Inverse PCR-Based Method for Isolating Novel SINEs from Genome

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	Inverse PCR-Based Method for Isolating Novel SINEs from Genome
	Han, Yawei 1,2; Chen, Liping 1; Guan, Lihong 2; He, Shunping 2
刊名	MOLECULAR BIOTECHNOLOGY
	2014-04-01
卷号	56 期号:4 页码:296-304
关键词	Inverse PCR Short interspersed elements Self-ligation of DNA Cyprinidaes
ISSN号	1073-6085
通讯作者	Han, YW (reprint author), Zhengzhou Univ Light Ind, Coll Food & Bioengn, Zhengzhou 450002, Henan, Peoples R China.
中文摘要	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.
英文摘要	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.
WOS标题词	Science & Technology ; Life Sciences & Biomedicine
类目[WOS]	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology
研究领域[WOS]	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology
关键词[WOS]	RNA-DERIVED SINES ; SHORT INTERSPERSED ELEMENTS ; 5S RIBOSOMAL-RNA ; EUKARYOTIC GENOMES ; VERTEBRATE GENOMES ; MAMMALIAN GENOME ; MOUSE GENOME ; SEQUENCES ; FAMILY ; DNA
收录类别	SCI
资助信息	National Natural Science Foundation of China [31172175]; Doctor Foundation of Zhengzhou University of Light Industry
语种	英语
WOS记录号	WOS:000332972300002
公开日期	2014-08-07
内容类型	期刊论文
源URL	[http://ir.ihb.ac.cn/handle/342005/19997]
专题	水生生物研究所_水生生物多样性与资源保护研究中心_期刊论文
作者单位	1.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
推荐引用方式 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.(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.