Regulation of the cohesin-loading factor NIPBL: Role of the lncRNA NIPBL-AS1 and identification of a distal enhancer element

PLoS Genet. 2017 Dec 20;13(12):e1007137. doi: 10.1371/journal.pgen.1007137. eCollection 2017 Dec.

Abstract

Cohesin is crucial for genome stability, cell division, transcription and chromatin organization. Its functions critically depend on NIPBL, the cohesin-loader protein that is found to be mutated in >60% of the cases of Cornelia de Lange syndrome (CdLS). Other mutations are described in the cohesin subunits SMC1A, RAD21, SMC3 and the HDAC8 protein. In 25-30% of CdLS cases no mutation in the known CdLS genes is detected. Until now, functional elements in the noncoding genome were not characterized in the molecular etiology of CdLS and therefore are excluded from mutation screening, although the impact of such mutations has now been recognized for a wide range of diseases. We have identified different elements of the noncoding genome involved in regulation of the NIPBL gene. NIPBL-AS1 is a long non-coding RNA transcribed upstream and antisense to NIPBL. By knockdown and transcription blocking experiments, we could show that not the NIPBL-AS1 gene product, but its actual transcription is important to regulate NIPBL expression levels. This reveals a possibility to boost the transcriptional activity of the NIPBL gene by interfering with the NIPBL-AS1 lncRNA. Further, we have identified a novel distal enhancer regulating both NIPBL and NIPBL-AS1. Deletion of the enhancer using CRISPR genome editing in HEK293T cells reduces expression of NIPBL, NIPBL-AS1 as well as genes found to be dysregulated in CdLS.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Cycle Proteins / genetics
  • Cell Cycle Proteins / metabolism
  • Chromosomal Proteins, Non-Histone / genetics
  • Chromosomal Proteins, Non-Histone / metabolism
  • Chromosome Segregation
  • De Lange Syndrome / genetics
  • Enhancer Elements, Genetic*
  • Gene Expression Regulation
  • Genome, Human
  • HEK293 Cells
  • Humans
  • Mutation
  • Oligonucleotides, Antisense / genetics*
  • Oligonucleotides, Antisense / metabolism*
  • Phenotype
  • Promoter Regions, Genetic
  • Proteins / genetics*
  • Proteins / metabolism*
  • RNA, Long Noncoding / genetics
  • RNA, Long Noncoding / metabolism
  • Sequence Analysis, DNA

Substances

  • Cell Cycle Proteins
  • Chromosomal Proteins, Non-Histone
  • NIPBL protein, human
  • Oligonucleotides, Antisense
  • Proteins
  • RNA, Long Noncoding
  • cohesins

Grant support

Work in the labs of KSW, EW and FJK was supported under the frame of E-Rare-2 (TARGET-CdLS) the ERA-Net for Research on Rare Diseases (http://www.erare.eu/financed-projects/target-cdls) by the respective national research agencies, Netherlands Organization for Health Research and Development (ZonMw, project 40188) (to KSW), the German Federal Ministry of Education and Research (BMBF) (to FJK) and the French National Research Agency (ANR) (to EW). JZ was supported by the Netherlands Organisation for Scientific Research (NWO)(ALW grant dossier 821.02.014) to KSW. FJK was supported by the DFG Research Unit FOR2488 and BMBF—Chromatin-Net (01GM1520C). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.