Gene regulatory network controlling neural crest derived formation of facial cartilage

点击翻译按钮获取中文摘要

In the previous grant period, we explored regulatory differences between cranial and trunk neural crest cells. Comparative transcriptomics coupled with functional perturbation revealed a premigratory “cranial-specific” neural crest GRN subcircuit that links anterior identity to ability to differentiate into facial cartilage. Here, we propose to elucidate the gene regulatory network (GRN) downstream of this cranial-specific subcircuit that confers ability to differentiate into facial skeleton. The goal is to understand the program underlying differentiation and pattern formation of craniofacial cartilage. First, we will explore regulatory changes in trunk neural crest cells after introduction of cranial crest subcircuit genes. Next, we will characterize late-migrating cranial crest cells as they condense to form facial cartilage at the single cell level to understand GRN changes as a function of time, at single cell resolution and a functional level. Finally, we propose to identify active enhancers and their direct inputs in late migrating and condensing cranial crest cells by combining in vivo electroporation of reporter constructs in the chick embryo with high throughput genomic approaches. To these ends, we will conduct the following aims: Specific Aim 1: Effects of “reprogramming” trunk neural crest cell identity. Ectopic expression of cranial crest subcircuit genes imbues trunk crest cells with chondrogenic potential after grafting to the head. Here we will: characterize transcriptional changes that occur in reprogrammed trunk crest cells over time; test the ability of reprogrammed trunk neural crest to form ectopic cartilage in their normal environment; test the ability of the cranial subcircuit to confer chondrogenic ability onto ES cells and crestosphere-derived cells. Specific Aim 2: Transcriptional profiling and functional validation of condensing cranial neural crest cells at high cell resolution using single cell RNA-seq and multiplex in situ hybridization. To gain insights into how neural crest-derived cells differentiate and what gene regulatory programs control their progression to facial skeleton, we propose to perform single cell RNA-seq of condensing cranial crest cells in the branchial arches with the goal of identifying candidate GRN components of the cartilage-forming module. We will validate expression of candidate transcription factors at high resolution and test their function using CRISPR-Cas9 knockout. Specific Aim 3: Construction of a cranial cartilage gene regulatory network (GRN) by identifying cis- regulatory elements and direct downstream targets of the cranial crest-specific subcircuit genes. In order to build regulatory linkages in branchial arch neural crest, we will characterize their chromatin landscape using low-input Assay for Transposase-Accessible Chromatin (ATAC-seq) optimized for as few as 1500 cells per replicate and perform CUT&RUN to confirm direct inputs downstream of subcircuit genes.