Bat Accelerated Regions Identify a Bat Forelimb Specific Enhancer in the HoxD Locus.
Bat Accelerated Regions Identify a Bat Forelimb Specific Enhancer in the HoxD Locus.
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DOI：
10.1371/journal.pgen.1005738
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发表时间：
2016-03
期刊：
影响因子：
4.5
通讯作者：
Ahituv N
中科院分区：
文献类型：
--
作者：
Booker BM;Friedrich T;Mason MK;VanderMeer JE;Zhao J;Eckalbar WL;Logan M;Illing N;Pollard KS;Ahituv N
导致蝙蝠翅膀发育的分子事件在很大程度上仍然未知，并且被认为部分是由肢体发育期间基因表达的变化引起的。这些表达变化可能是由基因调控增强子的变化引起的。在这里，我们使用比较基因组学方法来确定在蝙蝠祖先中迅速进化，但在其他脊椎动物中高度保守的区域。我们发现了166个蝙蝠加速区域（BAR），这些区域在发育中的小鼠肢体中与H3 K27 ac和p300 ChIP-seq峰重叠。使用小鼠增强子测定，我们表明，五个鼠耳蝠lucifugus BAR驱动基因表达在发展中的小鼠肢体，与大多数显示差异增强子活性相比，小鼠orthopathic BAR序列。这些包括BAR 116，其位于HoxD簇的端粒，并且对M. lucifugus序列，小鼠序列在胚胎第12.5天无活性。在长翼蝠中Hoxd 10-Hoxd 13的发育肢体表达分析显示，Hoxd 10-Hoxd 11的前肢高表达，后肢弱表达，与在M.在小鼠中的Lucifugus BAR 116，表明它可能参与调节蝙蝠HoxD复合物。结合起来，我们的研究结果突出了新的调控区域，可能有助于导致蝙蝠翅膀发育的形态差异。肢体是脊椎动物同源性的典型例子，并且由大范围的形态结构如鳍、腿和翅膀代表。这些结构的进化可能是由在发育过程中起关键作用的基因调控元件的改变驱动的。为了确定可能有助于蝙蝠翅膀发育的元件，我们描述了脊椎动物之间保守的序列，但在蝙蝠谱系中发生了显着变化。然后，我们将这些序列与ChIP-seq确定的预测发育肢体增强子重叠，发现166个蝙蝠加速序列（BAR）。在小鼠中测试增强子活性的五种BAR都驱动了肢体中的表达。测试小鼠的正向序列表明，与蝙蝠序列相比，三个序列的肢体增强子活性存在差异。其中，BAR 116是特别感兴趣的，因为它位于HoxD基因座附近，HoxD基因座是发育肢体的适当时空模式所需的必需基因复合体。蝙蝠BAR 116序列驱动了强大的前肢表达，但小鼠BAR 116序列没有显示增强子活性。这些实验对应于在发育中的蝙蝠肢体中HoxD基因表达的分析，其具有Hoxd 10 -11的强前肢相对于弱后肢表达。结合起来，我们的研究突出了特定的基因组区域，这些区域在形成导致蝙蝠翅膀发育的形态差异方面可能很重要。
The molecular events leading to the development of the bat wing remain largely unknown, and are thought to be caused, in part, by changes in gene expression during limb development. These expression changes could be instigated by variations in gene regulatory enhancers. Here, we used a comparative genomics approach to identify regions that evolved rapidly in the bat ancestor, but are highly conserved in other vertebrates. We discovered 166 bat accelerated regions (BARs) that overlap H3K27ac and p300 ChIP-seq peaks in developing mouse limbs. Using a mouse enhancer assay, we show that five Myotis lucifugus BARs drive gene expression in the developing mouse limb, with the majority showing differential enhancer activity compared to the mouse orthologous BAR sequences. These include BAR116, which is located telomeric to the HoxD cluster and had robust forelimb expression for the M. lucifugus sequence and no activity for the mouse sequence at embryonic day 12.5. Developing limb expression analysis of Hoxd10-Hoxd13 in Miniopterus natalensis bats showed a high-forelimb weak-hindlimb expression for Hoxd10-Hoxd11, similar to the expression trend observed for M. lucifugus BAR116 in mice, suggesting that it could be involved in the regulation of the bat HoxD complex. Combined, our results highlight novel regulatory regions that could be instrumental for the morphological differences leading to the development of the bat wing. The limb is a classic example of vertebrate homology and is represented by a large range of morphological structures such as fins, legs and wings. The evolution of these structures could be driven by alterations in gene regulatory elements that have critical roles during development. To identify elements that may contribute to bat wing development, we characterized sequences that are conserved between vertebrates, but changed significantly in the bat lineage. We then overlapped these sequences with predicted developing limb enhancers as determined by ChIP-seq, finding 166 bat accelerated sequences (BARs). Five BARs that were tested for enhancer activity in mice all drove expression in the limb. Testing the mouse orthologous sequence showed that three had differences in their limb enhancer activity as compared to the bat sequence. Of these, BAR116 was of particular interest as it is located near the HoxD locus, an essential gene complex required for proper spatiotemporal patterning of the developing limb. The bat BAR116 sequence drove robust forelimb expression but the mouse BAR116 sequence did not show enhancer activity. These experiments correspond to analyses of HoxD gene expressions in developing bat limbs, which had strong forelimb versus weak hindlimb expression for Hoxd10-11. Combined, our studies highlight specific genomic regions that could be important in shaping the morphological differences that led to the development of the bat wing.