Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks
Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks
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DOI：
10.1101/gr.239863.118
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发表时间：
2019-04-01
期刊：
影响因子：
7
通讯作者：
Larkin, Denis M.
中科院分区：
文献类型：
--
作者：
Farre, Marta;Kim, Jaebum;Larkin, Denis M.
染色体重排在驱动进化中的作用一直是进化生物学的一个长期问题。在这里，我们专注于反刍动物作为一个模型，以评估如何重排可能有助于基因调控的进化。使用重建的祖先的Cetartiodactyls，反刍动物，山核桃，牛科动物的核型，我们跟踪模式的总染色体变化。我们发现，从其他cetartiodactyls分裂后，导致反刍动物祖先的血统的特点是主要是染色体内的变化，而导致pecoran祖先（包括所有牲畜反刍动物）的血统包括多个染色体间的变化。我们观察到，在反刍动物的进化断点区域的肝细胞推定的增强子是高度富集的DNA序列的选择性限制作用于谱系特异性转座因子（TE）和一组25个特定的转录因子（TF）结合基序与最近活跃的TE。结合基因表达数据，我们发现反刍动物断点区域附近的基因在物种间表现出更趋分化的表达谱，特别是在牛中，这与这些断点区域的系统发育起源一致。这种分歧是显着更大的基因增强子，包含至少一个的25个特定的TF结合基序，并位于附近的牛科牛血统断点区域。综上所述，通过将祖先核型重建与顺式调控元件和基因表达进化分析相结合，我们的工作表明，与总染色体重排共定位的谱系特异性调控元件可能提供了有价值的功能修饰，有助于塑造反刍动物的进化。
The role of chromosome rearrangements in driving evolution has been a long-standing question of evolutionary biology. Here we focused on ruminants as a model to assess how rearrangements may have contributed to the evolution of gene regulation. Using reconstructed ancestral karyotypes of Cetartiodactyls, Ruminants, Pecorans, and Bovids, we traced patterns of gross chromosome changes. We found that the lineage leading to the ruminant ancestor after the split from other cetartiodactyls was characterized by mostly intrachromosomal changes, whereas the lineage leading to the pecoran ancestor (including all livestock ruminants) included multiple interchromosomal changes. We observed that the liver cell putative enhancers in the ruminant evolutionary breakpoint regions are highly enriched for DNA sequences under selective constraint acting on lineage-specific transposable elements (TEs) and a set of 25 specific transcription factor (TF) binding motifs associated with recently active TEs. Coupled with gene expression data, we found that genes near ruminant breakpoint regions exhibit more divergent expression profiles among species, particularly in cattle, which is consistent with the phylogenetic origin of these breakpoint regions. This divergence was significantly greater in genes with enhancers that contain at least one of the 25 specific TF binding motifs and located near bovidae-to-cattle lineage breakpoint regions. Taken together, by combining ancestral karyotype reconstructions with analysis of cis regulatory element and gene expression evolution, our work demonstrated that lineage-specific regulatory elements colocalized with gross chromosome rearrangements may have provided valuable functional modifications that helped to shape ruminant evolution.