Identification of transcription factor targets, gene expression profiles and accessible chromatin regions in the Caenorhabditis elegans epidermis using targeted DamID

Abstract

Development is an exceptionally complex process that is performed with exquisite control. A series of developmental programmes allow the orchestrated and tightly-regulated deployment of the genomic information, governing events like cell division, cell fate maintenance and differentiation. Understanding the complete regulatory states that instruct a selective decoding of the genome capable of bringing about morphogenetic events is central to developmental biology. Among all cells, stem cells maintain the potential to produce cells that undergo transitions in developmental trajectories and thus are particularly interesting. In this study, I have used the postembryonic development of the Caenorhabditis elegans epidermis driven by the stem cell-like seam cells, to begin exploring the gene regulatory network, transcriptional states and epigenomic regulation involved in cell fate patterning. To that end, I have adapted and present here the first application of the targeted DamID (TaDa) methodology in C. elegans, for assaying protein-DNA interactions, to use as a single technique in approaching all of the above objectives. I show that TaDa requires little starting material, is reproducible and tissue-specific. Using TaDa I identify targets for the transcription factors LIN-22 and NHR-25 that propose new biological functions for these regulators in epidermal development. I acquire gene expression profiles for the seam cells and hypodermis that lead to the discovery of novel transcription and chromatin factors, as well as new miRNAs. Finally, I produce the first cell-type-specific chromatin accessibility maps in C. elegans for the seam cells and hypodermis and use them to identify tissue-specific enhancers. These findings expand our knowledge of the mechanisms underlying fate decisions in epidermal patterning and provide a proof-of-concept for the application of TaDa in C. elegans.