Novel transcripts of human cytomegalovirus clinical strain found by cDNA library screening

Ma, Yong; Ruan, Qiang; Yh, Ji; Wang, N; Ml, Li; Qi, Yong; He, Rong; Zr, Sun; Gw, Ren

doi:10.4238/vol10-2gmr1059

Cited by 19 publications

(17 citation statements)

References 30 publications

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“…A cDNA library of the HCMV clinical strain H had been previously constructed using the pBluescript II SK vector [24]. The primary library consisted of 1.12 × 10 6 recombinant clones/mL.…”

Section: Methodsmentioning

confidence: 99%

Characterization of the transcripts of human cytomegalovirus UL144

Wang

et al. 2011

Virol J

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BackgroundThe genome of human cytomegalovirus (HCMV) has been studied extensively, particularly in the UL/b' region. In this study, transcripts of one of the UL/b' genes, UL144, were identified in 3 HCMV isolates obtained from urine samples of congenitally infected infants.MethodsNorthern blot hybridization, cDNA library screening, and RACE-PCR were used.ResultsWe identified at least 4 differentially regulated 3'-coterminal transcripts of UL144 in infected cells of 1,300, 1,600, 1,700, and 3,500 nucleotides (nt). The 1600 nt transcript was the major form of UL144 mRNA. The largest transcript initiated from the region within the UL141 open reading frame (ORF) and included UL141, UL142, UL143, UL144, and UL145 ORFs.ConclusionsThese findings reveal the complex nature of the transcription of the UL144 gene in clinical isolates.

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“…A cDNA library of the HCMV clinical strain H had been previously constructed using the pBluescript II SK vector [24]. The primary library consisted of 1.12 × 10 6 recombinant clones/mL.…”

Section: Methodsmentioning

confidence: 99%

Characterization of the transcripts of human cytomegalovirus UL144

Wang

et al. 2011

Virol J

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“…RNA2.7 functions in inhibiting apoptosis (13), the RNA5.0 homolog in murine cytomegalovirus is involved in virulence (14), and the role of RNA1.2 is unknown. Antisense transcripts (ASTs) form a second class of noncoding RNA, and are transcribed antisense to CRs (15,16). In addition, HCMV specifies several small, nonpolyA RNAs that may have regulatory roles, including microRNAs (miRNAs) (17) processed from longer transcripts and RNAs associated with the origin of DNA replication (18).…”

mentioning

confidence: 99%

High-resolution human cytomegalovirus transcriptome

Gatherer

Seirafian²,

Cunningham³

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

212

261

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Deep sequencing was used to bring high resolution to the human cytomegalovirus (HCMV) transcriptome at the stage when infectious virion production is under way, and major findings were confirmed by extensive experimentation using conventional techniques. The majority (65.1%) of polyadenylated viral RNA transcription is committed to producing four noncoding transcripts (RNA2.7, RNA1.2, RNA4.9, and RNA5.0) that do not substantially overlap designated protein-coding regions. Additional noncoding RNAs that are transcribed antisense to protein-coding regions map throughout the genome and account for 8.7% of transcription from these regions. RNA splicing is more common than recognized previously, which was evidenced by the identification of 229 potential donor and 132 acceptor sites, and it affects 58 proteincoding genes. The great majority (94) of 96 splice junctions most abundantly represented in the deep-sequencing data was confirmed by RT-PCR or RACE or supported by involvement in alternative splicing. Alternative splicing is frequent and particularly evident in four genes (RL8A, UL74A, UL124, and UL150A) that are transcribed by splicing from any one of many upstream exons. The analysis also resulted in the annotation of four previously unrecognized protein-coding regions (RL8A, RL9A, UL150A, and US33A), and expression of the UL150A protein was shown in the context of HCMV infection. The overall conclusion, that HCMV transcription is complex and multifaceted, has implications for the potential sophistication of virus functionality during infection. The study also illustrates the key contribution that deep sequencing can make to the genomics of nuclear DNA viruses.T he genetic repertoire of human cytomegalovirus (HCMV; species Human herpesvirus 5) is incompletely understood. Most bioinformatic investigations have focused on identifying open reading frames (ORFs) that are conserved in other organisms or that exhibit pattern-based similarities (e.g., in nucleotide or codon bias) to recognized protein-coding regions (CRs) (1). Our current map of the wild-type HCMV genome, based on strain Merlin, contains 166 protein-coding genes (2-5). It is entirely possible that additional, small protein-coding genes will be found. Candidates involve ORFs that overlap recognized CRs and for which there is some evidence for expression (6), ORFs highlighted in pattern-based bioinformatic (7) or proteomic analyses (8), and ORFs whose expression is presently unsuspected.Recognition of many protein-coding genes has been supplemented by information on protein expression and function. However, HCMV also specifies polyadenylated (polyA) transcripts that, because they lack sizeable, conserved ORFs, appear unlikely to function via translation. One class consists of noncoding, nonoverlapping transcripts (NNTs) that do not substantially overlap the designated CRs of other genes. These include an abundant 2.7-kb RNA (β2.7 or RNA2.7) (9), a 1.1-kb spliced RNA and associated 5-kb stable intron (RNA5.0) (10, 11), and a 1.2-kb RNA (RNA1.2) (12). RNA...

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“…In this study, the transcription of the AS strand of the HCMV UL87 gene area was investigated, and an 800 nt UL87 AS transcript was deeply characterized, which has been found as a cDNA clone in a late HCMV cDNA library [14]. The transcript was identified in three HCMV clinical strains.…”

Section: Discussionmentioning

confidence: 99%

“…However, two AS transcripts overlapping the UL87 gene were obtained by screening a HCMV cDNA library made during late infection, in the study by Zhang et al [10]. Moreover, we also found two cDNA clones in a late HCMV cDNA library containing the sequence of the UL87 AS strand [14]. …”

Section: Introductionmentioning

confidence: 98%

An antisense transcript in the human cytomegalovirus UL87 gene region

Wang

et al. 2011

Virol J

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BackgroundRapid advances in research on antisense transcripts are gradually changing our comprehension of genomic and gene expression aspects of the Herpesviridae. One such herpesvirus is the human cytomegalovirus (HCMV). Although transcription of the HCMV UL87 gene has not been specifically investigated, cDNA clones of UL87 antisense transcripts were found in HCMV cDNA libraries previously. In this study, the transcription of the UL87 antisense strand was investigated in three clinically isolated HCMV strains.ResultsFirst, an 800 nucleotides transcript having an antisense orientation to the UL87 gene was found in a late HCMV cDNA library. Then, the UL87 antisense transcript was confirmed by Rapid amplification of cDNA ends (RACE) and Northern blot in three HCMV clinical strains. Two ORFs were predicted in the antisense transcript. The putative protein of ORF 1 showed a high degree of conservation among HCMV and other CMV strains.ConclusionAn 800nt antisense transcript in the UL87 gene region exists in HCMV clinical strains.

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Novel transcripts of human cytomegalovirus clinical strain found by cDNA library screening

Cited by 19 publications

References 30 publications

Characterization of the transcripts of human cytomegalovirus UL144

Characterization of the transcripts of human cytomegalovirus UL144

High-resolution human cytomegalovirus transcriptome

An antisense transcript in the human cytomegalovirus UL87 gene region

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