Liu Wanfei, Zhao Yuhui, Cui Peng, Lin Qiang, Ding Feng, Xin Chengqi, Tan Xinyu, Song Shuhui, Yu Jun, Hu Songnian
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences Beijing, China.
Front Genet. 2011 Dec 26;2:93. doi: 10.3389/fgene.2011.00093. eCollection 2011.
The high-throughput next-generation sequencing technologies provide an excellent opportunity for the detection of less-abundance transcripts that may not be identifiable by previously available techniques. Here, we report a discovery of thousands of novel transcripts (mostly non-coding RNAs) that are expressed in mouse cerebrum, testis, and embryonic stem (ES) cells, through an in-depth analysis of rmRNA-seq data. These transcripts show significant associations with transcriptional start and elongation signals. At the upstream of these transcripts we observed significant enrichment of histone marks (histone H3 lysine 4 trimethylation, H3K4me3), RNAPII binding sites, and cap analysis of gene expression tags that mark transcriptional start sites. Along the length of these transcripts, we also observed enrichment of histone H3 lysine 36 trimethylation (H3K36me3). Moreover, these transcripts show strong purifying selection in their genomic loci, exonic sequences, and promoter regions, implying functional constraints on the evolution of these transcripts. These results define a collection of novel transcripts in the mouse genome and indicate their potential functions in the mouse tissues and cells.
高通量下一代测序技术为检测以前可用技术可能无法识别的低丰度转录本提供了绝佳机会。在此，我们通过对rmRNA-seq数据的深入分析，报告了在小鼠大脑、睾丸和胚胎干细胞（ES细胞）中表达的数千种新转录本（主要是非编码RNA）的发现。这些转录本与转录起始和延伸信号存在显著关联。在这些转录本的上游，我们观察到组蛋白标记（组蛋白H3赖氨酸4三甲基化，H3K4me3）、RNA聚合酶II结合位点以及标记转录起始位点的基因表达标签的帽分析显著富集。沿着这些转录本的长度，我们还观察到组蛋白H3赖氨酸36三甲基化（H3K36me3）的富集。此外，这些转录本在其基因组位点、外显子序列和启动子区域表现出强烈的纯化选择，这意味着这些转录本的进化受到功能限制。这些结果定义了小鼠基因组中的一组新转录本，并表明了它们在小鼠组织和细胞中的潜在功能。
