High GC content of simple sequence repeats in Herpes simplex virus type 1 genome

Ouyang, Qing; Zhao, Xiangyan; Feng, Haiping; You, Tian; Li, Dan; Li, Mingfu; Tan, Zhongyang

doi:10.1016/j.gene.2012.02.049

Cited by 20 publications

(17 citation statements)

References 35 publications

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“…The presence of functionally significant G4 DNA motifs in the human immunodeficiency virus (HIV) has been reported by us and others both in the promoter (12–14) and Nef coding regions (15). The herpes simplex virus-1 (HSV-1) genome has a very high GC content (68%) which peaks at 84.7% GC in simple sequence repeats (SSRs) (16). Recently we provided evidence for the presence of very stable G4-forming regions located in the HSV-1 inverted repeats (17).…”

Section: Introductionmentioning

confidence: 99%

Visualization of DNA G-quadruplexes in herpes simplex virus 1-infected cells

et al. 2016

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We have previously shown that clusters of guanine quadruplex (G4) structures can form in the human herpes simplex-1 (HSV-1) genome. Here we used immunofluorescence and immune-electron microscopy with a G4-specific monoclonal antibody to visualize G4 structures in HSV-1 infected cells. We found that G4 formation and localization within the cells was virus cycle dependent: viral G4s peaked at the time of viral DNA replication in the cell nucleus, moved to the nuclear membrane at the time of virus nuclear egress and were later found in HSV-1 immature virions released from the cell nucleus. Colocalization of G4s with ICP8, a viral DNA processing protein, was observed in viral replication compartments. G4s were lost upon treatment with DNAse and inhibitors of HSV-1 DNA replication. The notable increase in G4s upon HSV-1 infection suggests a key role of these structures in the HSV-1 biology and indicates new targets to control both the lytic and latent infection.

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Section: Introductionmentioning

confidence: 99%

Visualization of DNA G-quadruplexes in herpes simplex virus 1-infected cells

et al. 2016

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“…HSV-1 genomes are 68 to 86% GC rich, and the GC content of VNTR regions can approach 100% (9). A number of chemicals have been used to facilitate PCR assays of GC-rich regions.…”

Section: Discussionmentioning

confidence: 99%

“…These targets are guanine (G) and cytosine (C) rich (65 to 86%) and in some strains contain homopolymeric runs of cytosine and guanine. This base composition is found in sequence repeats throughout the HSV-1 genome (9). These characteristics make the sequencing of ReIV by conventional Sanger dideoxynucleotide sequencing methods extremely challenging and technically impractical.…”

mentioning

confidence: 99%

Molecular Method Development and Establishment of a Database for Clinical and Epidemiological Herpes Simplex Virus 1 Strain Comparisons

Dean

George

2014

J Clin Microbiol

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Previous methods of herpes simplex virus 1 (HSV-1) genotype analysis have lacked sufficient discriminatory power for strain analysis within genotypes. The hypervariable reiterative repeat regions in the US1 and US12 introns, known as ReIV, were targeted for strain comparison. PCR methods for these extremely GC-rich target regions were optimized to give reproducible amplicons that were visualized by capillary electrophoresis relative to size standards. Analysis of the size, shape, and pattern of the resulting signatures enabled strain discrimination. Primary clinical specimens were used to develop the assay and the analysis algorithm. A blinded clinical study of 147 in-state and 51 out-of-state samples, including matched specimen-isolate pairs, was then performed. All primary clinical samples had been collected between 2004 and 2011 for viral diagnosis and previously found to be positive for HSV-1 by real-time PCR. The combined database contained patterns from 264 samples collected from 199 patients with a total of 176 unique signatures, none of which were dominant in the population. Matches between the signatures of the more than 50 specimen-isolate pairs were always seen. Signatures also matched across multiple samples collected from individual patients (six such cases), as well as some additional signature matches where epidemiological links were likely. Results were reproducible on repeat testing of individual specimens, even after months in frozen storage. The protocol has multiple potential clinical and public health uses.

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“…In previous study of the HSV-1 genome, a total of only 1377 a The number shown in boldface and italics were neglected in previous studies (in previous studies, a sequence was defined as an repeats when the minimum number of iterations was set to 6, 3, 3, 3, 3 and 3 for mono-, di-, tri-, tetra-, penta-and hexanucleotide repeats, respectively). repeat tracts were identified [5]. Therefore, considerable parts of the short repeats (approximately 96%) were neglected in previous studies ( Table 2).…”

Section: Repeat Content In Panoramic Scopementioning

confidence: 99%

“…Like other creatures, the HSV-1 genome contains amounts of repeats. What's interesting is that the content of GC repeats is far high in the HSV-1 genome, which may be related to some pathogenesis of HSV-1 [5]. To our knowledge, the small scope of mutation in repeated regions can cause many diseases [6]; in addition, expansion or contraction of repeats can change the sequence length [7].…”

Section: Introductionmentioning

confidence: 99%

The genome of herpes simplex virus type 1 is prone to form short repeat sequences

Zhao¹,

Wu²,

Lv³

et al. 2013

JBM

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Herein, we report a very high content of simple sequence repeats (SSRs) covering 66.12% of the herpes simplex virus type 1 (HSV-1) genome when a low threshold is adopted to define SSRs, indicating that repeat sequence is a very important character of the HSV-1 genome. The repeats with two iterations account for 68.33% of the total repeats. In reality, the genome of HSV-1 is prone to form shorter repeat sequences. For mono-, di-and trinucleotide repeats, the repeat numbers decreased with the increase of repeats iterations, implicating that the formation tendency of SSRs might be from low iterations to high iterations. The high iterations SSRs might have subjected to strong selected pressure and survived to perform different functions. The analysis suggested that the repeats formation may be an essential evolutionary driving force for the HSV-1 genome, and the results might be helpful for studying the genome structure, repeats genesis and genome evolution of HSV-1.

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High GC content of simple sequence repeats in Herpes simplex virus type 1 genome

Cited by 20 publications

References 35 publications

Visualization of DNA G-quadruplexes in herpes simplex virus 1-infected cells

Visualization of DNA G-quadruplexes in herpes simplex virus 1-infected cells

Molecular Method Development and Establishment of a Database for Clinical and Epidemiological Herpes Simplex Virus 1 Strain Comparisons

The genome of herpes simplex virus type 1 is prone to form short repeat sequences

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