Transcriptional and Chromatin Dynamics of Muscle Regeneration after Severe Trauma

Abstract

SummaryFollowing injury, adult skeletal muscle undergoes a well-coordinated sequence of molecular and physiological events to promote repair and regeneration. However, a thorough understanding of the in vivo epigenomic and transcriptional mechanisms that control these reparative events is lacking. To address this, we monitored the in vivo dynamics of three histone modifications and coding and noncoding RNA expression throughout the regenerative process in a mouse model of traumatic muscle injury. We first illustrate how both coding and noncoding RNAs in tissues and sorted satellite cells are modified and regulated during various stages after trauma. Next, we use chromatin immunoprecipitation followed by sequencing to evaluate the chromatin state of cis-regulatory elements (promoters and enhancers) and view how these elements evolve and influence various muscle repair and regeneration transcriptional programs. These results provide a comprehensive view of the central factors that regulate muscle regeneration and underscore the multiple levels through which both transcriptional and epigenetic patterns are regulated to enact appropriate repair and regeneration.

Robust inflammatory and fibrotic signaling following volumetric muscle loss: a barrier to muscle regeneration

“…Using RNA-seq on the injured tissues and several types of bioinformatics analyses, the investigators found a series of enriched gene sets associated with chemotaxis and inflammation that were followed by pathways associated with excessive extracellular matrix (ECM) deposition and remodeling. These results were in contrast to many muscle regenerative studies 8 , where inflammatory pathways subsided after several days 9 . Instead, VML injury appears to stimulate complement, Wnt and TGF-β signaling in a sustained fashion, which in turn activates fibrosis development.…”

Single-cell analysis of adult skeletal muscle stem cells in homeostatic and regenerative conditions

“…The transitions experienced by MuSCs during development and regeneration are regulated by partially overlapping and dynamic transcriptional programs (Buckingham and Relaix, 2007;Sincennes et al, 2016;Chang et al, 2018). Bulk transcriptome analyses of MuSCs have contributed important mechanistic insights by providing static snapshots of averaged gene expression (Pallafacchina et al, 2010;Liu et al, 2013;Sousa-Victor et al, 2014;Yennek et al, 2014;Ryall et al, 2015b;Alonso-Martin et al, 2016;Aguilar et al, 2016;Machado et al, 2017;van Velthoven et al, 2017;Pala et al, 2018). The granularity required to identify distinct cell types, states, and their transcriptional dynamics can, however, be provided by single cell analysis.…”

Single Cell Deconstruction of Muscle Stem Cell Heterogeneity During Aging Reveals Sensitivity to the Neuromuscular Junction

“…To understand how MuSCs change with age, MuSCs were extracted from lower hind limb muscles (tibialis anterior-TA and gastrocnemius-Gas) of young (2-3 months) and aged (22-24 mos) wildtype mice using fluorescent activated cell sorting 21 (FACS, Fig. 1b), with both negative (Sca-1 -, CD45 -, Mac-1 -, Ter-119 -) and positive surface markers 22 (CXCR4 + & b1-integrin + ). To further verify these surface markers enriched a pure population of MuSCs, uninjured hindlimb muscles of transgenic mice harboring a Cre/LoxP-based system for MuSC lineage tracing Pax7Cre ER/+ ; Rosa26 mTmG/+ (P7 mTmG ) 23 were utilized.…”