High resolution annotation of zebrafish transcriptome using long-read sequencing.
High resolution annotation of zebrafish transcriptome using long-read sequencing.
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DOI：
10.1101/gr.223586.117
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发表时间：
2018-09
期刊：
影响因子：
7
通讯作者：
Zaslavsky E
中科院分区：
文献类型：
--
作者：
Nudelman G;Frasca A;Kent B;Sadler KC;Sealfon SC;Walsh MJ;Zaslavsky E
随着斑马鱼作为一种重要的模式生物的出现，对其转录组的研究已取得了一致的努力。然而，这一努力是有限的，在斑马鱼注释，这是特别明显的合子基因组激活（ZGA）过程中动态表达的成绩单的差距。迄今为止，短读段测序已成为斑马鱼转录组注释的主要技术。部分是因为这些序列读段太短，组装方法无法解决转录组的全部复杂性，目前的注释是初步的。通过提供对全长转录本的直接观察，最近改进的长读段测序平台可以显著提高注释覆盖率和准确性。在这里，我们利用SMRT平台研究ZGA前后斑马鱼胚胎的转录组。我们的分析揭示了斑马鱼转录组的额外新奇和复杂性，识别出2539个源自先前未注释基因座的高置信度新转录本和先前注释基因中的1835个高置信度新亚型。我们使用一套计算方法验证了这些发现，包括结构预测，序列同源性和功能保守性分析，以及通过短读测序数据的确证性转录定量。我们的分析提供了深入了解新的同源物和旁系同源物的功能重要的蛋白质和非编码RNA，异构体转换的发生，和不同类别的新的剪接事件。通过PCR实验验证了几种代表不同剪接事件的新型异构体，包括发现和验证跨越多个mir-430元件的新型8-kb转录本，这是早期发育的重要驱动因素。我们的研究提供了一个显着改善斑马鱼转录组注释资源。
With the emergence of zebrafish as an important model organism, a concerted effort has been made to study its transcriptome. This effort is limited, however, by gaps in zebrafish annotation, which are especially pronounced concerning transcripts dynamically expressed during zygotic genome activation (ZGA). To date, short-read sequencing has been the principal technology for zebrafish transcriptome annotation. In part because these sequence reads are too short for assembly methods to resolve the full complexity of the transcriptome, the current annotation is rudimentary. By providing direct observation of full-length transcripts, recently refined long-read sequencing platforms can dramatically improve annotation coverage and accuracy. Here, we leveraged the SMRT platform to study the transcriptome of zebrafish embryos before and after ZGA. Our analysis revealed additional novelty and complexity in the zebrafish transcriptome, identifying 2539 high-confidence novel transcripts that originated from previously unannotated loci and 1835 high-confidence new isoforms in previously annotated genes. We validated these findings using a suite of computational approaches including structural prediction, sequence homology, and functional conservation analyses, as well as by confirmatory transcript quantification with short-read sequencing data. Our analyses provided insight into new homologs and paralogs of functionally important proteins and noncoding RNAs, isoform switching occurrences, and different classes of novel splicing events. Several novel isoforms representing distinct splicing events were validated through PCR experiments, including the discovery and validation of a novel 8-kb transcript spanning multiple mir-430 elements, an important driver of early development. Our study provides a significantly improved zebrafish transcriptome annotation resource.
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影响因子：
16.6
作者：
Abdel-Ghany SE;Hamilton M;Jacobi JL;Ngam P;Devitt N;Schilkey F;Ben-Hur A;Reddy AS
通讯作者：
Reddy AS
影响因子：
48
作者：
Engstrom, Par G.;Steijger, Tamara;Sipos, Botond;Grant, Gregory R.;Kahles, Andre;Raetsch, Gunnar;Goldman, Nick;Hubbard, Tim J.;Harrow, Jennifer;Guigo, Roderic;Bertone, Paul
通讯作者：
Bertone, Paul
影响因子：
14.9
作者：
Griffiths-Jones, S;Bateman, A;Eddy, SR
通讯作者：
Eddy, SR
影响因子：
10.5
作者：
Cabili, Moran N.;Trapnell, Cole;Rinn, John L.
通讯作者：
Rinn, John L.
影响因子：
56.9
作者：
Giraldez, AJ;Mishima, Y;Schier, AF
通讯作者：
Schier, AF