Cancer-associated SF3B1 mutants recognize otherwise inaccessible cryptic 3' splice sites within RNA secondary structures.
Cancer-associated SF3B1 mutants recognize otherwise inaccessible cryptic 3' splice sites within RNA secondary structures.
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DOI：
10.1038/onc.2016.279
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发表时间：
2017-02-23
期刊：
影响因子：
8
通讯作者：
Pillai MM
中科院分区：
文献类型：
--
作者：
Kesarwani AK;Ramirez O;Gupta AK;Yang X;Murthy T;Minella AC;Pillai MM
核心剪接因子的复发性突变已在包括癌症在内的几种克隆性疾病中报道。SF3B1是U2剪接复合体的一个组成部分，其突变最为常见。SF3B1突变与使用隐蔽3'剪接位点（3'SS）的异常前mRNA剪接相关，但其选择机制尚不清楚。为了理解隐藏的3'SS是如何被选择的，我们对患者样本中与SF3B1突变相关的剪接和基因表达的转录组范围的变化以及诱导表达的实验模型进行了全面分析。在表达突变体SF3B1的细胞中，在整个基因组中可检测到数百个隐蔽的3'SS。这些3'SS通常被隔离在RNA二级结构内，并且与其相应的典型3'SS相比难以接近。我们假设这些隐蔽的3'SS在正常的剪接催化过程中是不可接近的，并且这种限制在含有突变体SF3B1的剪接体中被克服。在与SF3B1突变（骨髓增生异常综合征和慢性淋巴细胞白血病）相关的多个克隆过程中发现了这种二级结构依赖性选择隐蔽3'SS的模型。我们验证了我们的模型预测在微型基因剪接测定。此外，我们发现在剪接因子相关疾病中具有相关功能的蛋白质的表达失调，这与异常剪接相关，而没有相应的剪接变化。我们的研究结果表明，SF3B1突变与多个克隆过程中共享的独特剪接程序相关，并定义了改变3'SS选择的生化机制。
Recurrent mutations in core splicing factors have been reported in several clonal disorders, including cancers. Mutations in SF3B1, a component of the U2 splicing complex, are the most common. SF3B1 mutations are associated with aberrant pre-mRNA splicing using cryptic 3’ splice sites (3’SS) but the mechanism of their selection is not clear. To understand how cryptic 3’SS are selected, we performed comprehensive analysis of transcriptome-wide changes to splicing and gene expression associated with SF3B1 mutations in patient samples as well as an experimental model of inducible expression. Hundreds of cryptic 3’SS were detectable across the genome in cells expressing mutant SF3B1. These 3’SS are typically sequestered within RNA secondary structures and poorly accessible compared to their corresponding canonical 3’SS. We hypothesized that these cryptic 3’SS are inaccessible during normal splicing catalysis and that this constraint is overcome in spliceosomes containing mutant SF3B1. This model of secondary structure-dependent selection of cryptic 3’SS was found across multiple clonal processes associated with SF3B1 mutations (myelodysplastic syndrome and chronic lymphocytic leukemia). We validated our model predictions in mini-gene splicing assays. Additionally, we found deregulated expression of proteins with relevant functions in splicing factor-related diseases both in association with aberrant splicing and without corresponding splicing changes. Our results show that SF3B1 mutations are associated with a distinct splicing program shared across multiple clonal processes and define a biochemical mechanism for altered 3’SS choice.