Mapping the C-elegans noncoding transcriptome with a whole-genome tiling microarray
Mapping the C-elegans noncoding transcriptome with a whole-genome tiling microarray
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DOI：
10.1101/gr.6611807
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发表时间：
2007-10-01
期刊：
影响因子：
7
通讯作者：
Chen, Runsheng
中科院分区：
文献类型：
--
作者：
He, Housheng;Wang, Jie;Chen, Runsheng
秀丽线虫基因组中有注释的蛋白质编码基因的数量与其他动物相似，但其非蛋白质编码转录组的范围尚不清楚。将全基因组平铺微阵列应用于混合阶段线虫种群的表达谱分析，证实了71%的注释外显子的表达。只有一小部分(11%)的多腺苷化转录没有注释，似乎由类似于3200个缺失或替代外显子和7800个功能未知的小转录本(TUF)组成。几乎一半(44%)的检测到的转录产物是非多聚腺苷化的，可能不是蛋白质编码的，其中70%以复杂的方式与蛋白质编码基因的边界重叠。对小的非多聚腺苷化转录本的特殊分析证实了所有注释的小ncRNA的97%，并表明转录组包含类似于1200个小的(<；500个核苷酸)未注释的非编码区。在结合重叠的转录本后，我们估计至少有70%的线虫基因组是转录的。
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.