Genome-wide analysis of alternative splicing in Chlamydomonas reinhardtii.
Genome-wide analysis of alternative splicing in Chlamydomonas reinhardtii.
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DOI：
10.1186/1471-2164-11-114
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发表时间：
2010-02-17
期刊：
影响因子：
4.4
通讯作者：
Ben-Hur A
中科院分区：
文献类型：
--
作者：
Labadorf A;Link A;Rogers MF;Thomas J;Reddy AS;Ben-Hur A
对几种开花植物中可变剪接（AS）的全基因组计算分析表明，约30%的基因的前体mRNA会发生可变剪接。衣藻是一种简单的单细胞绿藻，属于包括陆生植物在内的谱系。然而，它在大约十亿年前从陆生植物中分化出来。因此，它是研究早期光合真核生物中可变剪接的良好模式系统，有助于深入了解植物中这一过程的演化，并比较简单的单细胞光合和非光合真核生物中的剪接。我们利用衣藻最近完成的基因组序列以及所有可用的EST和cDNA，对其进行了可变剪接的全面分析。
我们使用BLAT和Sircah工具的改进版本对AS进行分析，结果显示498个转录单元存在611个可变剪接事件，约占基因总数的3%。与陆生植物一样，内含子保留是最常见的可变剪接形式。保留的内含子和跳过的外显子往往比组成性剪接基因中的相应部分更短。所有类型的可变剪接事件中的剪接位点信号都比组成性剪接基因中的弱。此外，在可变剪接基因中，常见的剪接形式比不常见的形式具有更强的剪接位点信号。对组成性剪接内含子的分析表明，与参与内含子保留的内含子相比，具有简单重复元件的基序过多。在几乎所有情况下，可变剪接导致开放阅读框截断，产生的编码序列比常见剪接形式短约50%。通过RT - PCR，我们验证了两个基因的可变剪接，并表明它们产生的异构体比EST数据所显示的更多。所有cDNA/EST比对和剪接图都可在http://combi.cs.colostate.edu/as/chlamy网站上获取。
我们观察到的衣藻中可变剪接的程度远小于陆生植物，但远高于简单的单细胞异养真核生物。不同可变剪接事件的百分比与开花植物相似。衣藻中组成性剪接和可变剪接的普遍性，以及它的简单性、许多可用的公共资源以及针对该生物完善的遗传和分子工具，使其成为阐明光合真核生物中调控剪接机制的极佳模式系统。
Genome-wide computational analysis of alternative splicing (AS) in several flowering plants has revealed that pre-mRNAs from about 30% of genes undergo AS. Chlamydomonas, a simple unicellular green alga, is part of the lineage that includes land plants. However, it diverged from land plants about one billion years ago. Hence, it serves as a good model system to study alternative splicing in early photosynthetic eukaryotes, to obtain insights into the evolution of this process in plants, and to compare splicing in simple unicellular photosynthetic and non-photosynthetic eukaryotes. We performed a global analysis of alternative splicing in Chlamydomonas reinhardtii using its recently completed genome sequence and all available ESTs and cDNAs. Our analysis of AS using BLAT and a modified version of the Sircah tool revealed AS of 498 transcriptional units with 611 events, representing about 3% of the total number of genes. As in land plants, intron retention is the most prevalent form of AS. Retained introns and skipped exons tend to be shorter than their counterparts in constitutively spliced genes. The splice site signals in all types of AS events are weaker than those in constitutively spliced genes. Furthermore, in alternatively spliced genes, the prevalent splice form has a stronger splice site signal than the non-prevalent form. Analysis of constitutively spliced introns revealed an over-abundance of motifs with simple repetitive elements in comparison to introns involved in intron retention. In almost all cases, AS results in a truncated ORF, leading to a coding sequence that is around 50% shorter than the prevalent splice form. Using RT-PCR we verified AS of two genes and show that they produce more isoforms than indicated by EST data. All cDNA/EST alignments and splice graphs are provided in a website at http://combi.cs.colostate.edu/as/chlamy. The extent of AS in Chlamydomonas that we observed is much smaller than observed in land plants, but is much higher than in simple unicellular heterotrophic eukaryotes. The percentage of different alternative splicing events is similar to flowering plants. Prevalence of constitutive and alternative splicing in Chlamydomonas, together with its simplicity, many available public resources, and well developed genetic and molecular tools for this organism make it an excellent model system to elucidate the mechanisms involved in regulated splicing in photosynthetic eukaryotes.
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