A microarray configuration to quantify expression levels and relative abundance of splice variants.
A microarray configuration to quantify expression levels and relative abundance of splice variants.
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DOI：
10.1093/nar/gni047
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发表时间：
2005-03-10
影响因子：
14.9
通讯作者：
Cochet, Olivier
中科院分区：
文献类型：
--
作者：
Fehlbaum, Pascale;Guihal, Caroline;Bracco, Laurent;Cochet, Olivier
在过去的十年中，选择性RNA剪接引起了人们的极大兴趣，似乎在表达多样性的产生中具有高度重要性。这一调控过程在正常发育中起着至关重要的作用，它对人类疾病的发生和发展以及对药物药理性质的影响越来越被人们所认识。只有少数研究描述了特定的选择性剪接表达谱。微阵列策略已被设想用于解决备选剪接事件，但很少有实验数据与其提供真正定量值的能力相关。我们开发了一种特定的微阵列配置，依赖于每个剪接事件的几个优化探针。基本上，使用5个24mer探针来完全表征剪接事件。这些探针有两种类型，外显子探针和连接探针，它们要么特定于剪接事件，要么不是。这种“拼接阵列”的性能在合成模型系统和复杂生物材料上得到了验证。结果表明，基于该设计的DNA芯片结合了外显子和结衍生探针，可以检测剪接变异，并对剪接变异进行绝对和相对定量。此外，该策略与所有使用寡核苷酸探针的微阵列兼容。
Over the past decade, alternative RNA splicing has raised a great interest appearing to be of high importance in the generation of expression diversity. This regulatory process plays a critical role in the normal development and its impact on the initiation and development of human disorders as well as on the pharmacological properties of drugs is increasingly being recognized. Only few studies describe specific alternative splicing expression profiling. Microarray strategies have been conceived to address alternative splicing events but with very few experimental data related to their abilities to provide true quantification values. We have developed a specific microarray configuration relying on a few, well optimized probes per splice event. Basically, five probes of 24mer are used to fully characterize a splice event. These probes are of two types, exon probes and junction probes, and are either specific to a splice event or not. The performances of such a ‘splice array’ were validated on synthetic model systems and on complex biological materials. The results indicate that DNA chips based on this design combining exon and junction derived probes enable the detection and, absolute and relative quantification of splice variants. In addition, this strategy is compatible with all the microarrays that use oligonucleotide probes.