Large parental differences in chromatin organization in pancreatic beta cell line explaining diabetes susceptibility effects

Nat Commun. 2021 Jul 15;12(1):4338. doi: 10.1038/s41467-021-24635-2.


Previous GWAS studies identified non-coding loci with parent-of-origin-specific effects on Type 2 diabetes susceptibility. Here we report the molecular basis for one such locus near the KRTAP5-6 gene on chromosome 11. We determine the pattern of long-range contacts between an enhancer in this locus and the human INS promoter 460 kb away, in the human pancreatic β-cell line, EndoC-βH1. 3C long range contact experiments distinguish contacts on the two sister chromosomes. Coupling with allele-specific SNPs allows construction of maps revealing marked differences in organization of the two sister chromosomes in the entire region between KRTAP5-6 and INS. Further mapping distinguishes maternal and paternal alleles. This reveals a domain of parent-of-origin-specific chromatin structure extending in the telomeric direction from the INS locus. This suggests more generally that imprinted loci may extend their influence over gene expression beyond those loci through long range chromatin structure, resulting in parent-of-origin-biased expression patterns over great distances.

Publication types

  • Research Support, N.I.H., Intramural

MeSH terms

  • Adult
  • Cell Line
  • Chromatin / genetics*
  • Chromatin / metabolism
  • CpG Islands
  • Cytoskeletal Proteins / genetics
  • DNA Methylation
  • Diabetes Mellitus, Type 2 / genetics*
  • Female
  • Genetic Predisposition to Disease
  • Genome-Wide Association Study
  • Humans
  • Insulin / genetics
  • Insulin-Like Growth Factor II / genetics
  • Insulin-Secreting Cells / physiology*
  • Male
  • Mutant Chimeric Proteins / genetics*
  • Polymorphism, Single Nucleotide
  • Promoter Regions, Genetic


  • Chromatin
  • Cytoskeletal Proteins
  • IGF2 protein, human
  • INS-IGF2 protein, human
  • Insulin
  • Mutant Chimeric Proteins
  • keratin-associated protein 5 family, human
  • Insulin-Like Growth Factor II