Global identification of hnRNP A1 binding sites for SSO-based splicing modulation.
Global identification of hnRNP A1 binding sites for SSO-based splicing modulation.
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DOI：
10.1186/s12915-016-0279-9
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发表时间：
2016-07-05
期刊：
影响因子：
5.4
通讯作者：
Andresen BS
中科院分区：
文献类型：
--
作者：
Bruun GH;Doktor TK;Borch-Jensen J;Masuda A;Krainer AR;Ohno K;Andresen BS
许多病原遗传变异已被证明是在保存良好的剪接位点的剪接突变之外，剪接调节元素（SRE）的突变可能会消除剪接并引起疾病。其他带有剪接切换的寡核苷酸（SSO）的SRE。
在这里，我们使用了单个核苷酸分辨率交联免疫沉淀（ICLIP）来建立一个键剪接调节因子HNRNP A1的体内结合图，并生成HNRNP A1共识结合基序。对于抑制外显子。 ICLIP识别的HNRNP A1结合位点立即在5'剪接位点的下游。 5'剪接位点下游的识别的HNRNP A1结合位点可以被SSO阻断以激活外显子。
HNRNP A1结合图可用于鉴定基于SSO的治疗的潜在靶标。 mRNA剪接。
本文的在线版本（doi：10.1186/s12915-016-0279-9）包含补充材料，可供授权用户使用。
Many pathogenic genetic variants have been shown to disrupt mRNA splicing. Besides splice mutations in the well-conserved splice sites, mutations in splicing regulatory elements (SREs) may deregulate splicing and cause disease. A promising therapeutic approach is to compensate for this deregulation by blocking other SREs with splice-switching oligonucleotides (SSOs). However, the location and sequence of most SREs are not well known. Here, we used individual-nucleotide resolution crosslinking immunoprecipitation (iCLIP) to establish an in vivo binding map for the key splicing regulatory factor hnRNP A1 and to generate an hnRNP A1 consensus binding motif. We find that hnRNP A1 binding in proximal introns may be important for repressing exons. We show that inclusion of the alternative cassette exon 3 in SKA2 can be significantly increased by SSO-based treatment which blocks an iCLIP-identified hnRNP A1 binding site immediately downstream of the 5’ splice site. Because pseudoexons are well suited as models for constitutive exons which have been inactivated by pathogenic mutations in SREs, we used a pseudoexon in MTRR as a model and showed that an iCLIP-identified hnRNP A1 binding site downstream of the 5′ splice site can be blocked by SSOs to activate the exon. The hnRNP A1 binding map can be used to identify potential targets for SSO-based therapy. Moreover, together with the hnRNP A1 consensus binding motif, the binding map may be used to predict whether disease-associated mutations and SNPs affect hnRNP A1 binding and eventually mRNA splicing. The online version of this article (doi:10.1186/s12915-016-0279-9) contains supplementary material, which is available to authorized users.