scholarly journals Impacts of Genome-Wide Analyses on Our Understanding of Human Herpesvirus Diversity and Evolution

2017 ◽  
Vol 92 (1) ◽  
Author(s):  
Daniel W. Renner ◽  
Moriah L. Szpara
Keyword(s):  
High Throughput Sequencing ◽  
Evolutionary Dynamics ◽  
Human Herpesvirus ◽  
Ribosome Profiling ◽  
Genomic Diversity ◽  
Rna Seq ◽  
Dna Viruses ◽  
Double Stranded Dna ◽  
Genome Wide ◽  
Human Herpesviruses

ABSTRACTUntil fairly recently, genome-wide evolutionary dynamics and within-host diversity were more commonly examined in the context of small viruses than in the context of large double-stranded DNA viruses such as herpesviruses. The high mutation rates and more compact genomes of RNA viruses have inspired the investigation of population dynamics for these species, and recent data now suggest that herpesviruses might also be considered candidates for population modeling. High-throughput sequencing (HTS) and bioinformatics have expanded our understanding of herpesviruses through genome-wide comparisons of sequence diversity, recombination, allele frequency, and selective pressures. Here we discuss recent data on the mechanisms that generate herpesvirus genomic diversity and underlie the evolution of these virus families. We focus on human herpesviruses, with key insights drawn from veterinary herpesviruses and other large DNA virus families. We consider the impacts of cell culture on herpesvirus genomes and how to accurately describe the viral populations under study. The need for a strong foundation of high-quality genomes is also discussed, since it underlies all secondary genomic analyses such as RNA sequencing (RNA-Seq), chromatin immunoprecipitation, and ribosome profiling. Areas where we foresee future progress, such as the linking of viral genetic differences to phenotypic or clinical outcomes, are highlighted as well.

scholarly journals The Ins and Outs of Herpesviral Capsids: Divergent Structures and Assembly Mechanisms across the Three Subfamilies

Viruses ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 1913
Author(s):  
Elizabeth B. Draganova ◽  
Jonathan Valentin ◽  
Ekaterina E. Heldwein
Keyword(s):  
Capsid Protein ◽  
Severe Disease ◽  
Human Herpesvirus ◽  
Dna Viruses ◽  
Double Stranded Dna ◽  
Cryo Electron Microscopy ◽  
Protein Functions ◽  
Attractive Therapeutic Target ◽  
Key Steps ◽  
Human Herpesviruses

Human herpesviruses, classified into three subfamilies, are double-stranded DNA viruses that establish lifelong latent infections within most of the world’s population and can cause severe disease, especially in immunocompromised people. There is no cure, and current preventative and therapeutic options are limited. Therefore, understanding the biology of these viruses is essential for finding new ways to stop them. Capsids play a central role in herpesvirus biology. They are sophisticated vehicles that shelter the pressurized double-stranded-DNA genomes while ensuring their delivery to defined cellular destinations on the way in and out of the host cell. Moreover, the importance of capsids for multiple key steps in the replication cycle makes their assembly an attractive therapeutic target. Recent cryo-electron microscopy reconstructions of capsids from all three subfamilies of human herpesviruses revealed not only conserved features but also remarkable structural differences. Furthermore, capsid assembly studies have suggested subfamily-specific roles of viral capsid protein homologs. In this review, we compare capsid structures, assembly mechanisms, and capsid protein functions across human herpesvirus subfamilies, highlighting the differences.

scholarly journals Genome-Wide Profiling of Diadegma semiclausum Ichnovirus Integration in Parasitized Plutella xylostella Hemocytes Identifies Host Integration Motifs and Insertion Sites

2021 ◽  
Vol 11 ◽  
Author(s):  
Ze-hua Wang ◽  
Yue-nan Zhou ◽  
Jing Yang ◽  
Xi-qian Ye ◽  
Min Shi ◽  
...  
Keyword(s):  
Plutella Xylostella ◽  
Genomic Dna ◽  
Host Genome ◽  
Specific Mechanism ◽  
Diadegma Semiclausum ◽  
Dna Viruses ◽  
Double Stranded Dna ◽  
Genome Wide ◽  
Insertion Sites

Polydnaviruses (PDVs), classified into two genera, bracoviruses (BVs) and ichnoviruses (IVs), are large, double-stranded DNA viruses, which are beneficial symbionts of parasitoid wasps. PDVs do not replicate in their infected lepidopteran hosts. BV circles have been demonstrated to be integrated into host genomic DNA after natural parasitization. However, the integrations of IV circles in vivo remain largely unknown. Here, we analyzed the integration of Diadegma semiclausum ichnovirus (DsIV) in the genomic DNA of parasitized Plutella xylostella hemocytes. We found that DsIV circles are present in host hemocytes with non-integrated and integrated forms. Moreover, DsIV integrates its DNA circles into the host genome by two distinct strategies, conservatively, and randomly. We also found that four conserved-broken circles share similar motifs containing two reverse complementary repeats at their breaking sites, which were host integration motifs (HIMs). We also predicted HIMs of eight circles from other ichnoviruses, indicating that a HIM-mediated specific mechanism was conserved in IV integrations. Investigation of DsIV circle insertion sites of the host genome revealed the enrichment of microhomologies between the host genome and the DsIV circles at integration breakpoints. These findings will deepen our understanding of the infections of PDVs, especially IVs.

scholarly journals The landscape of accessible chromatin in quiescent and post-myocardial infarction cardiac fibroblasts

2021 ◽  
Author(s):  
Chaoyang Li ◽  
Jiangwen Sun ◽  
Qianglin Liu ◽  
Sanjeeva Dodlapati ◽  
Hao Ming ◽  
...  
Keyword(s):  
Gene Expression ◽  
Myocardial Infarction ◽  
High Throughput Sequencing ◽  
Cardiac Fibroblasts ◽  
Expression Profiles ◽  
Integrated Analysis ◽  
Matrix Remodeling ◽  
Rna Seq ◽  
Genome Wide ◽  
Accessible Chromatin

AbstractAfter myocardial infarction, quiescent cardiac fibroblasts are activated and undergo multiple proliferation and differentiation events, which contribute to the extracellular matrix remodeling of the infarcted myocardium. We recently found that cardiac fibroblasts of different differentiation states had distinct expression profiles closely related to their functions. Gene expression is directly regulated by chromatin state. However, the role of chromatin reorganization in the drastic gene expression changes during post-MI differentiation of cardiac fibroblast has not been revealed. In this study, the gene expression profiling and genome-wide mapping of accessible chromatin in mouse cardiac fibroblasts isolated from uninjured hearts and the infarcts at different time points were performed by RNA sequencing (RNA-seq) and the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq), respectively. ATAC-seq peaks were highly enriched in the promoter area and distal areas where enhancers might be located. A positive correlation was identified between the transcription level and promoter accessibility for many dynamically expressed genes. In addition, it was found that DNA methylation may contribute to the post-MI chromatin remodeling and gene expression in cardiac fibroblasts. Integrated analysis of ATAC-seq and RNA-seq datasets also identified transcription factors that possibly contributed to the differential gene expression between cardiac fibroblasts of different states.

scholarly journals RiboVIEW: a computational framework for visualization, quality control and statistical analysis of ribosome profiling data

2019 ◽  
Vol 48 (2) ◽  
pp. e7-e7 ◽  
Author(s):  
Carine Legrand ◽  
Francesca Tuorto
Keyword(s):  
Quality Control ◽  
Statistical Analysis ◽  
Computational Analysis ◽  
High Throughput Sequencing ◽  
Ribosome Profiling ◽  
Confounding Factors ◽  
Batch Effects ◽  
Sequencing Data ◽  
Computational Framework ◽  
Genome Wide

Abstract Recently, newly developed ribosome profiling methods based on high-throughput sequencing of ribosome-protected mRNA footprints allow to study genome-wide translational changes in detail. However, computational analysis of the sequencing data still represents a bottleneck for many laboratories. Further, specific pipelines for quality control and statistical analysis of ribosome profiling data, providing high levels of both accuracy and confidence, are currently lacking. In this study, we describe automated bioinformatic and statistical diagnoses to perform robust quality control of ribosome profiling data (RiboQC), to efficiently visualize ribosome positions and to estimate ribosome speed (RiboMine) in an unbiased way. We present an R pipeline to setup and undertake the analyses that offers the user an HTML page to scan own data regarding the following aspects: periodicity, ligation and digestion of footprints; reproducibility and batch effects of replicates; drug-related artifacts; unbiased codon enrichment including variability between mRNAs, for A, P and E sites; mining of some causal or confounding factors. We expect our pipeline to allow an optimal use of the wealth of information provided by ribosome profiling experiments.

scholarly journals Nuclease-mediated depletion biases in ribosome footprint profiling libraries

2020 ◽  
Author(s):  
Boris Zinshteyn ◽  
Jamie R Wangen ◽  
Boyang Hua ◽  
Rachel Green
Keyword(s):  
Ribosomal Rna ◽  
High Throughput Sequencing ◽  
Precise Determination ◽  
Ribosome Profiling ◽  
Rna Seq ◽  
Rna Sequences ◽  
Ribosomal Rna Sequences ◽  
Rna Fragments ◽  
Commercial Applications

AbstractRibosome footprint profiling is a high throughput sequencing based technique that provides detailed and global views of translation in living cells. An essential part of this technology is removal of unwanted, normally very abundant, ribosomal RNA sequences that dominate libraries and increase sequencing costs. The most effective commercial solution (Ribo-Zero) has been discontinued and a number of new, experimentally distinct commercial applications have emerged on the market. Here we evaluated several commercially available alternatives designed for RNA-seq of human samples and find them unsuitable for ribosome footprint profiling. We instead recommend the use of custom-designed biotinylated oligos, which were widely used in early ribosome profiling studies. Importantly, we warn that depletion solutions based on targeted nuclease cleavage significantly perturb the high-resolution information that can be derived from the data, and thus do not recommend their use for any applications that require precise determination of the ends of RNA fragments.

scholarly journals The genetic diversity of “papillomavirome” in bovine teat papilloma lesions

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Jéssica Tatiane Sauthier ◽  
Cíntia Daudt ◽  
Flavio Roberto Chaves da Silva ◽  
Christian Diniz Beduschi Travassos Alves ◽  
Fabiana Quoos Mayer ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
High Throughput Sequencing ◽  
Molecular Detection ◽  
Bos Taurus ◽  
Rolling Circle Amplification ◽  
Dna Viruses ◽  
Rolling Circle ◽  
Double Stranded Dna ◽  
Wide Range ◽  
Study Support

Abstract Background Papillomaviruses are small nonenveloped, circular double-stranded DNA viruses that belong to the Papillomaviridae family. To date, 29 Bos taurus papillomavirus (BPV) types have been described. Studies involving mixed BPV infections have rarely been reported in contrast to human papillomavirus (HPV), which is commonly described in numerous studies showing coinfections. Moreover, previous studies had shown that HPV coinfections increase the risk of carcinogenesis. In the present study, we used rolling-circle amplification followed by a high-throughput sequencing (RCA-HTS) approach in 23 teat papillomas from southern Brazil. Results Eleven well-characterized BPV types and 14 putative new BPV types were genetically characterized into the Xi, Epsilon and Dyoxipapillomavirus genera according to phylogenetic analysis of the L1 gene, which expands the previous 29 BPV types to 43. Moreover, BPV coinfections were detected in the majority (56.3%) of the papilloma lesions analyzed, suggesting a genetic diverse “papillomavirome” in bovine teat warts. Conclusions The data generated in this study support the possibility that a wide range of BPV is probably underdetected by conventional molecular detection tools, and that BPV coinfections are underestimated and probably genetic diverse. Additionally, 14 new BPV types were characterized, increasing the knowledge regarding BPV genetic diversity.

scholarly journals Transcriptome-wide interrogation of the functional intronome by spliceosome profiling

2017 ◽  
Author(s):  
Weijun Chen ◽  
Jill Moore ◽  
Hakan Ozadam ◽  
Hennady P. Shulha ◽  
Nicholas Rhind ◽  
...  
Keyword(s):  
Deep Sequencing ◽  
Rna Processing ◽  
Mrna Translation ◽  
Ribosome Profiling ◽  
Rna Seq ◽  
Full Understanding ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Nucleotide Resolution ◽  
Single Nucleotide Resolution

SUMMARYFull understanding of eukaryotic transcriptomes and how they respond to different conditions requires deep knowledge of all sites of intron excision. Although RNA-Seq provides much of this information, the low abundance of many spliced transcripts (often due to their rapid cytoplasmic decay) limits the ability of RNA-Seq alone to reveal the full repertoire of spliced species. Here we present “spliceosome profiling”, a strategy based on deep sequencing of RNAs co-purifying with late stage spliceosomes. Spliceosome profiling allows for unambiguous mapping of intron ends to single nucleotide resolution and branchpoint identification at unprecedented depths. Our data reveal hundreds of new introns in S. pombe and numerous others that were previously misannotated. By providing a means to directly interrogate sites of spliceosome assembly and catalysis genome-wide, spliceosome profiling promises to transform our understanding of RNA processing in the nucleus much like ribosome profiling has transformed our understanding mRNA translation in the cytoplasm.

scholarly journals A novel lineage of polyomaviruses identified in bark scorpions

2021 ◽  
Author(s):  
Kara Schmidlin ◽  
Simona Kraberger ◽  
Chelsea Cook ◽  
Dale F DeNardo ◽  
Rafaela S Fontenele ◽  
...  
Keyword(s):  
Evolutionary History ◽  
High Throughput Sequencing ◽  
Gene Array ◽  
Molecular Techniques ◽  
Dna Viruses ◽  
Circular Dna ◽  
Important Group ◽  
Double Stranded Dna ◽  
Centruroides Sculpturatus ◽  
History Of

Polyomaviruses are nonenveloped viruses with circular double stranded DNA genomes that range in size from ~4 to 7 kilobasepairs. Initially identified in mammals, polyomaviruses have now been identified in birds and a few fish species. Although fragmentary polyomavirus-like sequences have been detected as apparent 'hitchhikers' in shotgun genomics datasets for various arthropods, the possible diversity of these viruses in invertebrates remains unclear. In general, polyomaviruses are host-specific, showing strong evidence of host virus coevolution. Identification of polyomaviruses in a broader range of animals could shed useful light on the evolutionary history of this medically important group of viruses. Scorpions are predatory arachnids that are among the oldest terrestrial animals. Thus far, viromes of arachnids have been under sampled and understudied. Here, high throughput sequencing and traditional molecular techniques were used to explore the diversity of circular DNA viruses associated with bark scorpions (Centruroides sculpturatus) from the greater Phoenix area, Arizona, USA. The complete genomes of eight novel polyomaviruses were identified. Analysis of Centruroides transcriptomic datasets elucidated the splicing of the viral late gene array, which is more complex than that of vertebrate polyomaviruses. Phylogenetic analysis provides further evidence of co-divergence of polyomaviruses with their hosts, suggesting that at least one ancestral species of polyomaviruses was circulating amongst the primitive common ancestors of arthropods and chordates.

scholarly journals Characterization of the Burkholderia thailandensis SOS Response by Using Whole-Transcriptome Shotgun Sequencing

2013 ◽  
Vol 79 (19) ◽  
pp. 5830-5843 ◽  
Author(s):  
Ricky L. Ulrich ◽  
David DeShazer ◽  
Tara A. Kenny ◽  
Melanie P. Ulrich ◽  
Anna Moravusova ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Bacterial Species ◽  
Sos Response ◽  
Dependent Manner ◽  
Rna Seq ◽  
Adaptive Responses ◽  
Burkholderia Thailandensis ◽  
Content Type ◽  
Genome Wide ◽  
Induced Mutagenesis

ABSTRACTThe bacterial SOS response is a well-characterized regulatory network encoded by most prokaryotic bacterial species and is involved in DNA repair. In addition to nucleic acid repair, the SOS response is involved in pathogenicity, stress-induced mutagenesis, and the emergence and dissemination of antibiotic resistance. Using high-throughput sequencing technology (SOLiD RNA-Seq), we analyzed theBurkholderia thailandensisglobal SOS response to the fluoroquinolone antibiotic, ciprofloxacin (CIP), and the DNA-damaging chemical, mitomycin C (MMC). We demonstrate that aB. thailandensis recAmutant (RU0643) is ∼4-fold more sensitive to CIP in contrast to the parental strainB. thailandensisDW503. Our RNA-Seq results show that CIP and MMC treatment (P< 0.01) resulted in the differential expression of 344 genes inB. thailandensisand 210 genes in RU0643. Several genes associated with the SOS response were induced and includelexA,uvrA,dnaE,dinB,recX, andrecA. At the genome-wide level, we found an overall decrease in gene expression, especially for genes involved in amino acid and carbohydrate transport and metabolism, following both CIP and MMC exposure. Interestingly, we observed the upregulation of several genes involved in bacterial motility and enhanced transcription of aB. thailandensisgenomic island encoding aSiphoviridaebacteriophage designated ϕE264. UsingB. thailandensisplaque assays and PCR withB. malleiATCC 23344 as the host, we demonstrate that CIP and MMC exposure inB. thailandensisDW503 induces the transcription and translation of viable bacteriophage in a RecA-dependent manner. This is the first report of the SOS response inBurkholderiaspp. to DNA-damaging agents. We have identified both common and unique adaptive responses ofB. thailandensisto chemical stress and DNA damage.

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