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Gene expression analysis from placenta of Cornelia de Lange Syndrome (CdLS) mouse models

ABSTRACT: CdLS is caused by mutaion in cohesin and associated proteins, such as Nipbl and Hdac8. We performed RNA seq analysis from Nipbl+/- and Hdac8-/0 placenta with their respective wild type control at 14.5 dpc, to identify molecular pathways affected. To understand the effect of protein kinase R (PKR) on gene expression we also performed RNA seq analysis from Nipbl+/- and Hdac8-/0 placenta lacking PKR.

ORGANISM(S): Mus musculus

PROVIDER: GSE138687 | GEO | 2020/07/27

REPOSITORIES: GEO

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Project description:The Cohesin apparatus has a canonical role in sister chromatid cohesion. Heterozygous mutations in Nipped B-like (NIPBL), SMC1A, and SMC3 have been found in 60% of probands with Cornelia de Lange Syndrome (CdLS), a dominant multi-system genetic disorder with variable expression. We have performed a genome-wide transcription assessment as well as cohesin binding analysis using human lymphoblastoid cell lines (LCLs) from probands with CdLS and controls. Here, we report a unique profile of genes dysregulated in CdLS that correlates with different clinical presentations. Genome-wide analysis of cohesin binding demonstrates a preference for intergenic regions suggesting a cis-regulatory function mimicking that of an insulator. However, the binding sites are enriched within the promoter regions of the dysregulated genes and are significantly decreased in CdLS probands, indicating an alternative role of cohesin as a classic transcription factor. Cohesin also co-localizes with CTCF at the boundary elements affecting neighboring gene expression in CdLS probands. We propose that the CdLS phenotype is the result of dysregulated gene expression rather than defective sister chromatid cohesion. Phenotype specific expression profiles are also described. Experiment Overall Design: To identify differentially expressed genes between CdLS patients and controls, age and gender matched samples from 16 normal Caucasian controls and 17 clinical severely affected Caucasian patients with NIPBL protein truncating mutations (nonsense or frameshift) were chosen as the training set for the discriminate analysis. To validate the expression pattern obtained from the training set, 6 samples including 1 healthy control, 1 Egyptian CdLS patient, 2 Roberts syndrome patients, and 2 Alagille patients were used as the testing set. All the 39 cell lines were growing anonymously and the processing of these 39 cell lines were randomized by genotypes to eliminate batch effects that may contribute to genotype-specific gene expression

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Gene expression analysis from placenta of Cornelia de Lange Syndrome (CdLS) mouse models

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