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

NSF-BSF：基因调控网络共选择和形态新颖性的基因组观点

• 批准号: 2129903
• 负责人: Mark Rebeiz
• 金额: $ 102.5万
• 依托单位: University of Pittsburgh
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-05-15 至 2026-04-30
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2129903&HistoricalAwards=false
• 关键词: NSF; BSF; genomic; view; gene

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.

生物学中最大的谜团之一是我们星球上奇妙多样的生命是如何起源的。这个问题的一个重要方面是解剖学上的新奇性：新的结构是如何形成的？这个项目将研究醋蝇（Drosophila melanogaster）中一种新进化的结构是如何首先出现的。发育生物学领域的工作已经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，遗传网络控制组织发育时哪些基因子集在组织中表达。形态新奇的问题可以用这些网络来表达--构成新颖性基础的网络是如何产生的？这是一个非常困难的问题，该领域以令人满意的方式解决。由于这些网络是复杂的，我们将采用尖端的基因组方法来全面盘点可能的参与者，并确定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的经验性后续行动相结合，将允许对新结构进化时发生的分子变化进行深入研究。这样做将为其他生物中各种各样的类似发育和进化过程提供信息，这些生物缺乏操纵和严格验证的工具。该项目将产生许多额外的更广泛的影响，包括培训科学家，为科学背景不足的初中和高中学生开展外联活动，以及开发软件工具和数据库。后叶是黑腹果蝇分支特有的形态学新新奇。我们先前已经发现，后叶是通过与另一个器官系统的基因调控网络的共同选择而出现的，后气门首先在胚胎发育期间形成。然而，目前还不知道该协同选择事件上游的哪些基因被修饰以及它们是如何被修饰的。此外，目前还不清楚类似的基因调控网络如何产生两种完全不同的结构。这些问题将通过识别网络的监管层次结构的变化和下游细胞过程的差异来解决。这将通过使用后叶和气门特异性细胞标记物进行细胞分选，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环境特异性基因表达的调控序列。这些将通过CRISPR/Cas9基因编辑进行验证，以及在有叶和无叶物种中使用报告基因进行转录调控活性的比较研究。 还将建立资源以测试比较种属D中的调节元件。ananassae。总之，这项研究将建立一个首映系统，在该系统中，形态新奇背后的遗传变化将被追踪和体内测试，这是一个在任何系统中都难以解决的问题。该奖项反映了NSF的法定使命，并被认为值得通过使用基金会的智力价值和更广泛的影响审查标准进行评估来支持。