Role of Muscle-Specific Nuclear Envelope Transmembrane Protein NET39 in Myogenic Genome Organization

Abstract

Studies over the past decade have shown the importance of the nuclear envelope (NE) in regulating genome organization. However, the mechanisms by which different NE components regulate genome organization through space and time in a tissue- specific manner are not completely understood. We utilized the in-vitro C2C12 myogenesis system to study local and genome wide changes in nuclear architecture during myogenesis by correlative studies of Hi-C, DamID and Microarray datasets. Our results show that the genome undergoes dynamic changes in compartmentalization and NE association. Analysis of genes under Lamina Associated Domains (LAD) and Chromatin Compartment control reveals that LADs fine tune genes expression important for myogenesis. However, dynamic changes in LADs and Chromatin Compartments do not necessarily correlate with transcriptional control. Preliminary analysis suggests that LAD functions extend beyond traditional gene regulation to possibly modulate functions of regulatory elements like ncRNA and enhancers. We then investigated potential mechanisms by which a major muscle-specific Nuclear Envelope Transmembrane Protein (NET) NET39, which is known to regulate a subset of LADs, regulates genome organization during myogenesis directly or indirectly via partner proteins identified by analysis of ‘Interactome’ datasets. We report that NET39 does not exert its genome organizing functions by affecting the physical features of the nucleus such as tensional forces, chromocenter organization and nuclear topology. We further show that NET39 regulates deposition of repressive histone modification H3K9Me3 on genes which get repressed during myogenesis. Finally, we also show that a subset of genes that get repressed and localize to the nuclear periphery during myogenesis get reactivated and concomitantly reposition into the nuclear interior, suggesting plasticity in myogenic genome organization. Taken together, our study gives us interesting insights into NE-genome organization interplay in myogenesis.