Differential RNA-seq analysis of MB135iDUX4 with CRISPR/Cas9-mediated KLF18 knockouts

However, other factors that help regulate ZGA-like transcription in human development and disease are still not fully understood. Here we identify Krüppel-like factor 18 (KLF18) as a component of a DUX4 feed-forward network that is necessary for expression of KLF17 and a subset of the DUX4-regulated totipotency-associated genes.

We mapped the genome-wide binding profile of KLF18 downstream of DUX4 and showed that its activity is influenced by DUX4 and chromatin accessibility. We find that in contrast to the rodent ortholog, human KLF18 has a predicted beta-solenoid structure composed of a variable number of tandem repeats (VNTRs) with multiple different structural variants in the human population. Expression of different KLF18 variants in combination with DUX4 showed similar transcriptional activity, whereas assessment of KLF18 structural variants in individuals with FSHD1 showed inconsistent association with disease severity that requires further study as a modifier locus.