NSF-BSF:A genomic view of gene regulatory network co-option and morphological novelty

生物学中最大的谜团之一是我们星球上惊人的生命多样性是如何起源的。这个问题的一个重要方面是解剖学上的新颖性：新的结构是如何存在的？这个项目将研究醋蝇(黑腹果蝇)的一种新的进化结构是如何产生的。发育生物学领域的工作追踪了大多数解剖结构是如何通过遗传网络在基因组中进行遗传编码的，这些遗传网络控制着组织在发育过程中表达的基因子集。形态新颖性的问题可以用这些网络来表达--作为新颖性基础的网络是如何起源的？对于该领域来说，这是一个非常困难的问题，要以令人满意的方式解决。由于这些网络是复杂的，我们将使用尖端基因组方法来全面清点可能的参与者，并精确定位他们相关的基因功能改变突变。将这样的基因组描述与使用果蝇强大的遗传工具包进行的经验跟踪相结合，将使人们能够深入研究随着新结构的进化而发生的分子变化。这样做将为其他生物体提供各种各样类似的发育和进化过程，在这些过程中，缺乏操纵和严格验证的工具。该项目将产生许多其他更广泛的影响，包括培训科学家，为科学方面背景较少的初中生和高中生开展外联活动，以及开发软件工具和数据库。后叶是果蝇特有的形态特征。我们之前已经发现，后叶是由来自另一个器官系统的基因调控网络共同选择而产生的，后气孔最初形成于胚胎发育期间。然而，目前尚不清楚这一共选事件上游的哪些基因被修改，以及它们是如何被修改的。此外，目前还不清楚类似的基因调控网络是如何产生两种完全不同的结构的。这些问题将通过确定网络监管层次结构的变化和下游蜂窝流程的差异来解决。这将通过用后叶和气门特异的细胞标记进行细胞分选，然后进行RNA-seq和atac-seq分析来完成。后续研究将确定负责物种和特定背景基因表达的调控序列。这些将通过CRISPR/Cas9基因编辑以及在分叶和非分叶物种中转录调控活性与报告基因的比较研究来验证。还将建立资源，以测试比较物种Anansae中的调控元素。总而言之，这项研究将建立一个首推系统，其中潜在的形态新颖性的基因变化将在体内被跟踪和测试，这是一个在任何系统中都很难解决的问题。这一奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

One of the greatest mysteries in biology is how the marvelous diversity of life on our planet originated. An important facet of this problem is that of anatomical novelty: how do new structures come into existence? This project will study how a newly evolved structure in the vinegar fly (Drosophila melanogaster) first arose. Work in the developmental biology field has traced how most anatomical structures are genetically encoded in the genome by genetic networks that control which subset of genes are expressed in a tissue as it develops. The problem of morphological novelty can be expressed in terms of these networks – how do the networks that underlie novelties originate? This has been an exceedingly difficult problem for the field to tackle in a satisfying way. Because these networks are complex, we will employ cutting edge genomic approaches to holistically inventory likely participants and pinpoint their relevant gene function-altering mutations. Combining such genomic descriptions with empirical follow-up using the powerful genetic toolkit of Drosophila will permit a deep examination of the molecular changes that occur as new structures evolve. Doing so will inform a wide variety of similar developmental and evolutionary processes in other organisms in which the tools for manipulation and rigorous validation are lacking. This project will have numerous additional broader impacts, including training of scientists, outreach activities for middle school and high school students from backgrounds underrepresented in science, and development of software tools and databases. The posterior lobe is a morphological novelty specific to Drosophila melanogaster clade. We have previously discovered that the posterior lobe emerged by co-option of a gene regulatory network from another organ system, the posterior spiracle which first forms during embryonic development. However, it is not known which genes upstream of this co-option event were modified and how they were modified. In addition, it is unclear how a similar gene regulatory network generates two completely different structures. These issues will be addressed by identifying altered changes in the network’s regulatory hierarchy and differences in its downstream cellular processes. This will be done by cell sorting with posterior-lobe and spiracle-specific cellular markers, followed by RNA-seq and ATAC-seq analyses. Follow-up studies will identify regulatory sequences responsible for species and context-specific gene expression. These will be validated by CRISPR/Cas9 gene editing, as well as comparative studies of transcriptional regulatory activity with reporter genes in both lobed and non-lobed species. Resources will also be established to test regulatory elements in the comparison species D. ananassae. Together, this research will establish a premiere system in which the genetic changes underlying a morphological novelty will have been traced and tested in vivo, a problem that has been difficult to unravel in any system.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.