Mapping epigenetic divergence in the massive radiation of Lake Malawi cichlid fishes.
Mapping epigenetic divergence in the massive radiation of Lake Malawi cichlid fishes.
复制标题
绘制马拉维湖慈嘴鱼大规模辐射的表观遗传差异图。
DOI：
10.1038/s41467-021-26166-2
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发表时间：
2021-10-07
影响因子：
16.6
通讯作者：
Miska EA
中科院分区：
文献类型：
--
作者：
Vernaz G;Malinsky M;Svardal H;Du M;Tyers AM;Santos ME;Durbin R;Genner MJ;Turner GF;Miska EA
表观遗传变异调节基因表达，并且可以遗传。然而，知识的贡献表观遗传分歧适应性多样化的性质仍然有限。马拉维湖慈鲷鱼显示广泛的表型多样性，尽管序列差异极低的大规模进化辐射是一个很好的系统来研究表观基因组的适应贡献。在这里，我们提出了一个比较全基因组甲基化和转录组研究，集中在肝脏和肌肉组织的表型分歧慈鲷物种。在这两种组织中，我们发现物种之间存在大量的甲基化差异。差异甲基化区域（DMR），丰富的进化年轻的转座子，与生态相关基因的转录变化有关的能量消耗和脂质代谢，指出饮食生态和甲基化分歧之间的联系。出乎意料的是，所有物种特异性DMR中有一半是跨组织共享的，并且在发育基因中富集，这可能反映了不同的表观遗传发育程序。我们的研究揭示了大量的甲基化分歧密切相关的慈鲷鱼，并代表了一个资源，研究表观遗传学在物种多样化的作用。马拉维湖慈鲷鱼是极端脊椎动物辐射的一个例子;然而，物种之间的序列差异很小。在这里，作者提出了一个比较全基因组甲基化研究，表明DNA甲基化在这些鱼类广泛的表型多样性中发挥了重要作用。
Epigenetic variation modulates gene expression and can be heritable. However, knowledge of the contribution of epigenetic divergence to adaptive diversification in nature remains limited. The massive evolutionary radiation of Lake Malawi cichlid fishes displaying extensive phenotypic diversity despite extremely low sequence divergence is an excellent system to study the epigenomic contribution to adaptation. Here, we present a comparative genome-wide methylome and transcriptome study, focussing on liver and muscle tissues in phenotypically divergent cichlid species. In both tissues we find substantial methylome divergence among species. Differentially methylated regions (DMR), enriched in evolutionary young transposons, are associated with transcription changes of ecologically-relevant genes related to energy expenditure and lipid metabolism, pointing to a link between dietary ecology and methylome divergence. Unexpectedly, half of all species-specific DMRs are shared across tissues and are enriched in developmental genes, likely reflecting distinct epigenetic developmental programmes. Our study reveals substantial methylome divergence in closely-related cichlid fishes and represents a resource to study the role of epigenetics in species diversification. The Lake Malawi cichlid fishes are an example of extreme vertebrate radiation; however, there is very little sequence divergence among the species. Here the authors present a comparative genome-wide methylome study to suggest DNA methylation played a major role in the extensive phenotypic diversity amongst these fishes.
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DOI：
10.1038/nrm4043
发表时间：
2015-09
期刊：
Nature reviews. Molecular cell biology
影响因子：
--
作者：
Du J;Johnson LM;Jacobsen SE;Patel DJ
通讯作者：
Patel DJ
影响因子：
7.7
作者：
Dubin MJ;Zhang P;Meng D;Remigereau MS;Osborne EJ;Paolo Casale F;Drewe P;Kahles A;Jean G;Vilhjálmsson B;Jagoda J;Irez S;Voronin V;Song Q;Long Q;Rätsch G;Stegle O;Clark RM;Nordborg M
通讯作者：
Nordborg M
影响因子：
5.3
作者：
Hayhurst, GP;Lee, YH;Gonzalez, FJ
通讯作者：
Gonzalez, FJ
影响因子：
9.2
作者：
Conte, Matthew A.;Joshi, Rajesh;Kocher, Thomas D.
通讯作者：
Kocher, Thomas D.
影响因子：
4.9
作者：
Carleton, Karen L.;Conte, Matthew A.;Kocher, Thomas D.
通讯作者：
Kocher, Thomas D.