Theis Mirko, Paszkowski-Rogacz Maciej, Weisswange Ina, Chakraborty Debojyoti, Buchholz Frank
Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, Dresden, Germany Eupheria Biotech GmbH, Dresden, Germany
Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, Dresden, Germany Eupheria Biotech GmbH, Dresden, Germany.
J Biomol Screen. 2015 Sep;20(8):1018-26. doi: 10.1177/1087057115583448. Epub 2015 Apr 24.
Broad sequencing enterprises such as the FANTOM or ENCODE projects have substantially extended our knowledge of the human transcriptome. They have revealed that a large portion of genomic DNA is actively transcribed and have identified a plethora of novel transcripts. Many newly identified transcripts belong to the class of long noncoding RNAs (lncRNAs), which range from a few hundred bases to multiple kilobases in length and harbor no protein-coding potential. Although the biological activity of some lncRNAs is understood, the functions of most lncRNAs remain elusive. Tools that allow rapid and cost-effective access to functional data of lncRNAs are therefore essential. Here, we describe the construction and validation of an endoribonuclease-prepared siRNA (esiRNA) library designed to target 1779 individual human lncRNAs by RNA interference. We present a compendium of lncRNA expression data for 11 human cancer cell lines. Furthermore, we show that the resource is suitable for combined knockdown and localization analysis. We discuss challenges in sequence annotation of lncRNAs with respect to their often low and cell type-specific expression and specify esiRNAs that are suitable for targeting lncRNAs in commonly used human cell lines.
诸如FANTOM或ENCODE项目等大规模测序计划极大地拓展了我们对人类转录组的认识。这些计划揭示，基因组DNA的很大一部分都在活跃转录，并鉴定出了大量新的转录本。许多新鉴定出的转录本属于长链非编码RNA（lncRNA）类别，其长度从几百个碱基到几千个碱基不等，且不具备蛋白质编码潜力。尽管一些lncRNA的生物学活性已为人所知，但大多数lncRNA的功能仍不清楚。因此，能够快速且经济高效地获取lncRNA功能数据的工具至关重要。在此，我们描述了一种核糖核酸内切酶制备的小干扰RNA（esiRNA）文库的构建与验证，该文库旨在通过RNA干扰靶向1779个人类lncRNA。我们展示了11种人类癌细胞系的lncRNA表达数据汇总。此外，我们表明该资源适用于联合敲低和定位分析。我们讨论了lncRNA序列注释方面的挑战，这些挑战源于其通常较低且具有细胞类型特异性的表达，并指定了适用于在常用人类细胞系中靶向lncRNA的esiRNA。
