Combining computational and experimental methods of analyze gene expression divergence by loss of conserved non-coding elements

进化发育生物学中的一个具有挑战性的问题是哪些基因在物种之间表现出不同的表达模式。这里描述的项目旨在通过计算和实验分析来解决这个问题。高度保守的非蛋白质编码元件（CNE）通常与基因表达调控有关，这一点得到了有力的支持。我将进行系统的计算搜索，寻找在许多物种中高度保守但在另一个物种中丢失的基因组区域。由于强保守性意味着功能，潜在的假设是这样的CNE的丢失导致靶基因表达模式的变化。通过（i）验证CNE的顺式调节作用和（ii）比较具有CNE的基因与缺乏CNE的基因的表达模式，将对该假设进行实验检验。例如，实验可能揭示（i）CNE是脑特异性转录增强子，并且（ii）具有该CNE的物种中的靶基因在脑中表达，而缺乏该CNE的另一物种中的靶基因在脑中不表达。这种计算和实验的混合方法允许关联CNE损失与基因表达的分歧。实验之前的转录因子结合位点簇的计算分析，旨在引导实验的时空域中的相应的转录因子的表达，从而增加成功的实验的机会。该项目的目标是提供深入了解CNEs的进化，有助于我们理解保守区域对基因表达的调控，并将差异基因表达与丢失的保守元件联系起来。

A challenging question in evolutionary developmental biology is which genes show a different expression pattern between species. The project described here aims at addressing this question by computational and experimental analyses. There is strong support that highly conserved non-proteincoding elements (CNEs) are often associated with regulation of gene expression. I will conduct a systematic computational search for genomic regions that are highly conserved in many species but lost in another species. Since strong conservation implies function, the underlying hypothesis is that loss of such a CNE leads to changes in the expression pattern of a target gene. This hypothesis will be experimentally tested by (i) verifying a cis-regulatory role for the CNE and (ii) comparing the expression pattern of a gene having the CNE to a gene lacking the CNE. For example, the experiments might reveal that (i) a CNE is a brain-specific transcriptional enhancer and that (ii) the target gene in a species having this CNE is expressed in brain while the target gene in another species lacking this CNE is not expressed in brain. This computational and experimental hybrid approach allows to associate CNE loss with divergence in gene expression. The experiments are preceded by computational analyses of transcription factor binding site clusters aiming at directing the experiments to the spatio-temporal domain where the respective transcription factors are expressed, thus increasing the chance for successful experiments. The goal of this project is to provide insight into the evolution of CNEs, to contribute to our understanding of gene expression regulation by conserved regions and to associate diverged gene expression with lost conserved elements.