected that emerging digital gene expression (DGE) technologies will overtake microarray technologies in the near future for many functional genomics applications. One of the fundamental data analysis tasks, especially for gene expression studies, involves determining whether there is evidence that counts for a transcript or exon are significantly different across experimental conditions. edgeR is a Bioconductor software package for examining differential expression of replicated count data. An overdispersed Poisson model is used to account for both biological and technical variability. Empirical Bayes methods are used to moderate the degree of overdispersion across transcripts, improving the reliability of inference. The methodology can be used even with the most minimal levels of replication, provided at least one phenotype or experimental condition is replicated. The software may have other applications beyond sequencing data, such as proteome peptide count data. Availability: The package is freely available under the LGPL licence from the Bioconductor web site (http://bioconductor.org). Contact: mrobinson@wehi.edu.au
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              Cutadapt removes adapter sequences from high-throughput sequencing reads

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                Author and article information

                Contributors
                xiaodong.zhuang@ndm.ox.ac.uk
                jane.mckeating@ndm.ox.ac.uk
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                12 March 2021
                12 March 2021
                2021
                : 12
                : 1658
                Affiliations
                [1 ]GRID grid.4991.5, ISNI 0000 0004 1936 8948, Nuffield Department of Medicine, , University of Oxford, ; Oxford, UK
                [2 ]GRID grid.410795.e, ISNI 0000 0001 2220 1880, Department of Virology II, , National Institute of Infectious Diseases, ; Tokyo, Japan
                [3 ]RIKEN Cluster for Pioneering Research, Wako, Japan
                [4 ]GRID grid.11843.3f, ISNI 0000 0001 2157 9291, University of Strasbourg and Inserm, , UMR-S1110, Institut de Recherche sur les Maladies Virales et Hépatiques, ; Strasbourg, France
                [5 ]GRID grid.8348.7, ISNI 0000 0001 2306 7492, NIHR Oxford Biomedical Research Centre, , John Radcliffe Hospital, ; Oxford, UK
                [6 ]GRID grid.4991.5, ISNI 0000 0004 1936 8948, Oxford Centre for Diabetes, Endocrinology and Metabolism, , University of Oxford, ; Oxford, UK
                [7 ]GRID grid.5379.8, ISNI 0000000121662407, Division of Informatics, Imaging and Data Sciences, Faculty of Biology, Medicine and Health, , University of Manchester, ; Manchester, UK
                [8 ]GRID grid.5379.8, ISNI 0000000121662407, Division of Pharmacy and Optometry, School of Health Sciences and Manchester Academic Health Sciences Centre, , University of Manchester, ; Manchester, UK
                [9 ]GRID grid.16563.37, ISNI 0000000121663741, Department of Translational Medicine, , Università del Piemonte Orientale, ; Novara, Italy
                [10 ]GRID grid.258799.8, ISNI 0000 0004 0372 2033, Department of Applied Biological Sciences, Tokyo University of Science Graduate School of Science and Technology, Japan and Institute for Frontier Life and Medical Sciences, , Kyoto University, ; Kyoto, Japan
                [11 ]GRID grid.440891.0, ISNI 0000 0001 1931 4817, Pôle Hépato-Digestif, Institut Hopitalo-Universitaire (IHU), , Hopitaux Universitaire de Strasbourg, Strasbourg and Institut Universitaire de France, ; Paris, France
                Author information
                http://orcid.org/0000-0002-6870-9003
                http://orcid.org/0000-0001-6957-7463
                http://orcid.org/0000-0003-1880-3496
                http://orcid.org/0000-0002-2354-3281
                http://orcid.org/0000-0001-7269-7925
                http://orcid.org/0000-0001-5386-3609
                http://orcid.org/0000-0002-7548-9731
                http://orcid.org/0000-0002-6246-0876
                http://orcid.org/0000-0002-4739-6773
                http://orcid.org/0000-0002-8864-2168
                http://orcid.org/0000-0002-7229-5886
                Article
                21821
                10.1038/s41467-021-21821-0
                7955118
                33712578
                d18cdeb5-bfc7-44a5-a865-6bc272ea7116
                © The Author(s) 2021

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 7 June 2020
                : 2 February 2021
                Funding
                Funded by: FundRef https://doi.org/10.13039/100004440, Wellcome Trust (Wellcome);
                Award ID: 0005025
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/501100000265, RCUK | Medical Research Council (MRC);
                Award ID: MR/R022011/1
                Award Recipient :
                Categories
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                © The Author(s) 2021

                Uncategorized
                hepatitis b virus,virus-host interactions
                Uncategorized
                hepatitis b virus, virus-host interactions

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