CLIP-seq of eIF4AIII reveals transcriptome-wide mapping of the human exon junction complex
CLIP-seq of eIF4AIII reveals transcriptome-wide mapping of the human exon junction complex
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DOI：
10.1038/nsmb.2420
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发表时间：
2012-11-01
影响因子：
16.8
通讯作者：
Le Hir, Herve
中科院分区：
文献类型：
--
作者：
Sauliere, Jerome;Murigneux, Valentine;Le Hir, Herve
外显子连接复合物 (EJC) 是 mRNA 命运的核心效应器，将核加工与 mRNA 运输、翻译和监视联系起来。然而，人们对其转录组范围内的目标知之甚少。我们在人类细胞中使用交联和免疫沉淀方法以及高通量测序 (CLIP-seq) 来识别 EJC 核心组件 DEAD-box 解旋酶 eIF4AIII 的结合位点。 CLIP 读取形成的峰主要位于剪接的 mRNA 中。大多数表达的外显子在位于类似于外显子连接上游 24 个核苷酸的规范 EJC 区域或其他非规范区域中具有峰值。值得注意的是，这两种类型的峰都优先与含有 GAAGA 基序的非结构化且富含嘌呤的序列相关，该基序是 EJC 相关因子的潜在结合位点。因此，外显子之间的 EJC 位置在空间和数量上存在差异。人类 eIF4AIII 的全转录组图谱揭示了 EJC 意想不到的方面，并扩大了其对转录后调控的潜在影响。
The exon junction complex (EJC) is a central effector of the fate of mRNAs, linking nuclear processing to mRNA transport, translation and surveillance. However, little is known about its transcriptome-wide targets. We used cross-linking and immunoprecipitation methods coupled to high-throughput sequencing (CLIP-seq) in human cells to identify the binding sites of the DEAD-box helicase eIF4AIII, an EJC core component. CLIP reads form peaks that are located mainly in spliced mRNAs. Most expressed exons harbor peaks either in the canonical EJC region, located similar to 24 nucleotides upstream of exonic junctions, or in other noncanonical regions. Notably, both of these types of peaks are preferentially associated with unstructured and purine-rich sequences containing the motif GAAGA, which is a potential binding site for EJC-associated factors. Therefore, EJC positions vary spatially and quantitatively between exons. This transcriptome-wide mapping of human eIF4AIII reveals unanticipated aspects of the EJC and broadens its potential impact on post-transcriptional regulation.