Time-course profiling of bovine alphaherpesvirus 1.1 transcriptome using multiplatform sequencing

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Abstract

Long-read sequencing (LRS) has become a standard approach for transcriptome analysis in recent years. Bovine alphaherpesvirus 1 (BoHV-1) is an important pathogen of cattle worldwide. This study reports the profiling of the dynamic lytic transcriptome of BoHV-1 using two long-read sequencing (LRS) techniques, the Oxford Nanopore Technologies MinION, and the LoopSeq synthetic LRS methods, using multiple library preparation protocols. In this work, we annotated viral mRNAs and non-coding transcripts, and a large number of transcript isoforms, including transcription start and end sites, as well as splice variants of BoHV-1. Our analysis demonstrated an extremely complex pattern of transcriptional overlaps.

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Most cited references 63

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Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans.

Sarah E Calvo, David Pagliarini, Vamsi K Mootha (2009)

Upstream ORFs (uORFs) are mRNA elements defined by a start codon in the 5' UTR that is out-of-frame with the main coding sequence. Although uORFs are present in approximately half of human and mouse transcripts, no study has investigated their global impact on protein expression. Here, we report that uORFs correlate with significantly reduced protein expression of the downstream ORF, based on analysis of 11,649 matched mRNA and protein measurements from 4 published mammalian studies. Using reporter constructs to test 25 selected uORFs, we estimate that uORFs typically reduce protein expression by 30-80%, with a modest impact on mRNA levels. We additionally identify polymorphisms that alter uORF presence in 509 human genes. Finally, we report that 5 uORF-altering mutations, detected within genes previously linked to human diseases, dramatically silence expression of the downstream protein. Together, our results suggest that uORFs influence the protein expression of thousands of mammalian genes and that variation in these elements can influence human phenotype and disease.

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A dynamic and intricate regulatory network determines Pseudomonas aeruginosa virulence

Deepak Balasubramanian, Lisa Schneper, Hansi Kumari … (2012)

Pseudomonas aeruginosa is a metabolically versatile bacterium that is found in a wide range of biotic and abiotic habitats. It is a major human opportunistic pathogen causing numerous acute and chronic infections. The critical traits contributing to the pathogenic potential of P. aeruginosa are the production of a myriad of virulence factors, formation of biofilms and antibiotic resistance. Expression of these traits is under stringent regulation, and it responds to largely unidentified environmental signals. This review is focused on providing a global picture of virulence gene regulation in P. aeruginosa. In addition to key regulatory pathways that control the transition from acute to chronic infection phenotypes, some regulators have been identified that modulate multiple virulence mechanisms. Despite of a propensity for chaotic behaviour, no chaotic motifs were readily observed in the P. aeruginosa virulence regulatory network. Having a ‘birds-eye’ view of the regulatory cascades provides the forum opportunities to pose questions, formulate hypotheses and evaluate theories in elucidating P. aeruginosa pathogenesis. Understanding the mechanisms involved in making P. aeruginosa a successful pathogen is essential in helping devise control strategies.

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Functional 5′ UTR mRNA structures in eukaryotic translation regulation and how to find them

Maria Barna, Rhiju Das, Kathrin Leppek (2017)

RNA molecules can fold into intricate shapes that can provide an additional layer of control of gene expression beyond that of their sequence. In this Review, we discuss the current mechanistic understanding of structures in 5' untranslated regions (UTRs) of eukaryotic mRNAs and the emerging methodologies used to explore them. These structures may regulate cap-dependent translation initiation through helicase-mediated remodelling of RNA structures and higher-order RNA interactions, as well as cap-independent translation initiation through internal ribosome entry sites (IRESs), mRNA modifications and other specialized translation pathways. We discuss known 5' UTR RNA structures and how new structure probing technologies coupled with prospective validation, particularly compensatory mutagenesis, are likely to identify classes of structured RNA elements that shape post-transcriptional control of gene expression and the development of multicellular organisms.

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Author and article information

Contributors

Zsolt Boldogkői: boldogkoi.zsolt@med.u-szeged.hu

Journal

Journal ID (nlm-ta): Sci Rep

Journal ID (iso-abbrev): Sci Rep

Title: Scientific Reports

Publisher: Nature Publishing Group UK (London )

ISSN (Electronic): 2045-2322

Publication date (Electronic): 24 November 2020

Publication date PMC-release: 24 November 2020

Publication date Collection: 2020

Volume: 10

Electronic Location Identifier: 20496

Affiliations

[1 ]GRID grid.9008.1, ISNI 0000 0001 1016 9625, Department of Medical Biology, Faculty of Medicine, , University of Szeged, ; Somogyi B. u. 4., 6720 Szeged, Hungary

[2 ]GRID grid.417756.6, Institute for Veterinary Medical Research, , Centre for Agricultural Research, ; Hungária krt. 21, 1143 Budapest, Hungary

[3 ]GRID grid.260120.7, ISNI 0000 0001 0816 8287, Department of Biochemistry and Molecular Biology, Entomology and Plant Pathology, , Mississippi State University, ; 408 Dorman Hall, 32 Creelman St., Box 9655, Starkville, MS 39762 USA

Article

Publisher ID: 77520

DOI: 10.1038/s41598-020-77520-1

PMC ID: 7686369

PubMed ID: 33235226

SO-VID: c740e7a6-ecf5-4160-b5af-a77c882ef3bd

License:

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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/.

History

Date received : 20 June 2020

Date accepted : 4 November 2020

Funding

Funded by: FundRef http://dx.doi.org/10.13039/501100011019, Nemzeti Kutatási Fejlesztési és Innovációs Hivatal;

Award ID: FK 128252

Award ID: K 128247

Award Recipient : Dóra Tombácz Zsolt Boldogkői

Funded by: University of Szeged Open Access Fund

Award ID: 4813

Award Recipient : Zsolt Boldogkői

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ScienceOpen disciplines: Uncategorized

Keywords: gene expression analysis,gene expression profiling,transcriptomics,rna sequencing,virology

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ScienceOpen disciplines: Uncategorized

Keywords: gene expression analysis, gene expression profiling, transcriptomics, rna sequencing, virology

Time-course profiling of bovine alphaherpesvirus 1.1 transcriptome using multiplatform sequencing

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Abstract

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Genome Engineering using CRISPR

Most cited references 63

Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans.

A dynamic and intricate regulatory network determines Pseudomonas aeruginosa virulence

Functional 5′ UTR mRNA structures in eukaryotic translation regulation and how to find them

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