Mitochondrial DNA The Journal of DNA Mapping, Sequencing, and Analysis
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
Complete mitochondrial genome sequence and mutations of the laryngeal cancer model inbred nude rat strain Chao-Hui Zheng, Rong-Zhi Lin, En-Hui Qiu, Yi-Min Chen, Xiao-Fang Chen, ZhiHui Xu, Zhen-Yuan Liang & Yu-Ming Hong To cite this article: Chao-Hui Zheng, Rong-Zhi Lin, En-Hui Qiu, Yi-Min Chen, Xiao-Fang Chen, Zhi-Hui Xu, Zhen-Yuan Liang & Yu-Ming Hong (2015): Complete mitochondrial genome sequence and mutations of the laryngeal cancer model inbred nude rat strain, Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.1003904
Published online: 29 Jan 2015.
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Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: [Deakin University Library]
Date: 07 November 2015, At: 00:42
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2014.1003904
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome sequence and mutations of the laryngeal cancer model inbred nude rat strain Chao-Hui Zheng, Rong-Zhi Lin, En-Hui Qiu, Yi-Min Chen, Xiao-Fang Chen, Zhi-Hui Xu, Zhen-Yuan Liang, and Yu-Ming Hong
Mitochondrial DNA
The Second Clinical Medical College of Fujian Medical University, Quanzhou, China
Abstract
Keywords
In the present work, we undertook the complete mitochondrial genome sequencing of an important laryngeal cancer model inbred rat strain for the first time. The total length of the mitogenome was 16,308 bp. It harbored 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one non-coding control region (D-loop region). The mutation events were also reported.
Genome, laryngeal cancer, mitochondrion
Animals have been used by humans for centuries to understand their own biology. In laryngeal cancer research, animal models have allowed the study of laryngeal cancer disease in the early stages, as well as the investigation of the mechanisms of the pathogenesis of laryngeal cancer disease and the effects of drug intervention (Song et al., 2013). Laryngeal carcinoma is the most common malignancy of the upper respiratory tract. It is believed to result from complex interactions among many genetic and environmental factors. The estimated incidence, mortality and 5-year prevalence of laryngeal carcinoma worldwide are 156,877, 83,376, and 441,675, respectively. Laryngeal cancer represents the second most common malignancy of the head and neck worldwide. Given the fundamental role, the larynx plays in human speech and communication, determining the optimal management of laryngeal cancer is critical. Despite multiple and aggressive therapeutic interventions, there has been no fundamental improvement in the 5-year survival rates of the patients over the past decades (Dang et al., 2014; Lu et al., 2014). Inbred rat and mouse strains with variations in their mitochondrial genomic sequences serve as good substrates for construction of conplastic strains for examining genetic contributions. Several complex traits are controlled by genetic elements of the mitochondrial genome (Yue et al., 2014).
History Received 14 December 2014 Accepted 19 December 2014 Published online 29 January 2015
Here, we reported complete mitochondrial genome sequence of a laryngeal cancer inbred nude rat model. Total DNA was extracted from the laryngeal cancer tissue of a female individual that harbors a serious laryngeal cancer. Polymerase chain reaction (PCR) was carried out using 22 pairs of primers to amplify the entire mitochondrial genome. Mitochondrial DNA information of this strain is described in Table 1 and sequences from the current study were deposited in GenBank (accession no. KJ939361). The mitochondrial genome is 16,308 bp long including 13 proteincoding genes, two rRNA genes, 22 tRNA genes, and 1 control region. The total length of the protein-coding gene sequences is 11,437 bp. Most protein-coding genes initiate with ATG except for ND2, ND3, and ND5 which begin with ATA. Eight proteincoding genes terminate with TAA whereas the ND2, ND3, and COX3 genes terminate with TAG and the CytB gene terminates with AGA. The incomplete stop codon (T–) is used in ND4. A strong bias against G at the third codon position is observed in the protein-coding genes. The length of tRNA genes vary from 60 to 73 bp. Sequence data obtained from the current study were compared with the reference BN sequence (AC_000022.1). Eighty-nine variations in mtDNA were observed between these two strains. 35.5% of the variations were within gene-coding sequences, 18.7% were within noncoding RNA sequences, and 45.8% were synonymous variants.
Correspondence: Yu-ming Hong, The Second Clinical Medical College of Fujian Medical University, Quanzhou, 362000, China. E-mail: [email protected]
2
C.-H. Zheng et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Genes encoded by this mitochondrial genome. Position Gene
Mitochondrial DNA
Phe
tRNA 12S rRNA tRNAVal 16S rRNA tRNALeu ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn OL tRNACys tRNATyr COX1 tRNASer tRNAAsp COX2 tRNALys ATP8 ATP6 COX3 tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer tRNALeu ND5 ND6 tRNAGlu CytB tRNAThr tRNAPro
Base composition (%)
From
To
Size (bp)
A
C
G
T
362 432 1388 1455 3025 3102 4058 4124 4198 4267 5309 5377 5447 5520 5552 5619 5688 7230 7306 7375 8065 8130 8291 8971 9755 9824 10,171 10,240 10,530 11,908 11,978 12,039 12,110 13,914 14,442 14,515 15,658 15,727
429 1386 1454 3024 3099 4058 4126 4195 4266 5310 5375 5445 5519 5550 5618 5686 7232 7298 7373 8058 8127 8330 8971 9774 9823 10,180 10,239 10,536 11,907 11,977 12,037 12,109 13,930 14,441 14,510 15,654 15,727 15,789
67 955 67 1570 75 957 69 72 69 1044 67 69 73 31 67 68 1545 69 68 684 63 201 681 804 69 357 69 297 1378 70 60 71 1821 528 69 1140 70 66
35.8 36.8 38.8 37.7 33.3 31.9 40.6 25.0 27.5 36.4 37.3 27.6 23.3 35.5 25.4 33.8 28.8 26.1 36.8 34.2 34.9 39.8 33.6 26.5 31.9 30.3 40.6 32.3 32.3 41.4 31.7 38.0 32.7 22.2 29.0 31.2 34.3 24.2
25.4 22.7 19.4 21.0 21.3 27.9 13.0 9.7 24.6 26.4 20.9 10.1 16.4 29.0 20.9 16.2 25.3 14.5 13.2 23.8 17.5 23.9 27.4 28.7 18.8 29.4 10.1 24.6 28.2 15.7 18.3 14.1 29.3 8.7 11.6 30.2 21.4 13.7
17.9 18.0 11.9 17.7 16.0 12.6 14.5 29.2 18.9 8.9 16.4 23.2 31.5 25.8 25.4 20.6 16.3 27.5 17.6 14.6 17.5 7.9 11.1 14.8 16.0 12.9 10.1 11.5 10.9 8.6 16.7 18.3 10.5 28.2 20.3 13.4 17.1 28.8
20.9 22.5 29.9 23.6 29.4 27.6 31.9 36.1 29.0 28.3 25.4 39.1 28.8 9.7 28.3 29.4 29.6 31.9 32.4 27.4 30.1 28.4 27.9 30.0 33.3 27.4 39.2 31.6 28.6 34.3 33.3 29.6 27.5 40.9 39.1 25.2 27.2 33.3
Declaration of interest The authors report that they have no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Dang S, Qu Y, Wei J, Shao Y, Yang Q, Ji M, Shi B, et al. (2014). Low copy number of mitochondrial DNA (mtDNA) predicts worse prognosis in early-stage laryngeal cancer patients. Diagn Pathol 9:28. doi:10.1186/1746-1596-9-28.
Start codon
Stop codon
ATG
TAA
ATA
TAG
ATG
TAA
ATG
TAA
ATG ATG ATG
TAA TAA TAG
ATA
TAG
ATG ATG
TAA T–
ATA ATG
TAA TAA
ATG
AGA
Strand H H H H H H H L H H H L L L L L H L H H H H H H H H H H H H H H H L L H H L
Lu B, Li J, Gao Q, Yu W, Yang Q, Li X. (2014). Laryngeal cancer risk and common single nucleotide polymorphisms in nucleotide excision repair pathway genes ERCC1, ERCC2, ERCC3, ERCC4, ERCC5 and XPA. Gene 542:64–8. Song Y, Sun X, Bai WL, Ji WY. (2013). Antitumor effects of Dasatinib on laryngeal squamous cell carcinoma in vivo and in vitro. Eur Arch Otorhinolaryngol 270:1397–404. Yue H, Liu S, Liu Y, Zhang X, Fan Z. (2014). Mitochondrial genome of the Sichuan field mouse (Apodemus latronum). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2014.930835.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
Complete mitochondrial genome sequence and mutations of the laryngeal cancer model inbred nude rat strain Chao-Hui Zheng, Rong-Zhi Lin, En-Hui Qiu, Yi-Min Chen, Xiao-Fang Chen, ZhiHui Xu, Zhen-Yuan Liang & Yu-Ming Hong To cite this article: Chao-Hui Zheng, Rong-Zhi Lin, En-Hui Qiu, Yi-Min Chen, Xiao-Fang Chen, Zhi-Hui Xu, Zhen-Yuan Liang & Yu-Ming Hong (2015): Complete mitochondrial genome sequence and mutations of the laryngeal cancer model inbred nude rat strain, Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.1003904
Published online: 29 Jan 2015.
Submit your article to this journal
Article views: 9
View related articles
View Crossmark data
Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: [Deakin University Library]
Date: 07 November 2015, At: 00:42
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2014.1003904
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome sequence and mutations of the laryngeal cancer model inbred nude rat strain Chao-Hui Zheng, Rong-Zhi Lin, En-Hui Qiu, Yi-Min Chen, Xiao-Fang Chen, Zhi-Hui Xu, Zhen-Yuan Liang, and Yu-Ming Hong
Mitochondrial DNA
The Second Clinical Medical College of Fujian Medical University, Quanzhou, China
Abstract
Keywords
In the present work, we undertook the complete mitochondrial genome sequencing of an important laryngeal cancer model inbred rat strain for the first time. The total length of the mitogenome was 16,308 bp. It harbored 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one non-coding control region (D-loop region). The mutation events were also reported.
Genome, laryngeal cancer, mitochondrion
Animals have been used by humans for centuries to understand their own biology. In laryngeal cancer research, animal models have allowed the study of laryngeal cancer disease in the early stages, as well as the investigation of the mechanisms of the pathogenesis of laryngeal cancer disease and the effects of drug intervention (Song et al., 2013). Laryngeal carcinoma is the most common malignancy of the upper respiratory tract. It is believed to result from complex interactions among many genetic and environmental factors. The estimated incidence, mortality and 5-year prevalence of laryngeal carcinoma worldwide are 156,877, 83,376, and 441,675, respectively. Laryngeal cancer represents the second most common malignancy of the head and neck worldwide. Given the fundamental role, the larynx plays in human speech and communication, determining the optimal management of laryngeal cancer is critical. Despite multiple and aggressive therapeutic interventions, there has been no fundamental improvement in the 5-year survival rates of the patients over the past decades (Dang et al., 2014; Lu et al., 2014). Inbred rat and mouse strains with variations in their mitochondrial genomic sequences serve as good substrates for construction of conplastic strains for examining genetic contributions. Several complex traits are controlled by genetic elements of the mitochondrial genome (Yue et al., 2014).
History Received 14 December 2014 Accepted 19 December 2014 Published online 29 January 2015
Here, we reported complete mitochondrial genome sequence of a laryngeal cancer inbred nude rat model. Total DNA was extracted from the laryngeal cancer tissue of a female individual that harbors a serious laryngeal cancer. Polymerase chain reaction (PCR) was carried out using 22 pairs of primers to amplify the entire mitochondrial genome. Mitochondrial DNA information of this strain is described in Table 1 and sequences from the current study were deposited in GenBank (accession no. KJ939361). The mitochondrial genome is 16,308 bp long including 13 proteincoding genes, two rRNA genes, 22 tRNA genes, and 1 control region. The total length of the protein-coding gene sequences is 11,437 bp. Most protein-coding genes initiate with ATG except for ND2, ND3, and ND5 which begin with ATA. Eight proteincoding genes terminate with TAA whereas the ND2, ND3, and COX3 genes terminate with TAG and the CytB gene terminates with AGA. The incomplete stop codon (T–) is used in ND4. A strong bias against G at the third codon position is observed in the protein-coding genes. The length of tRNA genes vary from 60 to 73 bp. Sequence data obtained from the current study were compared with the reference BN sequence (AC_000022.1). Eighty-nine variations in mtDNA were observed between these two strains. 35.5% of the variations were within gene-coding sequences, 18.7% were within noncoding RNA sequences, and 45.8% were synonymous variants.
Correspondence: Yu-ming Hong, The Second Clinical Medical College of Fujian Medical University, Quanzhou, 362000, China. E-mail: [email protected]
2
C.-H. Zheng et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Genes encoded by this mitochondrial genome. Position Gene
Mitochondrial DNA
Phe
tRNA 12S rRNA tRNAVal 16S rRNA tRNALeu ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn OL tRNACys tRNATyr COX1 tRNASer tRNAAsp COX2 tRNALys ATP8 ATP6 COX3 tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer tRNALeu ND5 ND6 tRNAGlu CytB tRNAThr tRNAPro
Base composition (%)
From
To
Size (bp)
A
C
G
T
362 432 1388 1455 3025 3102 4058 4124 4198 4267 5309 5377 5447 5520 5552 5619 5688 7230 7306 7375 8065 8130 8291 8971 9755 9824 10,171 10,240 10,530 11,908 11,978 12,039 12,110 13,914 14,442 14,515 15,658 15,727
429 1386 1454 3024 3099 4058 4126 4195 4266 5310 5375 5445 5519 5550 5618 5686 7232 7298 7373 8058 8127 8330 8971 9774 9823 10,180 10,239 10,536 11,907 11,977 12,037 12,109 13,930 14,441 14,510 15,654 15,727 15,789
67 955 67 1570 75 957 69 72 69 1044 67 69 73 31 67 68 1545 69 68 684 63 201 681 804 69 357 69 297 1378 70 60 71 1821 528 69 1140 70 66
35.8 36.8 38.8 37.7 33.3 31.9 40.6 25.0 27.5 36.4 37.3 27.6 23.3 35.5 25.4 33.8 28.8 26.1 36.8 34.2 34.9 39.8 33.6 26.5 31.9 30.3 40.6 32.3 32.3 41.4 31.7 38.0 32.7 22.2 29.0 31.2 34.3 24.2
25.4 22.7 19.4 21.0 21.3 27.9 13.0 9.7 24.6 26.4 20.9 10.1 16.4 29.0 20.9 16.2 25.3 14.5 13.2 23.8 17.5 23.9 27.4 28.7 18.8 29.4 10.1 24.6 28.2 15.7 18.3 14.1 29.3 8.7 11.6 30.2 21.4 13.7
17.9 18.0 11.9 17.7 16.0 12.6 14.5 29.2 18.9 8.9 16.4 23.2 31.5 25.8 25.4 20.6 16.3 27.5 17.6 14.6 17.5 7.9 11.1 14.8 16.0 12.9 10.1 11.5 10.9 8.6 16.7 18.3 10.5 28.2 20.3 13.4 17.1 28.8
20.9 22.5 29.9 23.6 29.4 27.6 31.9 36.1 29.0 28.3 25.4 39.1 28.8 9.7 28.3 29.4 29.6 31.9 32.4 27.4 30.1 28.4 27.9 30.0 33.3 27.4 39.2 31.6 28.6 34.3 33.3 29.6 27.5 40.9 39.1 25.2 27.2 33.3
Declaration of interest The authors report that they have no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Dang S, Qu Y, Wei J, Shao Y, Yang Q, Ji M, Shi B, et al. (2014). Low copy number of mitochondrial DNA (mtDNA) predicts worse prognosis in early-stage laryngeal cancer patients. Diagn Pathol 9:28. doi:10.1186/1746-1596-9-28.
Start codon
Stop codon
ATG
TAA
ATA
TAG
ATG
TAA
ATG
TAA
ATG ATG ATG
TAA TAA TAG
ATA
TAG
ATG ATG
TAA T–
ATA ATG
TAA TAA
ATG
AGA
Strand H H H H H H H L H H H L L L L L H L H H H H H H H H H H H H H H H L L H H L
Lu B, Li J, Gao Q, Yu W, Yang Q, Li X. (2014). Laryngeal cancer risk and common single nucleotide polymorphisms in nucleotide excision repair pathway genes ERCC1, ERCC2, ERCC3, ERCC4, ERCC5 and XPA. Gene 542:64–8. Song Y, Sun X, Bai WL, Ji WY. (2013). Antitumor effects of Dasatinib on laryngeal squamous cell carcinoma in vivo and in vitro. Eur Arch Otorhinolaryngol 270:1397–404. Yue H, Liu S, Liu Y, Zhang X, Fan Z. (2014). Mitochondrial genome of the Sichuan field mouse (Apodemus latronum). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2014.930835.
