Genomic Reorganization of Lamin-Associated Domains in Cardiac Myocytes Is Associated With Differential Gene Expression and DNA Methylation in Human Dilated Cardiomyopathy

Abstract

Lamin A/C (LMNA), a nuclear membrane protein, interacts with genome through lamin-associated domains (LADs) and regulates gene expression. Mutations in the LMNA gene cause a diverse array of diseases, including dilated cardiomyopathy (DCM). DCM is the leading cause of death in laminopathies. To identify LADs and characterize their associations with CpG methylation and gene expression in human cardiac myocytes in DCM. LMNA chromatin immunoprecipitation-sequencing, reduced representative bisulfite sequencing, and RNA-sequencing were performed in 5 control and 5 LMNA-associated DCM hearts. LADs were identified using Enriched Domain Detector (EDD) program. Genome wide 331 ± 77 LADs with an average size of 2.1 ± 1.5 Mbp were identified in control human cardiac myocytes. LADs encompassed ~20% of the genome and were predominantly located in the heterochromatin and less so in the promoter and actively transcribed regions. LADs were redistributed in DCM as evidenced by a gain of 520 and loss of 149 genomic regions. Approximately, 4,500 coding genes and 800 long non-coding RNAs (lncRNAs), whose levels correlated with the transcript levels of coding genes in cis, were differentially expressed in DCM. TP53 was the most prominent amongst the dysregulated pathways. CpG sites were predominantly hypomethylated genome-wide in controls and DCM hearts, but overall CpG methylation was increased in DCM. LADs were associated with increased CpG methylation and suppressed gene expression. Integrated analysis identified genes whose expressions were regulated by LADs or CpG methylation, or by both, the latter pertained to genes involved in cell death, cell cycle, and metabolic regulation. LADs encompass ~20% of the genome in human cardiac myocytes comprised of several hundred coding and non-coding genes. LADs are redistributed in LMNA-associated DCM in association with markedly altered CpG methylation and gene expression. Thus, LADs through genomic alterations contribute to the pathogenesis of DCM in laminopathies.