Neonatal diabetes mutations disrupt a chromatin pioneering function that activates the human insulin gene

Abstract

Despite the central role of chromosomal context in gene transcription, human noncoding DNA variants are generally studied outside of their genomic location. This limits our understanding of disease-causing regulatory variants. INS promoter mutations cause recessive neonatal diabetes. We show that all INS promoter point mutations in 60 patients disrupt a CC dinucleotide, whereas none affect other elements important for episomal promoter function. To model CC mutations, we humanized an ∼3.1-kb region of the mouse Ins2 gene. This recapitulated developmental chromatin states and cell-specific transcription. A CC mutant allele, however, abrogated active chromatin formation during pancreas development. A search for transcription factors acting through this element revealed that another neonatal diabetes gene product, GLIS3, has a pioneer-like ability to derepress INS chromatin, which is hampered by the CC mutation. Our in vivo analysis, therefore, connects two human genetic defects in an essential mechanism for developmental activation of the INS gene.

This research was supported by the Birmingham Fellowship Programme, RD Lawrence Fellowship (Diabetes UK, 20/0006136), and Academy of Medical Sciences Springboard (SBF006\1140) to I.A. Other main funding sources (to J.F.) are Ministerio de Ciencia e Innovación (BFU2014-54284-R and RTI2018-095666-B-I00), Medical Research Council (MR/L02036X/1), a Wellcome Trust Senior Investigator Award (WT101033), European Research Council Advanced Grant (789055), and FP6-LIFESCIHEALTH 518153. E.D.F. is a Diabetes UK RD Lawrence Fellow (19/005971). A.T.H. and S.E. are the recipients of a Wellcome Trust Senior Investigator award (WT098395/Z/12/Z). S.E.F. has a Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (105636/Z/14/Z). Human islets for research were supported by the Juvenile Diabetes Research Foundation (2-RSC-2019-724-I-X). Work in CRG was supported by the CERCA Programme, Generalitat de Catalunya, and Centro de Excelencia Severo Ochoa (SEV-2015-0510). CRG acknowledges the support of the Spanish Ministry of Science and Innovation to the EMBL partnership