title: A cohesin-independent role for NIPBL at promoters provides insights in CdLS.
abstract: The cohesin complex is crucial for chromosome segregation during mitosis and has recently also been implicated in transcriptional regulation and chromatin architecture. The NIPBL protein is required for the loading of cohesin onto chromatin, but how and where cohesin is loaded in vertebrate cells is unclear. Heterozygous mutations of NIPBL were found in 50% of the cases of Cornelia de Lange Syndrome (CdLS), a human developmental syndrome with a complex phenotype. However, no defects in the mitotic function of cohesin have been observed so far and the links between NIPBL mutations and the observed developmental defects are unclear. We show that NIPBL binds to chromatin in somatic cells with a different timing than cohesin. Further, we observe that high-affinity NIPBL binding sites localize to different regions than cohesin and almost exclusively to the promoters of active genes. NIPBL or cohesin knockdown reduce transcription of these genes differently, suggesting a cohesin-independent role of NIPBL for transcription. Motif analysis and comparison to published data show that NIPBL co-localizes with a specific set of other transcription factors. In cells derived from CdLS patients NIPBL binding levels are reduced and several of the NIPBL-bound genes have previously been observed to be mis-expressed in CdLS. In summary, our observations indicate that NIPBL mutations might cause developmental defects in different ways. First, defects of NIPBL might lead to cohesin-loading defects and thereby alter gene expression and second, NIPBL deficiency might affect genes directly via its role at the respective promoters.
authors.affiliation: Department of Cell Biology, Erasmus MC, Rotterdam, Netherlands.
authors.forename: Jessica
authors.initials: J
authors.lastname: Zuin
authors.affiliation: Computational Biology Unit, Uni Computing, Uni Research AS, Bergen, Norway.
authors.forename: Vedran
authors.initials: V
authors.lastname: Franke
authors.affiliation: Center for Biomics, Erasmus MC, Rotterdam, Netherlands.
authors.forename: Wilfred F J
authors.initials: WF
authors.lastname: van Ijcken
authors.affiliation: Center for Biomics, Erasmus MC, Rotterdam, Netherlands.
authors.forename: Antoine
authors.initials: A
authors.lastname: van der Sloot
authors.affiliation: The Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America.
authors.forename: Ian D
authors.initials: ID
authors.lastname: Krantz
authors.affiliation: Department of Cell Biology, Erasmus MC, Rotterdam, Netherlands.
authors.forename: Michael I J A
authors.initials: MI
authors.lastname: van der Reijden
authors.affiliation: Laboratory of Genome Structure and Function, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan.
authors.forename: Ryuichiro
authors.initials: R
authors.lastname: Nakato
authors.affiliation: Computational Biology Unit, Uni Computing, Uni Research AS, Bergen, Norway ; Department of Biology, University of Bergen, Bergen, Norway.
authors.forename: Boris
authors.initials: B
authors.lastname: Lenhard
authors.affiliation: Department of Cell Biology, Erasmus MC, Rotterdam, Netherlands.
authors.forename: Kerstin S
authors.initials: KS
authors.lastname: Wendt
mesh_terms: D000076246:CCCTC-Binding Factor; D018797:Cell Cycle Proteins / Q000235:genetics* / Q000378:metabolism; D002843:Chromatin / Q000235:genetics; D002868:Chromosomal Proteins, Non-Histone / Q000235:genetics* / Q000378:metabolism; D020090:Chromosome Segregation / Q000235:genetics; D003635:De Lange Syndrome / Q000235:genetics* / Q000473:pathology; D005786:Gene Expression Regulation; D015894:Genome, Human; D006801:Humans; D009154:Mutation; D011401:Promoter Regions, Genetic; D011506:Proteins / Q000235:genetics* / Q000378:metabolism; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic; D000097722:Cohesins
chemical_list: D000076246:CCCTC-Binding Factor; D018797:Cell Cycle Proteins; D002843:Chromatin; D002868:Chromosomal Proteins, Non-Histone; D011506:Proteins; D012097:Repressor Proteins; D000097722:Cohesins; C000619697:CTCF protein, human; C487465:NIPBL protein, human