PT  - JOURNAL ARTICLE
AU  - Daniel A. Newkirk
AU  - Yen-Yun Chen
AU  - Richard Chien
AU  - Weihua Zeng
AU  - Jacob Biesinger
AU  - Ebony Flowers
AU  - Shimako Kawauchi
AU  - Rosaysela Santos
AU  - Anne L. Calof
AU  - Arthur D. Lander
AU  - Xiaohui Xie
AU  - Kyoko Yokomori
TI  - The effect of Nipped-B-Like (Nipbl) haploinsufficiency on genome-wide cohesin binding and target gene expression: modeling Cornelia de Lange Syndrome
AID  - 10.1101/134825
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 134825
4099  - http://biorxiv.org/content/early/2017/05/05/134825.short
4100  - http://biorxiv.org/content/early/2017/05/05/134825.full
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.