Alternative splicing plays a major role in shaping tissue-specific transcriptomes. Among the broad tissue types present in metazoans, the central nervous system contains some of the highest levels of alternative splicing. Although many documented examples of splicing differences between broad tissue types exist, there remains much to be understood about the splicing factors and the cis sequence elements controlling tissue and neuron subtype-specific splicing patterns. By using translating ribosome affinity purification coupled with deep-sequencing (TRAP-seq) in Caenorhabditis elegans, we have obtained high coverage profiles of ribosome-associated mRNA for three broad tissue classes (nervous system, muscle, and intestine) and two neuronal subtypes (dopaminergic and serotonergic neurons). We have identified hundreds of splice junctions that exhibit distinct splicing patterns between tissue types or within the nervous system. Alternative splicing events differentially regulated between tissues are more often frame-preserving, are more highly conserved across Caenorhabditis species, and are enriched in specific cis regulatory motifs, when compared with other types of exons. By using this information, we have identified a likely mechanism of splicing repression by the RNA-binding protein UNC-75/CELF via interactions with cis elements that overlap a 5′ splice site. Alternatively spliced exons also overlap more frequently with intrinsically disordered peptide regions than constitutive exons. Moreover, regulated exons are often shorter than constitutive exons but are flanked by longer intron sequences. Among these tissue-regulated exons are several highly conserved microexons <27 nt in length. Collectively, our results indicate a rich layer of tissue-specific gene regulation at the level of alternative splicing in C. elegans that parallels the evolutionary forces and constraints observed across metazoa.

中文翻译：

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跨组织和在秀丽隐杆线虫神经系统内选择性剪接的全球调控特征

选择性剪接在塑造组织特异性转录组方面起着重要作用。在后生动物中存在的广泛组织类型中，中枢神经系统包含一些最高水平的选择性剪接。尽管存在许多关于广泛组织类型之间剪接差异的文献实例，但关于控制组织和神经元亚型特异性剪接模式的剪接因子和顺式序列元件仍有很多需要了解的地方。通过在秀丽隐杆线虫中使用翻译核糖体亲和纯化结合深度测序（TRAP-seq），我们已经获得了三种广泛的组织类别（神经系统、肌肉和肠）和两种神经元亚型（多巴胺能和血清素能神经元）的核糖体相关 mRNA 的高覆盖率。我们已经确定了数百个剪接点，它们在组织类型之间或神经系统内表现出不同的剪接模式。与其他类型的外显子相比，在组织之间差异调节的选择性剪接事件通常是框架保留的，在Caenorhabditis物种中更加高度保守，并且富含特定的顺式调节基序。通过使用这些信息，我们确定了 RNA 结合蛋白 UNC-75/CELF 通过与顺式相互作用进行剪接抑制的可能机制。与 5' 剪接位点重叠的元素。与组成型外显子相比，选择性剪接的外显子与内在无序肽区域的重叠也更频繁。此外，受调控的外显子通常比组成型外显子短，但两侧是更长的内含子序列。在这些组织调节的外显子中，有几个高度保守的微外显子长度 <27 nt。总的来说，我们的结果表明，在线虫中选择性剪接水平上有一个丰富的组织特异性基因调控层，与在后生动物中观察到的进化力和约束平行。