Cohesin Mutations Induce Chromatin Conformation Perturbation of the H19/IGF2 Imprinted Region and Gene Expression Dysregulation in Cornelia de Lange Syndrome Cell Lines

Abstract

Traditionally, Cornelia de Lange Syndrome (CdLS) is considered a cohesinopathy caused by constitutive mutations in cohesin complex genes. Cohesin is a major regulator of chromatin architecture, including the formation of chromatin loops at the imprinted IGF2/H19 domain. We used 3C analysis on lymphoblastoid cells from CdLS patients carrying mutations in NIPBL and SMC1A genes to explore 3D chromatin structure of the IGF2/H19 locus and evaluate the influence of cohesin alterations in chromatin architecture. We also assessed quantitative expression of imprinted loci and WNT pathway genes, together with DMR methylation status of the imprinted genes. A general impairment of chromatin architecture and the emergence of new interactions were found. Moreover, imprinting alterations also involved the expression and methylation levels of imprinted genes, suggesting an association among cohesin genetic defects, chromatin architecture impairment, and imprinting network alteration. The WNT pathway resulted dysregulated: canonical WNT, cell cycle, and WNT signal negative regulation were the most significantly affected subpathways. Among the deregulated pathway nodes, the key node of the frizzled receptors was repressed. Our study provides new evidence that mutations in genes of the cohesin complex have effects on the chromatin architecture and epigenetic stability of genes commonly regulated by high order chromatin structure.

Cornelia de Lange syndrome mutations in NIPBL can impair cohesin-mediated DNA loop extrusion

“…Defects in loop extrusion could explain how NIPBL and cohesin mutations lead to developmental gene dysregulation in CdLS patients, since some of the chromatin loops formed by this process facilitate enhancer–promoter interactions ( 4 , 15 ), and since boundaries between TADs can insulate genes from activation by enhancers in other TADs ( 16 ). Consistent with this prediction, a recent study reported changes in chromatin interactions at the H19-IGF2 locus in CdLS cells ( 17 ). Since CdLS patients carry heterozygous and sometimes mosaic mutations in NIPBL and cohesin genes, and since mouse models have shown that Nipbl heterozygosity only reduces Nipbl transcript levels by 30% ( 9 ), genome architecture changes in CdLS patient-derived cells are expected to be subtle.…”

Cohesin composition and dosage independently affect early development in zebrafish

“…We and others have previously reported dysregulated Wnt signaling upon cohesin mutation (Chin et al, 2020; Grazioli et al, 2021; Mazzola et al, 2019; Medina et al, 2016; Pileggi et al, 2021; Schuster et al, 2015) but the directionality of Wnt signaling disturbance remains unclear. We have shown stabilization of β -catenin and both up- and downregulation of components of the Wnt signaling pathway, indicating that the effects of cohesin deficiency on Wnt are likely to be complex (Chin et al, 2020).…”

Dysfunction in IGF2R Pathway and Associated Perturbations in Autophagy and WNT Processes in Beckwith–Wiedemann Syndrome Cell Lines

“…We used Nanostring technology as it represents a medium-throughput platform to evaluate mRNA abundance profiles providing reproducible and fully automated analyses of the samples. The robustness of this technology is already validated in several papers [46,71,72]. The reliability of Nanostring technology is based on the ability to quantify the expression of multiple genes without amplification steps.…”

“…To investigate the possible involvement of WNT pathway alteration in BWS, we evaluated the expression of 180 genes of the WNT pathways using the Nanostring approach. Of these, 163 were expressed in our LCLs (Table S1) [46].…”