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

University Of Pittsburgh, Pittsburgh PA

Investigators

Abstract

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.