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Deng J, Wang Q, Zhang J, Ma Y, Qi Y, Liu Z, Li Y, Ruan Q, Huang Y. Identification and characterization of human cytomegalovirus-encoded circular RNAs. Front Cell Infect Microbiol 2022; 12:980974. [PMID: 36452301 PMCID: PMC9702070 DOI: 10.3389/fcimb.2022.980974] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 10/28/2022] [Indexed: 08/27/2023] Open
Abstract
Circular RNA (circRNA) exists extensively and plays essential roles in serving as microRNA (miRNA) or protein sponges and protein scaffolding in many organisms. However, the profiles and potential functions of the virus-encoded circRNA, including human cytomegalovirus (HCMV)-encoded circular RNAs, remain unclear. In the present study, HCMV-encoded circRNAs profile in human embryonic lung fibroblasts (HELF) with lytic infection was investigated using RNA deep sequencing and bioinformatics analysis. In total, 629 HCMV-encoded circRNAs were identified with various expression patterns in our results. The full sequences and alternative splicings of circUS12, circUL55, and circUL89 were verified by reverse transcriptase-PCR (RT-PCR) with divergent primers followed and Sanger sequencing. Transcription of circUL89 was validated by Northern blot. The HCMV-encoded circRNA-miRNA network analyses revealed the potential function of HCMV-encoded circRNAs during HCMV infection in HELFs. Collectively, HCMV infection deduced abundant HCMV-associated circRNAs during infection, and the HCMV-encoded circRNAs might play important roles in benefiting HCMV infection.
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Affiliation(s)
- Jingui Deng
- Department of Microorganism Laboratory, Shenyang Center for Disease Control and Prevention, Shenyang, China
- Virology Laboratory, Shengjing Hospital of China Medical University, Shenyang, China
| | - Qing Wang
- Virology Laboratory, Shengjing Hospital of China Medical University, Shenyang, China
| | - Jing Zhang
- Virology Laboratory, Shengjing Hospital of China Medical University, Shenyang, China
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yanping Ma
- Virology Laboratory, Shengjing Hospital of China Medical University, Shenyang, China
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Ying Qi
- Virology Laboratory, Shengjing Hospital of China Medical University, Shenyang, China
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Zhongyang Liu
- Virology Laboratory, Shengjing Hospital of China Medical University, Shenyang, China
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yibo Li
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
- Department of Obstetrics and Gynecology, Central Hospital Affiliated to Shenyang Medical College, Shenyang, China
| | - Qiang Ruan
- Virology Laboratory, Shengjing Hospital of China Medical University, Shenyang, China
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yujing Huang
- Virology Laboratory, Shengjing Hospital of China Medical University, Shenyang, China
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
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Identification and characterization of a novel group of natural anti-sense transcripts from RNA1.2 gene locus of human cytomegalovirus. Chin Med J (Engl) 2019; 132:1591-1598. [PMID: 31205077 PMCID: PMC6616230 DOI: 10.1097/cm9.0000000000000299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Background: Natural anti-sense transcripts (NATs), which are transcribed from the complementary DNA strand of annotated genes, exert regulatory function of gene expression. Increasing studies recognized anti-sense transcription widespread throughout human cytomegalovirus (HCMV) genome, whereas the anti-sense transcription of RNA1.2 gene locus has never been investigated. In this study, the transcription of the RNA1.2 anti-sense strand was investigated in clinically isolated HCMV strain. Methods: Strand-specific high-through RNA-sequencing (RNA-seq) was performed to find possible anti-sense transcripts (ASTs). For analyzing and visualization of RNA-seq data sets, Integrative Genomics Viewer software was applied. To confirm these possibilities, Northern blotting and rapid amplification of cDNA ends (RACE) were used. Results: Transcription of the opposite strand of RNA1.2 gene locus was detected by RNA-sequencing using RNAs extracted from human embryonic lung fibroblasts infected with HCMV clinical isolate HAN. At least three HCMV NATs, named RNA1.2 AST 1, RNA1.2 AST2, and RNA1.2 AST3, were characterized by Northern blotting and RACE analyses. These RNA1.2 ASTs orientated from the complementary strand of RNA1.2 locus during the late phase of HCMV infection. The 5′- and 3′-termini of these transcripts were located within the opposite sequence of the predicted RNA1.2 gene. Conclusion: A cluster of novel NATs was transcribed from the opposite sequence of the HCMV RNA1.2 gene region.
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Lu Y, Ma Y, Liu Z, Han L, Gao S, Zheng B, Liu C, Qi Y, Sun Z, Huang Y, Ruan Q. A cluster of 3' coterminal transcripts from US12-US17 locus of human cytomegalovirus. Virus Genes 2016; 52:334-45. [PMID: 26931512 DOI: 10.1007/s11262-016-1308-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 02/20/2016] [Indexed: 01/27/2023]
Abstract
Among all the human cytomegalovirus (HCMV) gene families, US12 family is relatively undefined in their transcriptional profile and biological functions. In this study, the transcription pattern and characteristics of HCMV US12-US17 gene region were studied extensively. Twenty-three clones harboring US12 cDNA sequence were screened out from a late cDNA library of an HCMV clinical isolate, Han. Using a set of US12-US17 gene-specific probes, six transcripts from US12-US17 locus were detected by northern blot at late kinetics of the clinical isolate. One additional transcript was found in late RNA of HCMV strain AD169. No evidence showing these transcripts contain introns by reverse transcription PCR. 3' and 5' termini of these transcripts were confirmed by Rapid Amplification of cDNA Ends. A novel protein-coding region was predicted in the shorter US14 transcript with an alternative in-frame 5' translation initiation site compared to that of the previously predicted US14 ORF. Our findings demonstrate the existence of a cluster of 3' coterminal unspliced transcripts with distinct 5' transcriptional initiation sites originated from US12-US17 gene region in the late infection phase of an HCMV clinical strain.
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Affiliation(s)
- Ying Lu
- Virus Laboratory, Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning, 121000, China
- Department of Pathogen Biology, College of Basic Medical Sciences, Liaoning Medical University, Jinzhou, Liaoning, 121000, China
| | - Yanping Ma
- Virus Laboratory, Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning, 121000, China.
| | - Zhongyang Liu
- Virus Laboratory, Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning, 121000, China
| | - Liying Han
- Virus Laboratory, Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning, 121000, China
| | - Shuang Gao
- The Clinical Laboratory, Shenyang Women's and Children's Hospital, Shenyang, Liaoning, 110014, China
| | - Bo Zheng
- The Pediatric Department, Shenyang Women's and Children's Hospital, Shenyang, Liaoning, 110014, China
| | - Chang Liu
- Virus Laboratory, Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning, 121000, China
| | - Ying Qi
- Virus Laboratory, Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning, 121000, China
| | - Zhengrong Sun
- Virus Laboratory, Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning, 121000, China
| | - Yujing Huang
- Virus Laboratory, Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning, 121000, China
| | - Qiang Ruan
- Virus Laboratory, Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning, 121000, China.
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Gao JX, Jing J, Yu CJ, Chen J. Construction of a High-Quality Yeast Two-Hybrid Library and Its Application in Identification of Interacting Proteins with Brn1 in Curvularia lunata. THE PLANT PATHOLOGY JOURNAL 2015; 31:108-14. [PMID: 26060429 PMCID: PMC4453991 DOI: 10.5423/ppj.oa.01.2015.0001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Revised: 04/01/2015] [Accepted: 04/07/2015] [Indexed: 05/24/2023]
Abstract
Curvularia lunata is an important maize foliar fungal pathogen that distributes widely in maize growing area in China, and several key pathogenic factors have been isolated. An yeast two-hybrid (Y2H) library is a very useful platform to further unravel novel pathogenic factors in C. lunata. To construct a high-quality full length-expression cDNA library from the C. lunata for application to pathogenesis-related protein-protein interaction screening, total RNA was extracted. The SMART (Switching Mechanism At 5' end of the RNA Transcript) technique was used for cDNA synthesis. Double-stranded cDNA was ligated into the pGADT7-Rec vector with Herring Testes Carrier DNA using homologous recombination method. The ligation mixture was transformed into competent yeast AH109 cells to construct the primary cDNA library. Eventually, a high qualitative library was successfully established according to an evaluation on quality. The transformation efficiency was about 6.39 ×10(5) transformants/3 μg pGADT7-Rec. The titer of the primary cDNA library was 2.5×10(8) cfu/mL. The numbers for the cDNA library was 2.46×10(5). Randomly picked clones show that the recombination rate was 88.24%. Gel electrophoresis results indicated that the fragments ranged from 0.4 kb to 3.0 kb. Melanin synthesis protein Brn1 (1,3,8-hydroxynaphthalene reductase) was used as a "bait" to test the sufficiency of the Y2H library. As a result, a cDNA clone encoding VelB protein that was known to be involved in the regulation of diverse cellular processes, including control of secondary metabolism containing melanin and toxin production in many filamentous fungi was identified. Further study on the exact role of the VelB gene is underway.
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Affiliation(s)
- Jin-Xin Gao
- School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai 200240,
P. R. China
- State Key Laboratory of Microbial Metabolism, Shanghai Jiaotong University, Shanghai 200240,
P. R. China
| | - Jing Jing
- School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai 200240,
P. R. China
- State Key Laboratory of Microbial Metabolism, Shanghai Jiaotong University, Shanghai 200240,
P. R. China
| | - Chuan-Jin Yu
- School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai 200240,
P. R. China
- State Key Laboratory of Microbial Metabolism, Shanghai Jiaotong University, Shanghai 200240,
P. R. China
| | - Jie Chen
- School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai 200240,
P. R. China
- State Key Laboratory of Microbial Metabolism, Shanghai Jiaotong University, Shanghai 200240,
P. R. China
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Gao S, Ruan Q, Ma Y, Li M, Wang L, Zheng B, Qi Y, Ji Y, Sun Z, Huang Y. Validation of three splice donor and three splice acceptor sites for regulating four novel low-abundance spliced transcripts of human cytomegalovirus UL21.5 gene locus. Int J Mol Med 2014; 35:253-62. [PMID: 25370414 DOI: 10.3892/ijmm.2014.1987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 10/23/2014] [Indexed: 11/06/2022] Open
Abstract
In a previous study, one spliced transcript of human cytomegalovirus (HCMV), named UL21.5 was identified. UL21.5 has been found to be one of the viral transcripts packaged within HCMV particles. The UL21.5 mRNA is translated into a secreted glycoprotein, which is a viral chemokine decoy receptor specifically interacting with regulated upon activation normal T cell expressed and secreted (RANTES). In the present study, four novel low-abundance 3'-coterminal spliced transcripts were identified to be transcribed from the UL21.5 gene region of a low-passage HCMV strain during the late infection phase by cDNA library screening, northern blot hybridization, reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE)-PCR. Three splicing donor and three splicing acceptor sites found in the UL21.5 gene region were validated to be functional in an in vitro expression system. In addition, the determinant regulatory region that is necessary for the splice donor site at nucleotide (nt) 25533 was located in a 9-bp sequence around the site; the regulatory regions for the splice acceptor sites at nt 26597 and nt 26633 were located in a 20-bp sequence upstream of the site at nt 26597 and in a 10-bp sequence from nt 26641 to nt 26650 downstream of the site at nt 26633, respectively.
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Affiliation(s)
- Shuang Gao
- Virus Laboratory, Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Qiang Ruan
- Virus Laboratory, Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Yanping Ma
- Virus Laboratory, Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Mali Li
- Virus Laboratory, Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Lin Wang
- Virus Laboratory, Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Bo Zheng
- Virus Laboratory, Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Ying Qi
- Virus Laboratory, Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Yaohua Ji
- Virus Laboratory, Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Zhengrong Sun
- Virus Laboratory, Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Yujing Huang
- Virus Laboratory, Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning 110004, P.R. China
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Zheng B, Li M, Gao S, Wang L, Qi Y, Ma Y, Ruan Q. Characterization of a novel group of antisense transcripts in human cytomegalovirus UL83 gene region. J Med Virol 2014; 86:2033-41. [PMID: 24615924 DOI: 10.1002/jmv.23887] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2013] [Indexed: 11/11/2022]
Abstract
The rapid advances in research on antisense transcripts are gradually changing our understanding of the expression of the Herpesviridae genome. In this study, the transcripts of the human cytomegalovirus (HCMV) UL83 antisense strand were investigated in three clinical isolates. Three cDNA clones containing sequences with an antisense orientation to the UL83 gene were identified in a late HCMV cDNA library. The UL83 antisense transcripts (UL83asts) were then shown to be transcribed only in the late infection phase of the three clinical HCMV strains, using rapid amplification of cDNA ends (RACE) and northern blotting. These UL83asts were identical at their 3' termini but different at 5' ends. Two open reading frames were predicted in the UL83asts.
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Affiliation(s)
- Bo Zheng
- Virus Laboratory, The affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning, China
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7
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Gao X, Jia R, Wang M, Zhu D, Chen S, Lin M, Yin Z, Wang Y, Chen X, Cheng A. Construction and identification of a cDNA library for use in the yeast two-hybrid system from duck embryonic fibroblast cells post-infected with duck enteritis virus. Mol Biol Rep 2013; 41:467-75. [PMID: 24293127 DOI: 10.1007/s11033-013-2881-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 11/21/2013] [Indexed: 12/30/2022]
Abstract
To explore and isolate genes related to duck embryonic fibroblast cells (DEFs) post-infected with duck enteritis virus (DEV), a cDNA library was established using SMART (Switching Mechanism At 5' end of the RNA Transcript) technique coupling with a homologous recombination method. The cells were harvested and total RNA was extracted at 48 h post infection. Then the mRNAs were purified and reverse transcribed to first-strand cDNAs using oligo (dT) primers (CDS III). Subsequently, long distance-PCR was performed, the double-stranded cDNAs were purified, and a transformation assay was carried out in that order. Eventually, a high qualitative library was successfully established according to an evaluation on quality. The transformation efficiency was about 2.33 × 10(6) transformants/4.34 μg pGADT7-Rec (>1.0 × 10(6)). The cell density of the library was 1.75 × 10(9) cells/mL (>2 × 10(7) cells/mL). The titer of the primary cDNA library and amplified cDNA library was 6.75 × 10(5) and 2.33 × 10(7) CFU/mL respectively. The numbers for the primary cDNA library and amplified cDNA library were 1.01 × 10(7) and 1.14 × 10(9), respectively, and the recombinant rate was 97.14 %. The sequence results of 27 randomly picked independent clones revealed the insert ranged from 0.323 to 2.017 kb with an average insert size of 0.807 kb. Full-length transcripts of DEV-CHv LORF3, UL26 and UL35 genes were acquired through sequence similarity analysis from the non-redundant nucleic acid or protein database. Five polyA sites were identified in the DEV-CHv genome. Also, a new transcript of 668 bp was found between the IRS gene and US1 gene of the DEV-CHv genome. Thus, we concluded that the constructed cDNA library will be a useful tool in proteomic analysis of interactions between the DEV and host DEFs, and discovery of biomarkers studies on the mechanism of DEV and subsequently exploitation original vaccines and antiviral drugs to prevent or cure diseases.
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Affiliation(s)
- Xinghong Gao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China,
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Ma Y, Li M, Zheng B, Wang N, Gao S, Wang L, Qi Y, Sun Z, Ruan Q. Overlapping transcription structure of human cytomegalovirus UL140 and UL141 genes. J Biosci 2013; 38:35-44. [PMID: 23385811 DOI: 10.1007/s12038-012-9293-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Transcription of human cytomegalovirus UL/b' region has been studied extensively for some genes. In this study, transcripts of the UL140 and UL141, two of the UL/b' genes, were identified in late RNAs of three HCMV isolates using Northern blot hybridization, cDNA library screening and RACE-PCR. At least three transcripts with length of 2800, 2400 and 1700 nt, as well as a group of transcripts of about 1000-1300 nt, were found in this gene region with an accordant 3' ends. Among the transcripts, two initiated upstream of the start code of the UL140 gene and contained the UL140 and UL141 open reading frame (ORF), one initiated in the middle of the UL140 gene, and could encode short ORFs upstream of the UL141 ORF. A group of transcripts initiated upstream or downstream of the start code of the UL141 gene, and could encode 'nested' ORFs, including the UL141 ORF. These 'nested' ORFs possess different initiation sites but the same termination site as that of the UL141 ORF.
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Affiliation(s)
- Yanping Ma
- Virus Laboratory, the Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning of P.R. China, 110004
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Analysis and mapping of a 3' coterminal transcription unit derived from human cytomegalovirus open reading frames UL30-UL32. Virol J 2013; 10:65. [PMID: 23446136 PMCID: PMC3600006 DOI: 10.1186/1743-422x-10-65] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 02/12/2013] [Indexed: 11/30/2022] Open
Abstract
Background It has been predicted that the UL31 gene originates from the positive strand of the human cytomegalovirus (HCMV) genome, whereas the UL30 and UL32 genes originate from the complementary strand. Except for the UL32 gene, the transcription of this gene region has not been investigated extensively. Methods Northern blotting, cDNA library screening, RACE-PCR,and RT-PCR were used. Results At least eight transcripts of the antisense orientation of UL31 were transcribed from the UL30–UL32 region during the late phase of HCMV infection. The 3′ coterminus of these transcripts was located within the predicted UL30 gene. The longest 6.0-kb transcript was initiated upstream of the predicted UL32 gene. Other transcripts were derived from the predicted UL30 and UL31 gene region. Except for the previously predicted UL32 open reading frame (ORF), three novel ORFs, named UL31anti-1, UL31anti-2 and UL31anti-3, were located in the transcripts from the UL31anti-UL32 transcription unit. No transcription was found in UL31. Conclusion A family of novel 3′ coterminal transcripts was transcribed from the UL30–UL32 gene region.
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Wang N, Ma Y, Li M, Gao S, Wang L, Qi Y, Ji Y, Sun Z, Ruan Q. Transcription characteristics of the human cytomegalovirus UL13 gene. Arch Virol 2012; 158:473-7. [PMID: 23065125 DOI: 10.1007/s00705-012-1461-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 07/20/2012] [Indexed: 11/25/2022]
Abstract
The human cytomegalovirus (HCMV) UL13 gene is located in the unique long (UL) region of its genome. The transcript structure of UL13 gene has not been investigated to date. By using cDNA library screening, northern blot, and rapid amplification of cDNA ends (RACE), the HCMV UL13 gene was demonstrated to be transcribed from the immediate early (IE) to the late (L) phase of infection, and at least one 1602-nt unspliced transcript was identified in the present study from three clinical isolates.
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Affiliation(s)
- Ning Wang
- Virus Laboratory, The Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning, 110004, China
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Ma Y, Wang N, Li M, Gao S, Wang L, Zheng B, Qi Y, Ruan Q. Human CMV transcripts: an overview. Future Microbiol 2012; 7:577-93. [PMID: 22568714 DOI: 10.2217/fmb.12.32] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The human CMV (HCMV) genome consists of an approximately 230-kb dsDNA and is predicted to contain over 165 open reading frames. Although the entire sequence of the laboratory-adapted AD169 strain of HCMV was first available in 1991, the precise number and nature of viral genes and gene products are still unclear. Fewer than 100 predicted genes have been convincingly elucidated with respect to their expression patterns, transcript structure and transcription characteristics. The high gene number of HCMV creates a crowded genome with many overlapping transcriptional units. 3´- or 5´-coterminal overlapping polycistronic transcripts could use a common promoter element or a poly-A signal. 3´-coterminal monocistronic transcripts could encode 'nested' open reading frames, which possess different initiation but the same termination sites. As a virus with eukaryotic cells as the host, HCMV has the capacity to splice out introns during transcription. Major alternately spliced mRNA species of HCMV originate primarily, but not exclusively, from the immediate early gene regions. Alternate splicing patterns of the mRNAs could encode a number of gene products with different sizes. In recent years, some antisense and noncoding transcripts of HCMV have been reported. These RNAs probably have functions in genomic replication or the regulation of gene expression.
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Affiliation(s)
- Yanping Ma
- Virus Laboratory, the Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning of PR China, China
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He R, Ma Y, Qi Y, Jiang S, Wang N, Li M, Ji Y, Sun Z, Ruan Q. Characterization of human cytomegalovirus UL146 transcripts. Virus Res 2012; 163:223-8. [DOI: 10.1016/j.virusres.2011.09.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Revised: 09/23/2011] [Accepted: 09/23/2011] [Indexed: 01/14/2023]
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Gatherer D, Seirafian S, Cunningham C, Holton M, Dargan DJ, Baluchova K, Hector RD, Galbraith J, Herzyk P, Wilkinson GWG, Davison AJ. High-resolution human cytomegalovirus transcriptome. Proc Natl Acad Sci U S A 2011; 108:19755-60. [PMID: 22109557 PMCID: PMC3241806 DOI: 10.1073/pnas.1115861108] [Citation(s) in RCA: 178] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
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 protein-coding 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.
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Affiliation(s)
- Derek Gatherer
- Medical Research Council–University of Glasgow Centre for Virus Research, Glasgow G11 5JR, United Kingdom
| | - Sepehr Seirafian
- School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom; and
| | - Charles Cunningham
- Medical Research Council–University of Glasgow Centre for Virus Research, Glasgow G11 5JR, United Kingdom
| | - Mary Holton
- Medical Research Council–University of Glasgow Centre for Virus Research, Glasgow G11 5JR, United Kingdom
| | - Derrick J. Dargan
- Medical Research Council–University of Glasgow Centre for Virus Research, Glasgow G11 5JR, United Kingdom
| | - Katarina Baluchova
- Medical Research Council–University of Glasgow Centre for Virus Research, Glasgow G11 5JR, United Kingdom
| | - Ralph D. Hector
- Medical Research Council–University of Glasgow Centre for Virus Research, Glasgow G11 5JR, United Kingdom
| | - Julie Galbraith
- Sir Henry Wellcome Functional Genomics Facility, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Pawel Herzyk
- Sir Henry Wellcome Functional Genomics Facility, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | | | - Andrew J. Davison
- Medical Research Council–University of Glasgow Centre for Virus Research, Glasgow G11 5JR, United Kingdom
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Ma Y, Wang N, Li M, Gao S, Wang L, Ji Y, Qi Y, He R, Sun Z, Ruan Q. An antisense transcript in the human cytomegalovirus UL87 gene region. Virol J 2011; 8:515. [PMID: 22074130 PMCID: PMC3223508 DOI: 10.1186/1743-422x-8-515] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Accepted: 11/11/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rapid 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. RESULTS First, 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. CONCLUSION An 800nt antisense transcript in the UL87 gene region exists in HCMV clinical strains.
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Affiliation(s)
- Yanping Ma
- Virus Laboratory, The Affiliated Shengjing Hospital, China Medical University, 110004 Shenyang, Liaoning of China, China
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Wang N, Ma Y, Sun Z, Qi Y, Ji Y, He R, Li M, Ruan Q. Transcriptional features and transcript structure of UL145 in different strains of human cytomegalovirus. J Med Virol 2011; 83:2151-6. [DOI: 10.1002/jmv.22241] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Human cytomegalovirus RL13 gene transcripts in a clinical strain. Virus Genes 2011; 43:327-34. [DOI: 10.1007/s11262-011-0641-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 06/29/2011] [Indexed: 12/23/2022]
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He R, Ma Y, Qi Y, Wang N, Li M, Ji Y, Sun Z, Jiang S, Ruan Q. Characterization of the transcripts of human cytomegalovirus UL144. Virol J 2011; 8:299. [PMID: 21669005 PMCID: PMC3141681 DOI: 10.1186/1743-422x-8-299] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Accepted: 06/14/2011] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The 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. METHODS Northern blot hybridization, cDNA library screening, and RACE-PCR were used. RESULTS We 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. CONCLUSIONS These findings reveal the complex nature of the transcription of the UL144 gene in clinical isolates.
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Affiliation(s)
- Rong He
- Clinical Genetics Department, The Affiliated Shengjing Hospital, China Medical University, 110004 Shenyang, Liaoning of China
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