Neonatal diabetes mutations disrupt a chromatin pioneering function that activates the human insulin gene
Despite the central role of chromosomal context in gene transcription, human noncoding DNA variants are generally studied outside of their endogenous genomic location. This limits our understanding of disease-causing regulatory variants. INS promoter mutations cause recessive neonatal diabetes. We studied 60 patients with such mutations, and show that all single base mutations disrupt a CC dinucleotide, while none affect elements important for INS promoter function in episomal assays. To model CC mutations, we humanized a ~3.1 kb region of the orthologous mouse Ins2 gene. This drove cell-specific transcription and recapitulated developmental chromatin states. A CC mutant allele, however, abrogated active chromatin formation during pancreas development. A search for transcription factors that act through this element revealed that another neonatal diabetes gene product, GLIS3, had a unique pioneer-like ability to derepress INS chromatin, which was hampered by the CC mutation. Our in vivo analysis, therefore, connects two human genetic defects in a pioneering mechanism that underlies developmental activation of the INS gene. This record contains the GLIS3 ChIP-seq and input control in human pancreatic islet cells revealing GLIS3 targets in human islet tissue. Overall design: In vivo analysis of GLIS3 and neonatal diabetes mutations reveal a pioneering essential step in the activation of the insulin gene: Chromatin immunoprecipitation was performed on donor-derived human islets (3000 IEQ). DNA was sequenced  using illumina HiSeq 2500. Raw reads were aligned to hg19 (human genome) and peaks were called using MACS2 against the input control file with q < 0.05.