Collaborative Research: cis-Regulatory architecture of color pattern convergence

理解生物多样性的起源和维持需要将分子水平上的遗传变异模式与个体、种群或物种之间的形态差异联系起来。在过去的十年中，许多适应性性状变异的例子都与基因表达的发育变化有关。位于基因之间的基因组区域包含调控基因表达的空间和时间模式的“调控元件”。这些调控区域被认为在性状适应中起着至关重要的作用。然而，我们对调控因素驱动形态多样化的具体机制的理解仍然有限。变化涉及的是影响较大的少数因素，还是影响较小的许多因素？新的基因表达模式是通过新元素的起源出现的，还是通过旧的祖先元素的变化出现的？单个元素的功能是如何变化的？某些因素在多大程度上促进了不同谱系的特征趋同？这个项目旨在解决这些问题。在这样做的过程中，它将破译一些控制结构、功能和调控元素演变的规则。具体来说，研究人员将把比较生物学与调节元件的机制研究结合起来，以了解蝴蝶重复颜色图案进化的调节基础。这项工作将包括在波士顿科学博物馆的公众参与。此外，这项工作将制定战略，增加从历史上代表性不足的群体中招收研究生。顺式调控元件（cre）包括启动子、增强子和沉默子。这些元素在表型进化中起着至关重要的作用，因为它们调节发育过程中的基因表达模式。尽管最近在识别和表征负责适应性性状变异的cre方面取得了进展，但仍存在许多问题。例如，序列分化、CRE内转录因子结合位点的基因组结构与CRE功能之间的关系是什么？解决这些问题是复杂的。CREs被假设为相对独立的控制组织特异性表达的模块。然而，越来越多的证据表明，CRE突变可能具有多种下游效应。在这里，我们建议在一个比较框架内使用重复进化的力量来解码控制CRE结构、功能和进化的规则。我们的研究解决了三个主要问题。首先，种群水平的序列差异是如何导致与Limenitis butterfly的染色质可及性和基因表达模式相关的翅膀图案模仿的？其次，在不同的系统发育时间尺度上，深层调控同源性在多大程度上构成了趋同进化的重复案例？第三，深层祖先与新近衍生的cre如何促进颜色图案的进化和收敛？我们将通过识别和功能表征控制两个基因WntA和optix表达的cre来回答这些问题。这些基因已被证明是蝴蝶物种内部和物种之间适应性模仿颜色模式差异的基础。然后，我们将利用在三个蝴蝶属中广泛发生的趋同进化来研究CRE增益和损失的大尺度进化模式。最终，我们的结果将阐明顺式调控元件是如何产生的，它们是如何决定表型的，以及是什么规则支配着它们的进化。该项目由生物科学理事会分子和细胞生物科学部的遗传机制项目共同资助。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

Understanding the origin and maintenance of biological diversity requires connecting patterns of genetic variation at the molecular level with morphological differences among individuals, populations, or species. Over the last decade, many examples of adaptive trait variation have been linked to developmental changes in gene expression. Regions of the genome that lie in between genes contain “regulatory elements” that regulate spatial and temporal patterns of gene expression. These regulatory regions are thought to play an essential role in trait adaptation. However, our understanding of the specific mechanisms through which regulatory elements have driven morphological diversification remains limited. Do changes involve a small number of elements with large effect, or many elements of minor effect? Do new gene expression patterns appear via origination of new elements, or changes in older ancestral elements? How do the functions of individual elements change? To what extent might some elements facilitate the convergence of traits across different linages? This project aims to address these questions. In doing so, it will decode some of the rules governing the structure, function, and evolution of regulatory elements. Specifically, the investigators will couple comparative biology with mechanistic studies of regulatory elements to understand the regulatory basis of repeated color pattern evolution in butterflies. The work will include public engagement at the Boston Science Museum. In addition, the work will develop strategies for increasing the recruitment of graduate students from historically underrepresented groups. Cis-regulatory elements (CREs) include promotors, enhancers, and silencers. These elements play an essential role in phenotypic evolution because they regulate patterns of gene expression during development. Despite recent progress in identifying and characterizing CREs responsible for adaptive trait variation, many questions remain. For example, what is the relationship between sequence divergence, the genomic architecture of transcription factor binding sites within CREs, and CRE function? Addressing these questions is complicated. CREs have been hypothesized to act as relatively independent modules controlling tissue-specific expression. However, growing evidence indicates that CRE mutations may have multiple downstream effects. Here, we propose to use the power of repeated evolution within a comparative framework to decode the rules governing CRE structure, function, and evolution. Our research addresses three primary questions. First, how is population-level sequence divergence responsible for wing pattern mimicry related to chromatin accessibility and patterns of gene expression in Limenitis butterflies? Second, to what extent does deep regulatory homology underlie repeated cases of convergent evolution across different phylogenetic timescales? Third, how do deeply ancestral vs. recently derived CREs contribute to color pattern evolution and convergence? We will answer these questions by identifying and functionally characterizing CREs controlling the expression of two genes, WntA and optix. These genes have been shown to underlie adaptive mimetic color pattern divergence within and between butterfly species. We will then leverage the widespread occurrence of convergent evolution across three butterfly genera to study broad-scale evolutionary patterns of CRE gain and loss. Ultimately, our results will shed light on how cis-regulatory elements arise, how they function to determine phenotype, and what rules govern their evolution.This project is co-funded by the Genetic Mechanisms program of the Molecular and Cellular Biosciences Division in the Biological Sciences Directorate.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.