Nanopore native RNA sequencing of a human poly(A) transcriptome.
Nanopore native RNA sequencing of a human poly(A) transcriptome.
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DOI：
10.1038/s41592-019-0617-2
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发表时间：
2019-12
期刊：
影响因子：
48
通讯作者：
Timp W
中科院分区：
文献类型：
--
作者：
Workman RE;Tang AD;Tang PS;Jain M;Tyson JR;Razaghi R;Zuzarte PC;Gilpatrick T;Payne A;Quick J;Sadowski N;Holmes N;de Jesus JG;Jones KL;Soulette CM;Snutch TP;Loman N;Paten B;Loose M;Simpson JT;Olsen HE;Brooks AN;Akeson M;Timp W
高通量cDNA测序技术已经推进了我们对转录组复杂性和调控的理解。然而，这些方法丢失了生物RNA中包含的信息，因为复制的读段通常很短，并且因为修饰不被保留。我们使用由Oxford Nanopore Technologies（ONT）开发的天然poly（A）RNA测序策略来解决这些限制。我们的研究使用六个机构的三十个MinION流动池为人类细胞系GM12878生成了990万个比对序列读数。这些天然RNA读段的中值长度为771个碱基，最大比对长度超过21，000个碱基。线粒体多聚腺苷酸读数提供了读数长度质量的内部测量。我们将这些长纳米孔读数与更高准确度的短读数和注释的GM12878启动子区域相结合，以鉴定33，984种合理的RNA同种型。我们描述了评估3′ poly（A）尾长、碱基修饰和转录单倍型的策略。
High throughput cDNA sequencing technologies have advanced our understanding of transcriptome complexity and regulation. However, these methods lose information contained in biological RNA because the copied reads are often short and because modifications are not retained. We address these limitations using a native poly(A) RNA sequencing strategy developed by Oxford Nanopore Technologies (ONT). Our study generated 9.9 million aligned sequence reads for the human cell line GM12878, using thirty MinION flow cells at six institutions. These native RNA reads had a median length of 771 bases, and a maximum aligned length of over 21,000 bases. Mitochondrial poly(A) reads provided an internal measure of read length quality. We combined these long nanopore reads with higher accuracy short-reads and annotated GM12878 promoter regions, to identify 33,984 plausible RNA isoforms. We describe strategies for assessing 3′ poly(A) tail length, base modifications, and transcript haplotypes.
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影响因子：
64.8
作者：
Ernst, Jason;Kheradpour, Pouya;Mikkelsen, Tarjei S.;Shoresh, Noam;Ward, Lucas D.;Epstein, Charles B.;Zhang, Xiaolan;Wang, Li;Issner, Robbyn;Coyne, Michael;Ku, Manching;Durham, Timothy;Kellis, Manolis;Bernstein, Bradley E.
通讯作者：
Bernstein, Bradley E.
影响因子：
12.3
作者：
Gonzàlez-Porta M;Frankish A;Rung J;Harrow J;Brazma A
通讯作者：
Brazma A
影响因子：
48
作者：
Molinie B;Wang J;Lim KS;Hillebrand R;Lu ZX;Van Wittenberghe N;Howard BD;Daneshvar K;Mullen AC;Dedon P;Xing Y;Giallourakis CC
通讯作者：
Giallourakis CC
DOI：
10.1038/nrm.2017.27
发表时间：
2017-07
期刊：
Nature reviews. Molecular cell biology
影响因子：
--
作者：
Baralle FE;Giudice J
通讯作者：
Giudice J
影响因子：
7
作者：
Eberle, Michael A.;Fritzilas, Epameinondas;Bentley, David R.
通讯作者：
Bentley, David R.