Insect New Genes Expression, Network and System: INGENeSys

• Applicant: Dr. Apolline Petit, Ph.D.
• Subject Area: Evolution, Anthropology ; General Genetics and Functional Genome Biology ; Bioinformatics and Theoretical Biology
• Term: since 2026
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 583693262

Understanding how genes become integrated into existing regulatory networks, the systems that control when and where genes are expressed, is essential for explaining, modelling, or engineering core biological processes. Yet, how new genes gain regulatory control remains largely unresolved. Most new genes arise through gene duplication followed by neo-functionalization, a long-recognized evolutionary mechanism, while others originate through de novo gene birth, a process more recently discovered. Although the emergence of both types of new genes has been extensively studied, the regulatory steps that follow, how local genomic context influences their expression, which cis-regulatory elements (CREs) such as promoters or enhancers are first involved, and how these factors shape gene survival, remain unresolved. Because the timing and location of expression determine a new gene’s fitness effects, these early regulatory events are likely decisive for whether a gene is purged or retained. The INGENeSys project aims to uncover how duplicated and de novo genes become integrated into regulatory networks across three insect species, testing the hypothesis that they follow comparable regulatory trajectories despite distinct origins. This topic will be explored through three research axes. 1) Assess whether new genes integrate into central or peripheral parts of regulatory networks. Theory suggests that new genes initially join small, tissue-specific subnetworks before expanding their regulatory influence. This objective will test this hypothesis through complementary analyses of new gene expression across multiple tissues in three insects: Drosophila melanogaster and the ants Temnothorax americanus and Temnothorax longispinosus. 2) Determine how local genomic context shapes regulatory integration. For new genes to acquire stable biological roles, they must not only produce functional transcripts but also adapt to their surrounding genomic environment. A key hypothesis is that early regulatory activity is influenced by neighboring genes. Through three complementary analyses, this objective will evaluate whether genomic neighborhood plays a role in the regulatory assimilation of new genes, and whether the genomic site of origin affects their long-term evolutionary fate. 3) Identify the regulatory elements associated with new genes. To become functional, new genes must acquire CREs that ensure appropriate spatial and temporal expression. Although theory predicts that new genes begin with minimal regulatory control and gradually accumulate CREs enabling specialization, empirical data on which CREs are first recruited is lacking. This objective will characterize CREs surrounding new genes to provide the first systematic assessment of regulatory innovation during gene birth.

• DFG Programme: Position