RT Journal Article
SR Electronic
T1 The effect of Nipped-B-Like (Nipbl) haploinsufficiency on genome-wide cohesin binding and target gene expression: modeling Cornelia de Lange Syndrome
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 134825
DO 10.1101/134825
A1 Daniel A. Newkirk
A1 Yen-Yun Chen
A1 Richard Chien
A1 Weihua Zeng
A1 Jacob Biesinger
A1 Ebony Flowers
A1 Shimako Kawauchi
A1 Rosaysela Santos
A1 Anne L. Calof
A1 Arthur D. Lander
A1 Xiaohui Xie
A1 Kyoko Yokomori
YR 2017
UL http://biorxiv.org/content/early/2017/05/05/134825.abstract
AB Cornelia de Lange Syndrome (CdLS) is a multisystem developmental disorder frequently associated with heterozygous loss-of-function mutations of Nipped-B-like (NIPBL), the human homolog of Drosophila Nipped-B. NIPBL loads cohesin onto chromatin. Cohesin mediates sister chromatid cohesion important for mitosis, but is also increasingly recognized as a regulator of gene expression. In CdLS patient cells and animal models, the presence of multiple gene expression changes with little or no sister chromatid cohesion defect suggests that disruption of gene regulation underlies this disorder. However, the effect of NIPBL haploinsufficiency on cohesin binding, and how this relates to the clinical presentation of CdLS, has not been fully investigated. Nipbl haploinsufficiency causes CdLS-like phenotype in mice. We examined genome-wide cohesin binding and its relationship to gene expression using mouse embryonic fibroblasts (MEFs) from Nipbl +/- mice that recapitulate the CdLS phenotype. We found a global decrease in cohesin binding, including at CCCTC-binding factor (CTCF) binding sites and repeat regions. Cohesin-bound genes were found to be enriched for histone H3 lysine 4 trimethylation (H3K4me3) at their promoters; were disproportionately downregulated in Nipbl mutant MEFs; and displayed evidence of reduced promoter-enhancer interaction. The results suggest that gene activation is the primary cohesin function sensitive to Nipbl reduction. Over 50% of significantly dysregulated transcripts in mutant MEFs come from cohesin target genes, including genes involved in adipogenesis that have been implicated in contributing to the CdLS phenotype. Thus, decreased cohesin binding at the gene regions directly contributes to disease-specific expression changes. Taken together, our Nipbl haploinsufficiency model allows us to analyze the dosage effect of cohesin loading on CdLS development.CTCFCCCCTC-binding factor3CChromatin conformation capture (3C)ChIPChromatin immunoprecipitationCdLSCornelia de Lange SyndromeFDRfalse discovery rateH3K4me3histone H3 lysine 4 trimethylationH3K4me1histone H3 lysine 4 monomethylationH3K27me3histone H3 lysine 27 trimethylationKS testKolmogorov-Smirnov testMEFsmouse embryonic fibroblastsmESCsmouse embryonic stem cellsNipblNipped-B-likePol IIRNA polymerase IIRPKMreads per kb per million total readssiRNAsmall interfering RNATSStranscription start siteTTStranscription termination site.