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

Silvana Pileggi,Patrizia Colapietro,Elisa Adele Colombo,Davide Rovina,Monica Miozzo,Annamaria Morotti,Marta La Vecchia,Giovanni Porta,Laura Fontana,Silvia Tabano,Myriam Alcalay,Silvia Maria Sirchia,Cristina Gervasini

doi:10.3390/biom11111622

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.

Highlights

Given that genetic defects in cohesin genes were found to be associated with a general impairment of the 3D chromatin structure of the IGF2/H19 imprinted domain, we investigated the expression profiles in Cornelia de Lange Syndrome (CdLS) lymphoblastoid cell lines (LCLs) in a panel of imprinted genes that are often regulated by a high order of chromatin structure [32,33]
Defects in cohesin function are associated with a group of diseases known as cohesinopathies, notably CdLS
Starting from the evidence that cohesin depletion causes a reduction in the looping interactions in the IGF2/H19 imprinted domain [29], we studied the 3D chromatin structure of this locus in LCLs from CdLS patients with mutations in the SMC1A or NIPBL genes, and evaluated whether constitutive genetic mutations in the cohesin subunit genes can alter chromatin architecture and, gene expression

Summary

Introduction

Cohesin is a ring-shaped complex composed of the SMC family proteins, SMC1 ( known as SMC1A) and SMC3, which function by forming heterodimers with two nonSMC components: RAD21 and SCC3. This core subunit orchestrates long-range DNA interactions to mediate sister chromatid cohesion during the cell cycle, essential for accurate chromosome segregation [4]. The removal of SMC3 from chromatin during prophase and anaphase is mediated by HDAC8, which functions as an SMC3 deacetylase to permit the correct dissolution of pro-cohesive elements and the recycling of “refreshed” cohesin for a new cell cycle [6].

Methods

Results

Conclusion