Large-scale analysis of branchpoint usage across species and cell lines.
Large-scale analysis of branchpoint usage across species and cell lines.
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DOI：
10.1101/gr.202820.115
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发表时间：
2017-04
期刊：
影响因子：
7
通讯作者：
Fairbrother WG
中科院分区：
文献类型：
--
作者：
Taggart AJ;Lin CL;Shrestha B;Heintzelman C;Kim S;Fairbrother WG
每个人类前mRNA的编码序列平均被11个内含子中断，这些内含子必须被剪接以进行适当的基因表达。每个内含子含有三个专性信号：一个5′剪接位点、一个分支位点和一个3′剪接位点。剪接位点的使用已经被详尽地映射到不同的物种、细胞类型和细胞状态。相比之下，只有一小部分分支位点被鉴定过一次。少数报道的分支位点的注释是不精确的，因为逆转录酶在穿过2-5键时跳过几个核苷酸。在这里，我们报告了来自三个不同物种和SF 3B 1 K700 E致癌突变体背景的深度测序数据的分支点的大规模映射。我们已经开发了一种新的方法，通过U2 snRNP/pre-mRNA碱基配对模型对原始的LIPR 4读数进行优化，以返回具有质量指标的分支点序列的最大当前数据集。该分析发现了U2 snRNA的新模式：前mRNA碱基配对在酵母中保守，并提供了深入了解内含子环的生物起源。最后，匹配分支位点的使用与异构体的选择，在广泛的面板的ENCODE RNA-seq数据集提供了洞察分支点的使用驱动选择性剪接的机制。
The coding sequence of each human pre-mRNA is interrupted, on average, by 11 introns that must be spliced out for proper gene expression. Each intron contains three obligate signals: a 5′ splice site, a branch site, and a 3′ splice site. Splice site usage has been mapped exhaustively across different species, cell types, and cellular states. In contrast, only a small fraction of branch sites have been identified even once. The few reported annotations of branch site are imprecise as reverse transcriptase skips several nucleotides while traversing a 2–5 linkage. Here, we report large-scale mapping of the branchpoints from deep sequencing data in three different species and in the SF3B1 K700E oncogenic mutant background. We have developed a novel method whereby raw lariat reads are refined by U2snRNP/pre-mRNA base-pairing models to return the largest current data set of branchpoint sequences with quality metrics. This analysis discovers novel modes of U2snRNA:pre-mRNA base-pairing conserved in yeast and provides insight into the biogenesis of intron circles. Finally, matching branch site usage with isoform selection across the extensive panel of ENCODE RNA-seq data sets offers insight into the mechanisms by which branchpoint usage drives alternative splicing.