Large introns in relation to alternative splicing and gene evolution: a case study of Drosophila bruno-3.
Large introns in relation to alternative splicing and gene evolution: a case study of Drosophila bruno-3.
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DOI：
10.1186/1471-2156-10-67
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发表时间：
2009-10-19
期刊：
影响因子：
2.9
通讯作者：
Noor MA
中科院分区：
文献类型：
--
作者：
Kandul NP;Noor MA
成熟mRNA的可变剪接（AS）能够从同一基因产生结构和功能不同的转录本。近期对现有基因组数据库的生物信息学分析推断内含子长度与可变剪接之间呈正相关。为了从经验上更详细地研究内含子长度与可变剪接之间的相互作用，我们分析了果蝇RNA结合蛋白Bruno - 3（Bru - 3）基因中可变剪接转录本（ASTs）的多样性。已知该基因编码13个外显子，这些外显子被不同大小的内含子分隔开，在黑腹果蝇中内含子长度从71到41973个核苷酸不等。尽管Bru - 3的结构预计有利于可变剪接，但此前仅描述了该基因的两种可变剪接转录本。
从代表三个不同果蝇谱系的四个物种中克隆整个开放阅读框（ORF）的逆转录聚合酶链反应（RT - PCR）产物，提供了一种进化视角、高灵敏度以及目前高通量方法无法实现的剪接选择的长程连续性。因此，我们鉴定出Bru - 3基因的三个新外显子、一个新外显子片段以及33种先前未知的可变剪接转录本。该基因中所有的外显子跳跃事件都定位在外显子上，这些外显子周围的内含子至少有800个核苷酸，而被小于250个核苷酸的内含子分隔的外显子在mRNA中总是连续剪接的。果蝇Bru - 3基因进化过程中外显子丢失和产生的情况也定位在大内含子内。值得注意的是，我们鉴定出一个真正的从头外显子获得：第8号外显子是在暗果蝇组的谱系中从所有被调查的果蝇物种中保守的隐蔽剪接位点之间的内含子序列产生的。代表暗果蝇组所有主要分支的物种在成熟mRNA中都包含第8号外显子。据我们所知，第8号外显子的起源是脊椎动物之外内含子序列外显子化的首个有记录的案例。
我们发现大内含子在进化过程中可通过外显子跳跃和外显子更替促进可变剪接，这可能是由于它们从成熟mRNA中去除时经常出错。大内含子可能是遗传多样性的一个储存库，因为它们比短内含子有更多的可变位点。综上所述，基因结构可以约束和/或促进基因进化。
Alternative splicing (AS) of maturing mRNA can generate structurally and functionally distinct transcripts from the same gene. Recent bioinformatic analyses of available genome databases inferred a positive correlation between intron length and AS. To study the interplay between intron length and AS empirically and in more detail, we analyzed the diversity of alternatively spliced transcripts (ASTs) in the Drosophila RNA-binding Bruno-3 (Bru-3) gene. This gene was known to encode thirteen exons separated by introns of diverse sizes, ranging from 71 to 41,973 nucleotides in D. melanogaster. Although Bru-3's structure is expected to be conducive to AS, only two ASTs of this gene were previously described. Cloning of RT-PCR products of the entire ORF from four species representing three diverged Drosophila lineages provided an evolutionary perspective, high sensitivity, and long-range contiguity of splice choices currently unattainable by high-throughput methods. Consequently, we identified three new exons, a new exon fragment and thirty-three previously unknown ASTs of Bru-3. All exon-skipping events in the gene were mapped to the exons surrounded by introns of at least 800 nucleotides, whereas exons split by introns of less than 250 nucleotides were always spliced contiguously in mRNA. Cases of exon loss and creation during Bru-3 evolution in Drosophila were also localized within large introns. Notably, we identified a true de novo exon gain: exon 8 was created along the lineage of the obscura group from intronic sequence between cryptic splice sites conserved among all Drosophila species surveyed. Exon 8 was included in mature mRNA by the species representing all the major branches of the obscura group. To our knowledge, the origin of exon 8 is the first documented case of exonization of intronic sequence outside vertebrates. We found that large introns can promote AS via exon-skipping and exon turnover during evolution likely due to frequent errors in their removal from maturing mRNA. Large introns could be a reservoir of genetic diversity, because they have a greater number of mutable sites than short introns. Taken together, gene structure can constrain and/or promote gene evolution.
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影响因子：
64.8
作者：
Clark, Andrew G.;Eisen, Michael B.;MacCallum, Iain
通讯作者：
MacCallum, Iain
影响因子：
10.7
作者：
Betrán, E;Wang, W;Long, MY
通讯作者：
Long, MY
影响因子：
10.7
作者：
Chen, FC;Wang, SS;Chuang, TJ
通讯作者：
Chuang, TJ
DOI：
10.1073/pnas.0506139102
发表时间：
2005-09-06
影响因子：
11.1
作者：
Baek, D;Green, P
通讯作者：
Green, P
影响因子：
14.9
作者：
Delaunay, J;Mée, GL;Aït-Ahmed, O
通讯作者：
Aït-Ahmed, O