The role of the genome organizer CTCF in cell-specific gene expression and differentiation

Abstract

Organismal development requires precise spatio-temporal control of gene expression, which is achieved by integrating inputs from multiple cell stimuli through transcription factor binding at enhancers. The architectural protein CTCF organizes chromatin into domains, such as topologically associated domains (TADs) that direct enhancer-gene interactions in vertebrates. TADs are evolutionary conserved providing the backbone for conserved gene expression patterns, while changes are often associated with new expression patterns and the emergence of phenotypical innovations during evolution. Although CTCF function has been extensively studied in vitro, its function during embryonic development and for tissue-specific gene expression programs needs further investigation. Here we investigate Ctcf function in vivo, using a zebrafish zygotic knockout model. The progressive loss of maternal Ctcf over developmental time allows us to determine Ctcf function and loss of chromatin domains at the tissue level and during the whole organism’s development. Interestingly, although gene expression is severely impaired in this mutant, differentiation defects are observed only in some tissues, suggesting a tissue- or stage-specific role of CTCF. We hypothesize that Ctcf is essential to establish enhancer-promoter interactions during cell differentiation and thus, tissue development. To test this, we follow the differentiation of cell populations by single-cell RNA-seq and modulate the timepoint of Ctcf loss-offunction during embryonic development. The results will refine the current theory of the role of chromatin domains in gene expression and will advance our knowledge on the regulatory mechanisms behind cell differentiation, which could likewise shape cell type evolution.