Dynamic splicing and trans-splicing in the model organism Caenorhabditis elegans

基因组测序项目的一个令人惊讶的发现是，基因组大小或注释基因的数量与相应生物体的感知复杂性之间缺乏令人信服的相关性。选择性基因剪接是生物体复杂性的一种可能机制。然而，许多转录本尚未被注释，包括被忽视的低全球表达，禁止其用于评估生物体的复杂性。本研究的目的是测试的假设，大量的全球罕见的转录本是“本地丰富”，在特定的细胞在特定的发育阶段，功能重要，线虫秀丽隐杆线虫作为模型系统。拟议的研究包括两个目标。首先，我们将使用对应于发育阶段和单个细胞的转录组数据来定义这些“全球罕见”但“局部丰富”（GRLA）的转录本，这些转录组数据最近才由于技术进步而可用。GRLA内含子和外显子通过搜索代表总组合的内含子和外显子的<1%而在文库中分别对应于特定发育阶段或细胞类型的= 1%的鉴定的内含子和外显子的实例来鉴定。我们将研究GRLA转录本的功能意义，并描述其转录调控。我们还将研究反式剪接在定义GRLA转录本的瞬时表达中所起的作用。 第二个目的是鉴定线虫C. briggsae的进化关系进行了比较。elegans和C.布里格塞C. briggsae与C. elegans，并已建立了一个强大的平台，比较基因组学。C. elegans和C. briggsae与人类和小鼠之间的相似。尽管存在分歧，但它们显示出染色体组织和同线性，发育细胞谱系和信号传导途径（包括Wnt信号传导）的广泛保守性。我们在C语言中有注释的抄本。briggsae通过RNA-Seq和鉴定剪接和反式剪接活动的快速进化。尽管有这些发现，对C。briggsae在C.优雅我们计划构建与发育阶段和细胞类型相对应的RNA-Seq文库，利用它们来鉴定GRLA转录本，并研究它们在C. briggsae，并研究了GRLA在线虫中的进化。 这些研究目标的完成将使研究的功能的重要性，在特定的细胞类型在特定的发育阶段的瞬时基因表达，并探索GRLA转录在进化中的功能意义。拟议的研究计划还为基因组学，生物信息学和分子生物学的学生提供了极好的跨学科培训机会。

A surprising finding from genome sequencing projects is the lack of convincing correlation between either genome size or number of annotated genes and the perceived complexity of corresponding organisms. Alternative gene splicing is a possible mechanism underlying organismal complexity. However, many transcripts have yet been annotated including the neglected ones with low global expression, prohibiting their use in evaluating organismal complexity. The goal of this research is to test the hypothesis that a large number of globally rare transcripts are "locally abundant" and functionally important in specific cells at specific developmental stages, using the nematode Caenorhabditis elegans as a model system. The proposed research consists of two objectives. First, we will define these "globally rare" but "locally abundant" (GRLA) transcripts using transcriptome data corresponding to developmental stages and to individual cells, which have been made available only recently due to technological advances. GRLA introns and exons are identified by searching for instances of identified introns and exons that represent <1% of the total combined introns and exons, while = 1% in libraries that correspond to specific developmental stages or cell types, respectively. We will study the functional significance of GRLA transcripts and characterize their transcriptional regulation. We will also examine the role that trans-splicing plays in defining transient expression of GRLA transcripts. The second objective is to identify GRLA transcripts in the nematode C. briggsae and compare the evolutionary relationship between GRLA in C. elegans and C. briggsae. C. briggsae is closely related to C. elegans and has been established as a powerful platform for comparative genomics. The evolutionary distance between C. elegans and C. briggsae is similar to that between human and mouse. Despite the divergence, they display extensive conservation of chromosomal organization and synteny, developmental cell linage, and signaling pathways including Wnt signaling. We have annotated transcripts in C. briggsae through RNA-Seq and identified fast evolution of splicing and trans-splicing activities. Despite these findings, research on transcription in C. briggsae lags far behind that in C. elegans. We plan to generate RNA-Seq libraries that correspond to developmental stage and cell types, use them to identify GRLA transcripts and study their expression and function in C. briggsae, and investigate the evolution of GRLA in nematodes. Completion of these research objectives will enable studies of the functional importance of transient gene expression in specific cell types at specific developmental stages, and exploring the functional implications of GRLA transcripts in evolution. The proposed research program also provides excellent interdisciplinary training opportunities for students in genomics, bioinformatics, and molecular biology.