Splicing of designer exons informs a biophysical model for exon definition.
Splicing of designer exons informs a biophysical model for exon definition.
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DOI：
10.1261/rna.048009.114
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发表时间：
2015-02
期刊：
影响因子：
--
通讯作者：
Chasin LA
中科院分区：
文献类型：
--
作者：
Arias MA;Lubkin A;Chasin LA
人类中的前mRNA分子主要包含较短的内部外显子，两侧是较长的内含子。为了解释这种内含子的去除，已经提出了外显子识别而不是内含子识别。我们使用设计者外显子（DE）研究了这种外显子定义，设计者外显子（DE）由我们自己设计的三个原型模块组成：外显子剪接增强子（ESE），外显子剪接沉默子（ESS）和参考序列（R）预测两者都不是。每个DE作为三外显子小基因中的中心外显子进行检查。由R模块组成的DE显示出明显的大小依赖性，短于14 nt和长于174 nt的外显子剪接不良。改变剪接位点的强度改善了较长的外显子剪接，但恶化了较短的外显子剪接，有效地将曲线向右移动。对于ESE，我们意外地发现，其增强效率与其在外显子中的位置无关。对于ESS，我们发现其作用在位置上呈阶梯式增加;它在外显子的3 '末端最有效。为了定量应用这些结果，我们开发了一个生物物理模型进行共转录剪接的内部外显子的外显子定义。该模型的特点是在下游外显子合成之前承诺包含，之后跳跃和包含命运之间的竞争。合并两个外显子末端碰撞形成外显子定义复合物以解释大小效应;在稳定化/不稳定化的基础上对ESE/ESS效应进行建模。该模型准确地预测了更复杂的DE的独立实验的结果，结合ESEs和ESS。
Pre-mRNA molecules in humans contain mostly short internal exons flanked by longer introns. To explain the removal of such introns, exon recognition instead of intron recognition has been proposed. We studied this exon definition using designer exons (DEs) made up of three prototype modules of our own design: an exonic splicing enhancer (ESE), an exonic splicing silencer (ESS), and a Reference Sequence (R) predicted to be neither. Each DE was examined as the central exon in a three-exon minigene. DEs made of R modules showed a sharp size dependence, with exons shorter than 14 nt and longer than 174 nt splicing poorly. Changing the strengths of the splice sites improved longer exon splicing but worsened shorter exon splicing, effectively displacing the curve to the right. For the ESE we found, unexpectedly, that its enhancement efficiency was independent of its position within the exon. For the ESS we found a step-wise positional increase in its effects; it was most effective at the 3′ end of the exon. To apply these results quantitatively, we developed a biophysical model for exon definition of internal exons undergoing cotranscriptional splicing. This model features commitment to inclusion before the downstream exon is synthesized and competition between skipping and inclusion fates afterward. Collision of both exon ends to form an exon definition complex was incorporated to account for the effect of size; ESE/ESS effects were modeled on the basis of stabilization/destabilization. This model accurately predicted the outcome of independent experiments on more complex DEs that combined ESEs and ESSs.
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影响因子：
9.8
作者：
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通讯作者：
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影响因子：
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作者：
Borensztajn, Keren;Sobrier, Marie-Laure;Duquesnoy, Philippe;Fischer, Anne-Marie;Tapon-Bretaudiere, Jacqueline;Amselem, Serge
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通讯作者：
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DOI：
10.1073/pnas.1119057109
发表时间：
2012-01-17
影响因子：
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作者：
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作者：
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