Identifying non-coding sources of mammalian craniofacial variation

Facial variations play a crucial role in human identity and social interactions, with craniofacial malformations being among the most prevalent congenital disorders. However, our understanding of the genetic factors governing mammalian craniofacial morphogenesis is still limited. The complexity in deciphering the genetic architecture of facial shape comes from its highly polygenic nature, as indicated by genome-wide association studies (GWAS). Many quantitative trait loci (QTLs) associated with facial shape and abnormalities are located in non-coding regions, which are thought to be cis-regulatory elements like enhancers. Enhancers can influence gene expression through alterations in sequences and/or enhancer–promoter interactions, and consequently affect phenotypic outcomes. Nevertheless, identifying the causal variants within QTLs is challenging because physically close non-causal ones can also reach statistical significance as a result of linkage disequilibrium. Understanding the impact of enhancer variants is further complicated by the fact that, in mammalian genomes, most developmental enhancers regulate more distal genes rather than the nearest ones, as shown in my preliminary data. Therefore, this proposal aims to identify and functional test non-coding elements and their variants to advance our understanding of genetic mechanisms underlying craniofacial variations and anomalies, ultimately informing targeted therapeutic interventions. For the K99 phase in this proposal, the objective is to use comparative genomics and dog breeds as a model system to uncover enhancers associated with craniofacial variations and validate their function through transgenic reporter assay (Aim 1.1). The impacts of specific variants on enhancer function and target gene expression will be tested using CRISPR/Cas9 genome editing (Aim 1.2). For the R00 phase, the research goal is to employ novel Micro-C technology to link thousands of enhancers to their target genes during craniofacial development (Aim 2.1), and to identify the variants potentially affecting transcription factor binding on enhancers (Aim 2.2). Completion of this proposal will provide a more comprehensive view of the genetic architecture underlying craniofacial morphogenesis in mammals. The research training will include: 1) Learning statistical methods for association studies and QTL mapping 2) Genetic control of craniofacial development and morphogenesis, and 3) Micro-C technology development in embryonic facial tissues. My career development plan will focus on enhancing skills critical to the proposed research, attending related courses and workshops, developing leadership and mentorship skills, and securing a faculty position. To ensure rigorous oversight of my progress, a distinguished research advisory committee has been assembled, consisting of my primary mentor, Dr. Evgeny Kvon, and co-mentor, Dr. Thomas Schilling, along with esteemed collaborators Drs. Licia Selleri, Timothy Cox and Anthony Long, which will provide me both research training and career guidance, facilitating my transition to independence. Project Number: 1K99DE034828-01A1 | Fiscal Year: 2026 | NIH Institute/Center: National Institute of Dental and Craniofacial Research (NIDCR) | Principal Investigator: Zhuoxin Chen | Institution: UNIVERSITY OF CALIFORNIA-IRVINE, IRVINE, CA | Award Amount: $128,191 | Activity Code: K99 | Study Section: Special Emphasis Panel[ZRG1 MSOS-F (80)] View on NIH RePORTER: https://reporter.nih.gov/project-details/11301154