Predicting long non-coding RNAs using RNA sequencing
Predicting long non-coding RNAs using RNA sequencing
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DOI：
10.1016/j.ymeth.2013.03.019
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发表时间：
2013-09-01
期刊：
影响因子：
4.8
通讯作者：
Ponting, Chris P.
中科院分区：
文献类型：
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作者：
Ilott, Nicholas E.;Ponting, Chris P.
下一代测序技术的出现，特别是RNA测序（RNA-seq）技术，扩大了我们对人类和其他动物基因组转录能力的了解。特别是，最近的RNA-seq研究表明，转录在哺乳动物基因组中广泛存在，导致来自已知蛋白质编码基因内部和之间的推定转录本数量大幅增加。似乎缺乏蛋白质编码潜力的长转录物（长非编码RNA，lncRNA）一直是最近研究的焦点，部分原因是观察到它们的细胞类型和发育时间点限制的表达模式。目前有多种测序方案可用于鉴定lncRNA，包括RNA聚合酶II占有率、染色质状态图和深度RNA测序（本文的重点）。此外，有许多分析方法可用于映射读数和组装转录模型，这些转录模型可从RNA-seq数据预测lncRNA的存在和结构。在这里，我们回顾了目前使用RNA-seq实验的大规模测序数据识别lncRNA的方法，并强调了进行此类项目时所需的分析考虑因素。(C)2013 Elsevier Inc. All rights reserved.
The advent of next-generation sequencing, and in particular RNA-sequencing (RNA-seq), technologies has expanded our knowledge of the transcriptional capacity of human and other animal, genomes. In particular, recent RNA-seq studies have revealed that transcription is widespread across the mammalian genome, resulting in a large increase in the number of putative transcripts from both within, and intervening between, known protein-coding genes. Long transcripts that appear to lack protein-coding potential (long non-coding RNAs, lncRNAs) have been the focus of much recent research, in part owing to observations of their cell-type and developmental time-point restricted expression patterns. A variety of sequencing protocols are currently available for identifying lncRNAs including RNA polymerase II occupancy, chromatin state maps and - the focus of this review - deep RNA sequencing. In addition, there are numerous analytical methods available for mapping reads and assembling transcript models that predict the presence and structure of lncRNAs from RNA-seq data. Here we review current methods for identifying lncRNAs using large-scale sequencing data from RNA-seq experiments and highlight analytical considerations that are required when undertaking such projects. (C) 2013 Elsevier Inc. All rights reserved.