德國科學(xué)家最近利用下一代測序技術(shù)和分析方法,,得到了對于人類轉(zhuǎn)錄組(transcriptome)的嶄新認(rèn)識,。相關(guān)論文7月3日在線發(fā)表于《科學(xué)》雜志,。
到目前為止,,人類轉(zhuǎn)錄組的功能復(fù)雜性尚未完全闡明,。在最新研究中,,通過對源自人類兩大細(xì)胞系——胚腎和B細(xì)胞系的轉(zhuǎn)錄子(本)進(jìn)行“鳥槍法測序”(shotgun sequencing,,一種隨機(jī)且高通量的序列測定方法),,德國馬普分子遺傳學(xué)研究所和Genomatix測序軟件公司的科學(xué)家揭示出人類轉(zhuǎn)錄組前所未有的復(fù)雜性和可變性。
他們發(fā)現(xiàn),,50%的轉(zhuǎn)錄子對應(yīng)于特定的基因組域,,其中有80%吻合已知的外顯子(exon)。多聚腺苷酸化的轉(zhuǎn)錄組(polyadenylated transcriptome)的66%對應(yīng)于已知基因,,其余的34%則對應(yīng)在未標(biāo)注的基因組域中,。很明顯,還有大量的新基因候選活躍在被研究的細(xì)胞系中,。而根據(jù)已知的轉(zhuǎn)錄子,,研究人員發(fā)現(xiàn),RNA測序可以比微陣列多探測到25%的基因,。
此外,,研究人員還進(jìn)行了一項關(guān)于信使RNA剪接(mRNA splicing)的全局研究,。他們共確定出94241個剪接位點,其中有4096個是全新的,。該研究還表明外顯子跳躍(exon skipping)是選擇性剪接(alternative splicing)的一種普遍形式,。關(guān)于這兩項研究的相關(guān)數(shù)據(jù)可以從http://www.genomatix.de/MPI.html開放獲取。
領(lǐng)導(dǎo)該項研究的馬普分子遺傳學(xué)研究所Marie-Laure Yaspo博士說,,“深度測序(deep sequencing)讓我們首次直接探索人類轉(zhuǎn)錄組的復(fù)雜性和動力學(xué)成為可能,。而此次的細(xì)胞內(nèi)和細(xì)胞間選擇性剪接的對比研究,以及對基因表達(dá)的同步分析是此前從未進(jìn)行過的,。新的研究結(jié)果將導(dǎo)致遠(yuǎn)超出現(xiàn)有程度的全新哺乳動物基因組注釋圖,。此外,一個越來越明顯的情況就是,,目前可用的方法只能帶來哺乳動物細(xì)胞的部分表達(dá)圖譜,,尤其是當(dāng)考慮到基因調(diào)控分析時。”
Genomatix公司的Martin Seifert博士也認(rèn)為,,“新研究的主要影響在于觀察到復(fù)雜性和可變性的新維度,。我們的分析清楚地表明,轉(zhuǎn)錄是一個高度動態(tài)和可變的過程,。”(生物谷Bioon.com)
生物谷推薦原始出處:
Science,,DOI: 10.1126/science.1160342,Marc Sultan, Martin Seifert, Marie-Laure Yaspo
A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome
Marc Sultan 1, Marcel H. Schulz 2, Hugues Richard 3, Alon Magen 1, Andreas Klingenhoff 4, Matthias Scherf 4, Martin Seifert 4, Tatjana Borodina 1, Aleksey Soldatov 1, Dmitri Parkhomchuk 1, Dominic Schmidt 1, Sean O’Keeffe 3, Stefan Haas 3, Martin Vingron 3, Hans Lehrach 1, Marie-Laure Yaspo 1*
1 Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestr. 73, 14195 Berlin, Germany.
2 Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestr. 73, 14195 Berlin, Germany.; International Max Planck Research School for Computational Biology and Scientific Computing.
3 Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestr. 73, 14195 Berlin, Germany.
4 Genomatix Software Gmbh, Bayerstr. 85a, 80335 Munich, Germany.
* To whom correspondence should be addressed.
Marie-Laure Yaspo , E-mail: [email protected]
These authors contributed equally to this work.
The functional complexity of the human transcriptome is not yet fully elucidated. We report a high-throughput sequence of the human transcriptome from a human embryonic kidney and a B cell line. Shotgun sequencing of transcripts was used to generate randomly distributed reads. Of these, 50% mapped to unique genomic location, of which 80% corresponded to known exons. We found that 66% of the polyadenylated transcriptome mapped to known genes and 34% to non-annotated genomic regions. Based on known transcripts, RNAseq can detect 25% more genes than microarrays. A global survey of mRNA splicing events identified 94,241 splice junctions, of which 4,096 are novel, and showed that exon skipping is the most prevalent form of alternative splicing.