Genome-wide profiling of nardilysin target genes reveals its role in epigenetic regulation and cell cycle progression

Sci Rep. 2017 Nov 1;7(1):14801. doi: 10.1038/s41598-017-14942-4.

Abstract

Post-translational histone modifications, such as acetylation and methylation, are prerequisites for transcriptional regulation. The metalloendopeptidase nardilysin (Nrdc) is a H3K4me2-binding protein that controls thermoregulation and β-cell functions through its transcriptional coregulator function. We herein combined high-throughput ChIP-seq and RNA-seq to achieve the first genome-wide identification of Nrdc target genes. A ChIP-seq analysis of immortalized mouse embryo fibroblasts (iMEF) identified 4053 Nrdc-binding sites, most of which were located in proximal promoter sites (2587 Nrdc-binding genes). Global H3K4me2 levels at Nrdc-binding promoters slightly increased, while H3K9ac levels decreased in the absence of Nrdc. Among Nrdc-binding genes, a comparative RNA-seq analysis identified 448 candidates for Nrdc target genes, among which cell cycle-related genes were significantly enriched. We confirmed decreased mRNA and H3K9ac levels at the promoters of individual genes in Nrdc-deficient iMEF, which were restored by the ectopic introduction of Nrdc. Reduced mRNA levels, but not H3K9ac levels were fully restored by the reintroduction of the peptidase-dead mutant of Nrdc. Furthermore, Nrdc promoted cell cycle progression at multiple stages, which enhanced cell proliferation in vivo. Collectively, our integrative studies emphasize the importance of Nrdc for maintaining a proper epigenetic status and cell growth.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cell Cycle*
  • Cell Line, Tumor
  • Epigenesis, Genetic*
  • Gene Expression Profiling*
  • Genome-Wide Association Study*
  • Metalloendopeptidases / genetics
  • Metalloendopeptidases / metabolism*
  • Mice
  • Mice, Knockout

Substances

  • Metalloendopeptidases
  • nardilysin