Organization of the Caenorhabditis elegans small non-coding transcriptome: Genomic features, biogenesis, and expression

doi:10.1101/gr.4139206

	Organization of the Caenorhabditis elegans small non-coding transcriptome: Genomic features, biogenesis, and expression
	Deng, W ; Zhu, XP ; Skogerbo, G ; Zhao, Y ; Fu, Z ; Wang, YD ; He, HS ; Cai, L ; Sun, H ; Liu, CN ; Li, B ; Bai, BY ; Wang, J ; Jia, D ; Sun, SW ; He, H ; Cui, Y ; Wang, Y ; Bu, DB ; Chen, RS
	2006
发表期刊	GENOME RESEARCH
ISSN	1088-9051
卷号	16 期号:1 页码:20-29
摘要	Recent evidence points to considerable transcription occurring in non-protein-coding regions of eukaryote genomes. However, their lack of conservation and demonstrated function have created controversy over whether these transcripts are functional. Applying a novel cloning strategy, we have cloned 100 novel and 61 known or predicted Caenorhabditis elegans full-length ncRNAs. Studying the genomic environment and transcriptional characteristics have shown that two-thirds of all ncRNAs, including many intronic snoRNAs, are independently transcribed under the control of ncRNA-specific upstream promoter elements. Furthermore, the transcription levels of at least 60% of the ncRNAs vary with developmental stages. We identified two new classes of ncRNAs, stern-bulge RNAs (sbRNAs) and snRNA-like RNAs (snIRNAs), both featuring distinct internal motifs, secondary structures, upstream elements, and high and developmentally variable expression. Most of the novel ncRNAs are conserved in Caenorhabditis briggsae, but only one homolog was found outside the nematodes. Preliminary estimates indicate that the C elegans transcriptome contains -2700 small non-coding RNAs, potentially acting as regulatory elements in nematode development.
DOI	10.1101/gr.4139206
收录类别	SCI
语种	英语
WOS研究方向	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS类目	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS记录号	WOS:000235598000003
出版者	COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
引用统计	被引频次：100[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/10598
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Chen, RS
作者单位	1.Chinese Acad Sci, Inst Biophys, Bioinformat Lab, Beijing 100101, Peoples R China 2.Chinese Acad Sci, Comp Technol Inst, Key Lab Intelligent Informat Proc, Bioinformat Res Grp, Beijing 100080, Peoples R China 3.Chinese Natl Human Genome Ctr, Beijing 100176, Peoples R China 4.Univ Tennessee, Ctr Hlth Sci, Dept Mol Sci, Ctr Genom & Bioinformat, Memphis, TN 38163 USA 5.Chinese Acad Sci, Grad Sch, Beijing 100080, Peoples R China 6.Peking Univ, Sch Oncol, Beijing Canc Hosp, Beijing 100036, Peoples R China
推荐引用方式 GB/T 7714	Deng, W,Zhu, XP,Skogerbo, G,et al. Organization of the Caenorhabditis elegans small non-coding transcriptome: Genomic features, biogenesis, and expression[J]. GENOME RESEARCH,2006,16(1):20-29.
APA	Deng, W.,Zhu, XP.,Skogerbo, G.,Zhao, Y.,Fu, Z.,...&Chen, RS.(2006).Organization of the Caenorhabditis elegans small non-coding transcriptome: Genomic features, biogenesis, and expression.GENOME RESEARCH,16(1),20-29.
MLA	Deng, W,et al."Organization of the Caenorhabditis elegans small non-coding transcriptome: Genomic features, biogenesis, and expression".GENOME RESEARCH 16.1(2006):20-29.