BioProject

Interactions between distal loci in mammalian genomes, including those involving enhancers and promoters, are thought to be a central mechanism of gene regulation in mammals, yet the protein regulators of these interactions remain largely undetermined. More...

Interactions between distal loci in mammalian genomes, including those involving enhancers and promoters, are thought to be a central mechanism of gene regulation in mammals, yet the protein regulators of these interactions remain largely undetermined. The zinc finger transcription factor ZNF143/ZFP143 has been strongly implicated as a factor that regulates chromatin interactions, functioning either with or without CTCF. However, ZNF143/ZFP143’s role in this process and its function with or without CTCF are not well understood. Here, we tagged both CTCF and ZNF143/ZFP143 with dual-purpose degron/imaging tags to combinatorically assess their loop function and effect on each other. We find that ZNF143/ZFP143 possesses no general looping function, and that it largely functions independently to CTCF. Instead, ZNF143/ZFP143 is an essential and highly conserved transcription factor possessing an extremely stable chromatin residence time (>20 min) that regulates an important subset of mitochondrial and ribosomal genes. Overall design: We generated two replicates of Micro-C, ZFP143 ChIP-seq, CTCF ChIP-seq, and PRO-seq per cell line and condition in two mouse embryonic stem cell (mESC) cell lines with the following conditions: untreated, three-hour ZFP143 depletion by 5-Ph-IAA/HaloPROTAC3 treatment, three-hour CTCF depletion by dTag-13 treatment, or three-hour depletion of both ZFP143 and CTCF. We also generated two replicates of Micro-C, ZFP143 ChIP-seq, CTCF ChIP-seq, and PRO-seq per condition in an additional mESC cell line with untreated and three-hour ZFP143 depletion by dTag-13 conditions. Additionally, we performed two replicates of Micro-C per condition in a HEK293T cell line with untreated and three-hour ZNF143 depletion by IAA conditions. Less...