Neighboring Genes Show Correlated Evolution in Gene Expression.
Neighboring Genes Show Correlated Evolution in Gene Expression.
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DOI：
10.1093/molbev/msv053
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发表时间：
2015-07
影响因子：
10.7
通讯作者：
Hurst LD
中科院分区：
文献类型：
--
作者：
Ghanbarian AT;Hurst LD
当考虑基因表达谱的进化时，我们通常认为这不受其基因组邻域的影响。然而，这与我们所知道的现存分类群中基因表达谱中相邻基因之间缺乏自主性相反。事实上，在所有真核基因组中，具有相似表达谱的基因倾向于聚集，反映了染色质水平的动态。这是否意味着，如果一个基因在一个特定的谱系中表达增加，那么基因组邻居的表达也会增加，或者基因表达进化是自主的？为了解决这个问题，我们考虑人类基因表达的进化，因为人类-黑猩猩的共同祖先，允许在估计当前的表达水平和误差贝叶斯估计的祖先状态的变化。我们发现，在所有组织和两种性别中，一个焦点基因的基因表达变化平均预测了邻居的基因表达变化。该效应在紧邻区域（<100 kb）非常明显，但延伸得更远。性别特异性表达变化也是基因组聚类的。由于基因在人类中增加表达往往会避免核纤层结构域，并富集基因激活剂5-羟甲基胞嘧啶，我们得出结论，最有可能是由于染色质水平控制基因表达，一个基因的基因表达变化可能会影响邻居的表达演变，我们称之为表达捎带，搭便车的类似物。
When considering the evolution of a gene’s expression profile, we commonly assume that this is unaffected by its genomic neighborhood. This is, however, in contrast to what we know about the lack of autonomy between neighboring genes in gene expression profiles in extant taxa. Indeed, in all eukaryotic genomes genes of similar expression-profile tend to cluster, reflecting chromatin level dynamics. Does it follow that if a gene increases expression in a particular lineage then the genomic neighbors will also increase in their expression or is gene expression evolution autonomous? To address this here we consider evolution of human gene expression since the human-chimp common ancestor, allowing for both variation in estimation of current expression level and error in Bayesian estimation of the ancestral state. We find that in all tissues and both sexes, the change in gene expression of a focal gene on average predicts the change in gene expression of neighbors. The effect is highly pronounced in the immediate vicinity (<100 kb) but extends much further. Sex-specific expression change is also genomically clustered. As genes increasing their expression in humans tend to avoid nuclear lamina domains and be enriched for the gene activator 5-hydroxymethylcytosine, we conclude that, most probably owing to chromatin level control of gene expression, a change in gene expression of one gene likely affects the expression evolution of neighbors, what we term expression piggybacking, an analog of hitchhiking.
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影响因子：
14.9
作者：
Flicek P;Amode MR;Barrell D;Beal K;Billis K;Brent S;Carvalho-Silva D;Clapham P;Coates G;Fitzgerald S;Gil L;Girón CG;Gordon L;Hourlier T;Hunt S;Johnson N;Juettemann T;Kähäri AK;Keenan S;Kulesha E;Martin FJ;Maurel T;McLaren WM;Murphy DN;Nag R;Overduin B;Pignatelli M;Pritchard B;Pritchard E;Riat HS;Ruffier M;Sheppard D;Taylor K;Thormann A;Trevanion SJ;Vullo A;Wilder SP;Wilson M;Zadissa A;Aken BL;Birney E;Cunningham F;Harrow J;Herrero J;Hubbard TJ;Kinsella R;Muffato M;Parker A;Spudich G;Yates A;Zerbino DR;Searle SM
通讯作者：
Searle SM
影响因子：
9.2
作者：
Barton, Robert A.;Venditti, Chris
通讯作者：
Venditti, Chris
影响因子：
7
作者：
Fan, Y;Linardopoulou, E;Trask, BJ
通讯作者：
Trask, BJ
影响因子：
64.8
作者：
Guelen, Lars;Pagie, Ludo;van Steensel, Bas
通讯作者：
van Steensel, Bas
影响因子：
16
作者：
Cho, RJ;Campbell, MJ;Davis, RW
通讯作者：
Davis, RW