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

Jessica Zuin; Valentina Casa; Jelena Pozojevic; Petros Kolovos; Mirjam C G N van den Hout; Wilfred F J van Ijcken; Ilaria Parenti; Diana Braunholz; Yorann Baron; Erwan Watrin; Frank J Kaiser; Kerstin S Wendt

doi:10.1371/journal.pgen.1007137

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.

Authors

Affiliations

¹ Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands.
² Section for Functional Genetics at the Institute of Human Genetics, University of Lübeck, Lübeck, Germany.
³ Center for Biomics, Erasmus MC, Rotterdam, The Netherlands.
⁴ Centre National de la Recherche Scientifique, UMR 6290, Rennes, France.
⁵ Institut de Génétique et Développement de Rennes, Faculté de Médecine, Rennes, France.

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
Cohesins
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

Grants and funding

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.