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Characterization of the transcripts of human cytomegalovirus UL144.

He R, Ma Y, Qi Y, Wang N, Li M, Ji Y, Sun Z, Jiang S, Ruan Q - Virol. J. (2011)

Bottom Line: 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.These findings reveal the complex nature of the transcription of the UL144 gene in clinical isolates.

View Article: PubMed Central - HTML - PubMed

Affiliation: Clinical Genetics Department, The Affiliated Shengjing Hospital, China Medical University, 110004 Shenyang, Liaoning of China.

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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Related in: MedlinePlus

Summary of UL144 mapping results. Transcripts of the HCMV UL144 gene demonstrated in this study are indicated. All of the transcripts share the same 3' end at nt 12844-12846. Nucleotide numbers are based on the UL/b' region sequence of isolate H (GenBank accession number GQ981646).
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Figure 3: Summary of UL144 mapping results. Transcripts of the HCMV UL144 gene demonstrated in this study are indicated. All of the transcripts share the same 3' end at nt 12844-12846. Nucleotide numbers are based on the UL/b' region sequence of isolate H (GenBank accession number GQ981646).

Mentions: In this study, we provide evidence for the existence of at least 4 differentially regulated UL144 transcripts of 1,300, 1,600, 1,700, and 3,500 nt (Table 2, Figure 3). The 5' ends of the 1,300, 1,600, and 1,700 nt transcripts are within the region between the UL143 and UL144 ORFs and the transcripts all contain the same 2 ORFs of UL144 and UL145. The 1,600 nt transcript appears to be the major form since its presence was confirmed by all of the methods used in this study, including Northern blot hybridization, RACE-PCR, and cDNA library screening. At the same time, this transcript is the most abundant based on its prevalence in the cDNA library (15 of 22 cDNA clones) and the strength of its band in the Northern blot assay. Potential TATA and CCAAT promoter elements at 29 and 70 bp upstream of its initiation site, respectively, further support the existence of this transcript. The 1,300 nt and 1,700 nt transcripts were not as prevalent as the 1,600 nt transcript. The 1,300 nt transcript was found in 4 of 22 clones from the cDNA library and while its genomic sequence contains a potential TATA promoter element 13 bases upstream of its initiation site, it does not contain a CAT box. The transcript of 1,700 nt was present in only 1 of the 22 specific cDNA clones and was not detected by Northern blot, most likely due to its low prevalence. It has potential TATTA and CACAT promoter elements at 50 and 90 bases upstream its initiation site, respectively. The largest transcript, 3,500 nt in length, initiates from within the UL141 ORF and includes UL142, UL143, UL144, UL145, and part of UL141 ORFs. This transcript was found by Northern blot only at long exposure times and its initiation site was demonstrated in two separate 5' RACE experiments using RNA preparations from isolate H. A potential promoter (TTACTTTTAA) and a "CCAAAT" were found at -15 and -29 of its initiation site, respectively. However, the presence of the 3500 nt transcript was not confirmed in the cDNA library. The long length of the transcript may have prevented its ligation during the construction of the cDNA library.


Characterization of the transcripts of human cytomegalovirus UL144.

He R, Ma Y, Qi Y, Wang N, Li M, Ji Y, Sun Z, Jiang S, Ruan Q - Virol. J. (2011)

Summary of UL144 mapping results. Transcripts of the HCMV UL144 gene demonstrated in this study are indicated. All of the transcripts share the same 3' end at nt 12844-12846. Nucleotide numbers are based on the UL/b' region sequence of isolate H (GenBank accession number GQ981646).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3141681&req=5

Figure 3: Summary of UL144 mapping results. Transcripts of the HCMV UL144 gene demonstrated in this study are indicated. All of the transcripts share the same 3' end at nt 12844-12846. Nucleotide numbers are based on the UL/b' region sequence of isolate H (GenBank accession number GQ981646).
Mentions: In this study, we provide evidence for the existence of at least 4 differentially regulated UL144 transcripts of 1,300, 1,600, 1,700, and 3,500 nt (Table 2, Figure 3). The 5' ends of the 1,300, 1,600, and 1,700 nt transcripts are within the region between the UL143 and UL144 ORFs and the transcripts all contain the same 2 ORFs of UL144 and UL145. The 1,600 nt transcript appears to be the major form since its presence was confirmed by all of the methods used in this study, including Northern blot hybridization, RACE-PCR, and cDNA library screening. At the same time, this transcript is the most abundant based on its prevalence in the cDNA library (15 of 22 cDNA clones) and the strength of its band in the Northern blot assay. Potential TATA and CCAAT promoter elements at 29 and 70 bp upstream of its initiation site, respectively, further support the existence of this transcript. The 1,300 nt and 1,700 nt transcripts were not as prevalent as the 1,600 nt transcript. The 1,300 nt transcript was found in 4 of 22 clones from the cDNA library and while its genomic sequence contains a potential TATA promoter element 13 bases upstream of its initiation site, it does not contain a CAT box. The transcript of 1,700 nt was present in only 1 of the 22 specific cDNA clones and was not detected by Northern blot, most likely due to its low prevalence. It has potential TATTA and CACAT promoter elements at 50 and 90 bases upstream its initiation site, respectively. The largest transcript, 3,500 nt in length, initiates from within the UL141 ORF and includes UL142, UL143, UL144, UL145, and part of UL141 ORFs. This transcript was found by Northern blot only at long exposure times and its initiation site was demonstrated in two separate 5' RACE experiments using RNA preparations from isolate H. A potential promoter (TTACTTTTAA) and a "CCAAAT" were found at -15 and -29 of its initiation site, respectively. However, the presence of the 3500 nt transcript was not confirmed in the cDNA library. The long length of the transcript may have prevented its ligation during the construction of the cDNA library.

Bottom Line: 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.These findings reveal the complex nature of the transcription of the UL144 gene in clinical isolates.

View Article: PubMed Central - HTML - PubMed

Affiliation: Clinical Genetics Department, The Affiliated Shengjing Hospital, China Medical University, 110004 Shenyang, Liaoning of China.

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.

Show MeSH
Related in: MedlinePlus