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Inverse PCR-Based Method for Isolating Novel SINEs from Genome
Han, Yawei1,2; Chen, Liping1; Guan, Lihong2; He, Shunping2; Han, YW (reprint author), Zhengzhou Univ Light Ind, Coll Food & Bioengn, Zhengzhou 450002, Henan, Peoples R China.
2014-04-01
Source PublicationMOLECULAR BIOTECHNOLOGY
ISSN1073-6085
Volume56Issue:4Pages:296-304
AbstractShort interspersed elements (SINEs) are moderately repetitive DNA sequences in eukaryotic genomes. Although eukaryotic genomes contain numerous SINEs copy, it is very difficult and laborious to isolate and identify them by the reported methods. In this study, the inverse PCR was successfully applied to isolate SINEs from Opsariichthys bidens genome in Eastern Asian Cyprinid. A group of SINEs derived from tRNA(Ala) molecular had been identified, which were named Opsar according to Opsariichthys. SINEs characteristics were exhibited in Opsar, which contained a tRNA(Ala)-derived region at the 5' end, a tRNA-unrelated region, and AT-rich region at the 3' end. The tRNA-derived region of Opsar shared 76 % sequence similarity with tRNA(Ala) gene. This result indicated that Opsar could derive from the inactive or pseudogene of tRNA(Ala). The reliability of method was tested by obtaining C-SINE, Ct-SINE, and M-SINEs from Ctenopharyngodon idellus, Megalobrama amblycephala, and Cyprinus carpio genomes. This method is simpler than the previously reported, which successfully omitted many steps, such as preparation of probes, construction of genomic libraries, and hybridization.; Short interspersed elements (SINEs) are moderately repetitive DNA sequences in eukaryotic genomes. Although eukaryotic genomes contain numerous SINEs copy, it is very difficult and laborious to isolate and identify them by the reported methods. In this study, the inverse PCR was successfully applied to isolate SINEs from Opsariichthys bidens genome in Eastern Asian Cyprinid. A group of SINEs derived from tRNA(Ala) molecular had been identified, which were named Opsar according to Opsariichthys. SINEs characteristics were exhibited in Opsar, which contained a tRNA(Ala)-derived region at the 5' end, a tRNA-unrelated region, and AT-rich region at the 3' end. The tRNA-derived region of Opsar shared 76 % sequence similarity with tRNA(Ala) gene. This result indicated that Opsar could derive from the inactive or pseudogene of tRNA(Ala). The reliability of method was tested by obtaining C-SINE, Ct-SINE, and M-SINEs from Ctenopharyngodon idellus, Megalobrama amblycephala, and Cyprinus carpio genomes. This method is simpler than the previously reported, which successfully omitted many steps, such as preparation of probes, construction of genomic libraries, and hybridization.
SubtypeArticle
KeywordInverse Pcr Short Interspersed Elements Self-ligation Of Dna Cyprinidaes
Department[Han, Yawei; Chen, Liping] Zhengzhou Univ Light Ind, Coll Food & Bioengn, Zhengzhou 450002, Henan, Peoples R China; [Han, Yawei; Guan, Lihong; He, Shunping] Chinese Acad Sci, Inst Hydrobiol, Wuhan 430072, Hubei, Peoples R China
DOI10.1007/s12033-013-9708-y
WOS HeadingsScience & Technology ; Life Sciences & Biomedicine
Funding OrganizationNational Natural Science Foundation of China [31172175]; Doctor Foundation of Zhengzhou University of Light Industry ; National Natural Science Foundation of China [31172175]; Doctor Foundation of Zhengzhou University of Light Industry ; National Natural Science Foundation of China [31172175]; Doctor Foundation of Zhengzhou University of Light Industry ; National Natural Science Foundation of China [31172175]; Doctor Foundation of Zhengzhou University of Light Industry
Indexed BySCI
Language英语
WOS Research AreaBiochemistry & Molecular Biology ; Biotechnology & Applied Microbiology
WOS SubjectBiochemistry & Molecular Biology ; Biotechnology & Applied Microbiology
WOS IDWOS:000332972300002
WOS KeywordRNA-DERIVED SINES ; SHORT INTERSPERSED ELEMENTS ; 5S RIBOSOMAL-RNA ; EUKARYOTIC GENOMES ; VERTEBRATE GENOMES ; MAMMALIAN GENOME ; MOUSE GENOME ; SEQUENCES ; FAMILY ; DNA
Funding OrganizationNational Natural Science Foundation of China [31172175]; Doctor Foundation of Zhengzhou University of Light Industry ; National Natural Science Foundation of China [31172175]; Doctor Foundation of Zhengzhou University of Light Industry ; National Natural Science Foundation of China [31172175]; Doctor Foundation of Zhengzhou University of Light Industry ; National Natural Science Foundation of China [31172175]; Doctor Foundation of Zhengzhou University of Light Industry
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Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/342005/19997
Collection水生生物多样性与资源保护研究中心_期刊论文
Corresponding AuthorHan, YW (reprint author), Zhengzhou Univ Light Ind, Coll Food & Bioengn, Zhengzhou 450002, Henan, Peoples R China.
Affiliation1.Zhengzhou Univ Light Ind, Coll Food & Bioengn, Zhengzhou 450002, Henan, Peoples R China
2.Chinese Acad Sci, Inst Hydrobiol, Wuhan 430072, Hubei, Peoples R China
Recommended Citation
GB/T 7714
Han, Yawei,Chen, Liping,Guan, Lihong,et al. Inverse PCR-Based Method for Isolating Novel SINEs from Genome[J]. MOLECULAR BIOTECHNOLOGY,2014,56(4):296-304.
APA Han, Yawei,Chen, Liping,Guan, Lihong,He, Shunping,&Han, YW .(2014).Inverse PCR-Based Method for Isolating Novel SINEs from Genome.MOLECULAR BIOTECHNOLOGY,56(4),296-304.
MLA Han, Yawei,et al."Inverse PCR-Based Method for Isolating Novel SINEs from Genome".MOLECULAR BIOTECHNOLOGY 56.4(2014):296-304.
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