Mapping the C-elegans noncoding transcriptome with a whole-genome tiling microarray

被引：45

作者：

He, Housheng

Wang, Jie

Liu, Tao

Liu, X. Shirley

Li, Tiantian

Wang, Yunfei

Qian, Zuwei

Zheng, Haixia

Zhu, Xiaopeng ^{[1
]}

Wu, Tao

Shi, Baochen

Deng, Wei

Zhou, Wei

Skogerbo, Geir

Chen, Runsheng

机构：

[1] Chinese Acad Sci, Inst Biophys, Bioinformat Lab, Beijing 100101, Peoples R China

[2] Chinese Acad Sci, Inst Biophys, Natl Lab Biomacromol, Beijing 100101, Peoples R China

[3] Chinese Acad Sci, Grad Sch, Beijing 100080, Peoples R China

[4] Harvard Univ, Sch Med, Dana Farber Canc Inst, Dept Biostat & Computat Biol, Boston, MA 02115 USA

[5] Harvard Univ, Sch Publ Hlth, Boston, MA 02115 USA

[6] Affymetrix Inc, Santa Clara, CA 95051 USA

[7] Chinese Acad Sci, Inst Comp Technol, Key Lab Intelligent Informat Proc, Bioinformat Res Grp, Beijing 100080, Peoples R China

[8] Chinese Natl Human Genome Ctr, Beijing 100176, Peoples R China

来源：

GENOME RESEARCH | 2007年 / 17卷 / 10期

关键词：

D O I：

10.1101/gr.6611807

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The number of annotated protein coding genes in the genome of Caenorhabditis elegans is similar to that of other animals, but the extent of its non- protein- coding transcriptome remains unknown. Expression profiling on whole- genome tiling microarrays applied to a mixed- stage C. elegans population verified the expression of 71% of all annotated exons. Only a small fraction ( 11%) of the polyadenylated transcription is non- annotated and appears to consist of similar to 3200 missed or alternative exons and 7800 small transcripts of unknown function ( TUFs). Almost half ( 44%) of the detected transcriptional output is non- polyadenylated and probably not protein coding, and of this, 70% overlaps the boundaries of protein- coding genes in a complex manner. Specific analysis of small non- polyadenylated transcripts verified 97% of all annotated small ncRNAs and suggested that the transcriptome contains similar to 1200 small (< 500 nt) unannotated noncoding loci. After combining overlapping transcripts, we estimate that at least 70% of the total C. elegans genome is transcribed.

引用

页码：1471 / 1477

页数：7

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