Linkages between changes in the 3D organization of the genome and transcription during myotube differentiation in vitro

Malina D Doynova,Mark H Vickers,David Cameron-Smith,Justin M O’Sullivan,James F Markworth

doi:10.1186/s13395-017-0122-1

Malina D Doynova, Mark H Vickers + Show 3 more

Open Access

https://doi.org/10.1186/s13395-017-0122-1

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Journal: Skeletal Muscle	Publication Date: Apr 5, 2017
Citations: 48	License type: open-access

Affiliation: University of Auckland

Abstract

BackgroundThe spatial organization of eukaryotic genomes facilitates and reflects the underlying nuclear processes that are occurring in the cell. As such, the spatial organization of a genome represents a window on the genome biology that enables analysis of the nuclear regulatory processes that contribute to mammalian development.MethodsIn this study, Hi-C and RNA-seq were used to capture the genome organization and transcriptome in mouse muscle progenitor cells (C2C12 myoblasts) before and after differentiation to myotubes, in the presence or absence of the cytidine analogue AraC.ResultsWe observed significant local and global developmental changes despite high levels of correlation between the myotubes and myoblast genomes. Notably, the genes that exhibited the greatest variation in transcript levels between the different developmental stages were predominately within the euchromatic compartment. There was significant re-structuring and changes in the expression of replication-dependent histone variants within the HIST1 locus. Finally, treating terminally differentiated myotubes with AraC resulted in additional changes to the transcriptome and 3D genome organization of sets of genes that were all involved in pyroptosis.ConclusionsCollectively, our results provide evidence for muscle cell-specific responses to developmental and environmental stimuli mediated through a chromatin structure mechanism.

Highlights

The spatial organization of eukaryotic genomes facilitates and reflects the underlying nuclear processes that are occurring in the cell
Our results provide evidence for (1) differential and ongoing expression of replicative histone variants within the HIST1 locus during muscle cell development and (2) muscle cell-specific responses to developmental and environmental stimuli mediated through a chromatin structure mechanism
Gene Ontology (GO) terms enriched amongst the genes corresponded to transcription start sites (TSS) having their First principal component (PC1) values and transcript levels decreased during the switch from myoblasts to myotubes

Summary

Introduction

The spatial organization of eukaryotic genomes facilitates and reflects the underlying nuclear processes that are occurring in the cell. Skeletal muscle development (myogenesis) is a complex, multistep process that converts multipotent mesodermal cells into myotubes and, subsequently, muscle fibres [1, 2]. This developmental process commences with progenitor proliferation, continues with exit from the cell cycle, early differentiation, alignment and fusion of the mononucleated myoblasts into multinucleated myotubes (late/terminal differentiation) [1,2,3]. Myod regulates cell cycle arrest by inducing p21 (Cdkn1a), which is a major cyclin-dependent kinase (CDKs) inhibitor; the expression of which results in cell cycle withdrawal [10, 11]. The post-mitotic state of differentiated cells is achieved by the expression of CDK inhibitors and, mainly, p21 (Cdkn1a) [10, 11]

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