Evolution of transcriptional regulation as motor of morphological diversification in cichlid fishes

进化生物学的最终目标之一是了解表型多样性特征的遗传基础。基因组调控环境的进化变化通过协调细胞增殖、身份和交流的变化，具有产生适应性表型复杂性的能力。越来越多的证据支持这样的假设，即非编码DNA的变化构成了表型进化的主要催化剂。一旦不再使用垃圾DNA这个名称，人们才刚刚开始探索非编码DNA的作用。最近有人提出，通过控制基因表达模式和水平，非编码DNA确实构成了表型进化的主要催化剂。它们可能解释了物种内部和物种之间的许多甚至大多数表型差异。我的研究项目旨在调查转录调控的变化，这些变化被认为是推动表型进化的因素。我使用慈嘴鱼作为模型，因为它们被认为是最多样化和物种最丰富的脊椎动物家族之一。慈鱼以其惊人的表型多样性而闻名，这使它们成为研究编码区和非编码元件(如顺式调节元件)进化作用的极佳模型。它们的物种形成和多样化的极端速度仍然令人费解。因此，慈鱼是分析进化的遗传基础的合适模型。通过RNA测序法(RNA-SEQ)和染色质免疫沉淀高通量测序法(CHIP-SEQ)对基因表达水平和活性调控元件丰度的比较分析，旨在揭示基因调控和转录的进化动力学。为了从功能上探索顺式调节元件在进化背景下的重要性，我利用我将在慈鱼体内执行的转基因方法来分析体内调节元件的活性。

One of the ultimate goals of evolutionary biology is to understand the genetic basis of phenotypically diverse traits. Evolutionary alterations to genomic regulatory landscapes have the power to generate adaptive phenotypic complexity, through orchestrating changes in cellular proliferation, identity and communication. There is growing evidence supporting the hypothesis that changes in non-coding DNA constitute a major catalyst for phenotypic evolution. Once relegated the name >>junk DNA<<, the role of non-coding DNA has only begun to be explored. It has recently been suggested that non-coding DNA indeed constitute a major catalyst for phenotypic evolution by controlling gene expression patterns and levels. They might explain many or even most phenotypic differences within and between species. My research project aims to investigate changes in transcriptional regulation that have been suggested to drive phenotypic evolution. I use cichlid fishes as a model since they are considered as one of the most diverse and species-rich families of vertebrates. Cichlids are famous for their astonishing rate of phenotypic diversification, making them excellent models for the investigation of the evolutionary role of coding regions but also non-coding elements such as cis-regulatory elements. Their extreme rate of speciation and diversification are still puzzling. Therefore, cichlids are a suitable model in which to analyze the genetic bases of evolution. By comparative analyses of gene expression levels using RNA-sequencing (RNA-seq) and abundance of active regulatory elements using Chromatin-immuno-precipiation with high-throughput sequencing (ChIP-seq) I aim to reveal the evolutionary dynamics of gene regulation and transcriptomes. To functionally explore the importance of cis-regulatory elements in an evolutionary context, I take advantage of transgenic approaches I will perform within cichlids to analyze the activity of regulatory elements in vivo.