使用转录组方法研究Alu元件的外显子化

熊荣川 编译

    Alu元件作为灵长类动物基因组进化和基因调控的主要贡献者而被人们所认识。Alu元件大约在6000万年前随着灵长动物的进化而出现，在人类基因组中大概有100万个拷贝，占所有DNA的10%左右，是含量最丰富的可移动元件。以前，曾认为Alu元件为基因组中的垃圾元件，没有明显的功能。然而近年来的研究表明其在基因调控和基因组进化中有着多种多样的作用。

    Alu元件的外显子化被认为是人类和灵长动物中外显子再创造的重要途径之一。Alu元件的通用序列包含有类似外显子5′和3′端剪接信号位点的序列位点。这样的Alu元件插入既有基因的内含子区域后，特定的突变可能导致这些位点的激活，或者引入新的剪接调控信号，从而创造出新的外显子。虽然很少有Alu元件被整合成转录产物，最近的一些表达序列标签、外显子芯片研究表明少量的Alu元件具有很高的剪接活性或者组织特异性剪接模式。一些实验性研究证明了Alu外显子在少数一些基因中对与基因功能的影响及其进化史。这些数据表明Alu元件的外显子化在人类和灵长动物的适应性进化中发挥了一定的贡献作用。

    本研究对使用高精RNA测序方法得到的转录组数据进行Alu外显子剪接分析。这种方法比起之前的表达序列标签和外显子芯片等方法，基因覆盖率和精度都有显著的提高，并且能对包含Alu外显子的转录产物进行量化评估。重要的是，研究发现Alu外显子多分布在基因的5′端非编码区域，且分布于这一区域的Alu外显子显著地改变mRNA的转录效率。这一结果暗示Alu元件的外显子化在人类和灵长动物转录调控的进化中扮演了重要的角色。

   关键词：转录组进化 可转移元件 选择性剪接 深度测序 上游开放阅读框

原文

Widespread establishment and regulatory impact of Alu exons in human genes

   Alu elements have emerged as a major contributor to gene regulation and genome evolution in primates (1–3). Created ∼60 million years ago during primate evolution, Alu is the most abundant type of mobile elements in the human genome, with more than 1 million copies occupying ∼10% of the human genomic DNA (3). Historically, Alu elements were regarded as “junk DNA” with no apparent function. However, studies in the past decade have revealed diverse roles for Alu elements in gene regulation and genome evolution (1–3).

   The exonization of Alu elements is a major mechanism for de novo exon creation in primate and human genomes (4). The consensus sequence of Alu harbors sites that resemble the 5′ and 3′ splice site signals (5, 6). After the insertion of an Alu element into the intronic region of an existing gene, subsequent mutations could activate these splice sites or introduce additional splicing regulatory signals, leading to the creation of a new exon (6). Although the vast majority of Alu exons are rarely incorporated into transcripts (7), the analyses of expressed sequence tags (ESTs) and exon array data recently have revealed a small number of Alu exons with high splicing activities or tissue-specific splicing profiles (8, 9). In a few genes, the functional impact and evolutionary history of Alu exons have been characterized experimentally (9–12). These data suggest that Alu exonization contributed to the adaptive evolution of primates and humans.

   In this work, we carried out a genome-wide analysis of Alu exon splicing using transcriptome profiles generated by deep RNA sequencing (RNA-Seq) (13). Previous studies of Alu exons using ESTs and exon arrays were limited by the incomplete exon coverage and low resolution of these technologies. By contrast, deep RNA-Seq enabled an unbiased analysis of Alu exonization events and allowed us to estimate quantitatively the transcript inclusion levels of Alu exons. Importantly, we found that Alu exons with high splicing activities were strongly enriched in the 5′-UTR, and a large fraction of 5′-UTR Alu exons significantly altered mRNA translational efficiency. These results suggest an important role for Alu exonization in the evolution of translational regulation in primates and humans. (Shen et al., 2011)

Keywords：transcriptome evolution； transposable element； alternative splicing； deep sequencing； uORF

参考文献

Shen Shihao, Lin Lan, Cai James J., Jiang Peng, Kenkel Elizabeth J., Stroik Mallory R., Sato Seiko, Davidson Beverly L.,Xing Yi (2011). "Widespread establishment and regulatory impact of Alu exons in human genes." Proceedings of the National Academy of Sciences 108(7): 2837-2842.