近日，相關(guān)成果論文在Frontiers in Genetics雜志發(fā)表了中國科學院北京基因組研究所胡松年項目組的研究成果,。研究人員利用新一代測序數(shù)據(jù),，運用生物信息學方法,，在小鼠的幾個組織中發(fā)現(xiàn)了幾千個新的轉(zhuǎn)錄本。該研究成果的完成拓寬了轉(zhuǎn)錄組數(shù)據(jù)分析的思路,，有利于更全面地認識小鼠的轉(zhuǎn)錄組組成,，并進一步補充了其基因組的注釋。
本研究運用通過去除核糖體技術(shù)構(gòu)建的轉(zhuǎn)錄組文庫的二代測序數(shù)據(jù),，該項技術(shù)理論上可以捕獲較全面的RNA分子,。通過深入分析，在小鼠的大腦,、睪丸和胚胎干細胞中發(fā)現(xiàn)了幾千個新的轉(zhuǎn)錄本（大部分是非編碼RNA）,。這些新檢測到的轉(zhuǎn)錄本與轉(zhuǎn)錄起始和延伸的信號密切相關(guān),，在這些轉(zhuǎn)錄本上游，科研人員看到了H3K4me3,RNAPII結(jié)合位點和CAGE等標志轉(zhuǎn)錄起始的特征,。而且這些轉(zhuǎn)錄本的基因組位置,、外顯子序列和啟動子經(jīng)過了進化的選擇，由此可以看出它們潛在的功能性,。
這些結(jié)果定義了一個小鼠基因組的新的轉(zhuǎn)錄本集合,，這些轉(zhuǎn)錄本在小鼠的細胞和組織中有一定的功能。
新鑒定的轉(zhuǎn)錄本示意,，分別定位于基因Tmem180的內(nèi)含子區(qū)域（上）和基因Sap130鄰近的基因間區(qū)
轉(zhuǎn)錄組研究是一種被廣泛應(yīng)用的,、從整體的層次研究材料中基因表達與調(diào)控的研究手段，在探索生命過程以及形形色色的生物學問題,，如疾病發(fā)生等的研究中發(fā)揮重要的作用。以前的轉(zhuǎn)錄組研究主要側(cè)重于對mRNA的研究,，隨著不同類型RNA分子的發(fā)現(xiàn)以及其重要生物學功能的揭示,，轉(zhuǎn)錄組的研究內(nèi)容也隨之拓展。新一代測序技術(shù)以其高通量數(shù)據(jù)的產(chǎn)出為鑒定低豐度表達的轉(zhuǎn)錄本提供了機會,，另一方面,，文庫構(gòu)建技術(shù)的發(fā)展也使科研人員有機會更高效全面的捕獲RNA分子。人們將有機會更全面深入地認識轉(zhuǎn)錄組,，并在此基礎(chǔ)上開展研究,。（生物谷Bioon.com）
doi:10.3389/fgene.2011.00093
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Thousands of novel transcripts identified in mouse cerebrum, testis, and ES cells based on ribo-minus RNA sequencing
Wanfei Liu, Yuhui Zhao, Peng Cui, Qiang Lin, Feng Ding, Chengqi Xin, Xinyu Tan, Shuhui Song, Jun Yu and Songnian Hu
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.
