Gene length and expression level shape genomic novelties.
Gene length and expression level shape genomic novelties.
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DOI：
10.1101/gr.169722.113
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发表时间：
2014-09
期刊：
影响因子：
7
通讯作者：
Yanai I
中科院分区：
文献类型：
--
作者：
Grishkevich V;Yanai I
基因复制和选择性剪接是产生基因组新颖性的重要机制。以前的研究表明，基因的家庭大小和它产生的剪接变体的数量是负相关的，尽管潜在的原因还没有被很好地理解。在这里，我们报告了基因长度和表达水平共同解释了这种关系。我们发现，基因长度与基因复制和选择性剪接相关：更长的基因不太可能产生重复，而更有可能表现出选择性剪接。我们发现，基因长度是一个动态属性，随着进化时间的延长而增加--部分原因是转座元件的插入--以及部分基因复制后的减少。然而，基因长度本身并不能解释选择性剪接和基因复制之间的关系。基因的表达水平似乎既对其长度施加了强烈的限制，又限制了基因的复制。此外，高基因表达促进了选择性剪接，特别是对于长基因，或者，低表达水平的短基因具有大的基因家族。我们对人类和小鼠基因组的分析表明，基因长度和表达水平是主要的基因属性，它们共同解释了基因复制和选择性剪接之间的关系，并偏离了基因组中新奇事物的起源。
Gene duplication and alternative splicing are important mechanisms in the production of genomic novelties. Previous work has shown that a gene’s family size and the number of splice variants it produces are inversely related, although the underlying reason is not well understood. Here, we report that gene length and expression level together explain this relationship. We found that gene lengths correlate with both gene duplication and alternative splicing: Longer genes are less likely to produce duplicates and more likely to exhibit alternative splicing. We show that gene length is a dynamic property, increasing with evolutionary time—due in part to the insertions of transposable elements—and decreasing following partial gene duplications. However, gene length alone does not account for the relationship between alternative splicing and gene duplication. A gene’s expression level appears both to impose a strong constraint on its length and to restrict gene duplications. Furthermore, high gene expression promotes alternative splicing, in particular for long genes, and alternatively, short genes with low expression levels have large gene families. Our analysis of the human and mouse genomes shows that gene length and expression level are primary genic properties that together account for the relationship between gene duplication and alternative splicing and bias the origin of novelties in the genome.
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DOI：
10.1038/nrg2810
发表时间：
2010-07
期刊：
Nature reviews. Genetics
影响因子：
--
作者：
通讯作者：
--
影响因子：
30.8
作者：
Morgante, M;Brunner, S;Rafalski, A
通讯作者：
Rafalski, A
影响因子：
14.9
作者：
Flicek P;Ahmed I;Amode MR;Barrell D;Beal K;Brent S;Carvalho-Silva D;Clapham P;Coates G;Fairley S;Fitzgerald S;Gil L;García-Girón C;Gordon L;Hourlier T;Hunt S;Juettemann T;Kähäri AK;Keenan S;Komorowska M;Kulesha E;Longden I;Maurel T;McLaren WM;Muffato M;Nag R;Overduin B;Pignatelli M;Pritchard B;Pritchard E;Riat HS;Ritchie GR;Ruffier M;Schuster M;Sheppard D;Sobral D;Taylor K;Thormann A;Trevanion S;White S;Wilder SP;Aken BL;Birney E;Cunningham F;Dunham I;Harrow J;Herrero J;Hubbard TJ;Johnson N;Kinsella R;Parker A;Spudich G;Yates A;Zadissa A;Searle SM
通讯作者：
Searle SM
影响因子：
56.9
作者：
Lev-Maor, G;Sorek, R;Ast, G
通讯作者：
Ast, G
影响因子：
56.9
作者：
Lynch, M;Conery, JS
通讯作者：
Conery, JS