An initial blueprint for myogenic differentiation

Abstract

We have combined genome-wide transcription factor binding and expression profiling to assemble a regulatory network controlling the myogenic differentiation program in mammalian cells. We identified a cadre of overlapping and distinct targets of the key myogenic regulatory factors (MRFs)-MyoD and myogenin-and Myocyte Enhancer Factor 2 (MEF2). We discovered that MRFs and MEF2 regulate a remarkably extensive array of transcription factor genes that propagate and amplify the signals initiated by MRFs. We found that MRFs play an unexpectedly wide-ranging role in directing the assembly and usage of the neuromuscular junction. Interestingly, these factors also prepare myoblasts to respond to diverse types of stress. Computational analyses identified novel combinations of factors that, depending on the differentiation state, might collaborate with MRFs. Our studies suggest unanticipated biological insights into muscle development and highlight new directions for further studies of genes involved in muscle repair and responses to stress and damage.[Keywords: ChIP-on-chip; myogenesis; transcriptional regulation network] Supplemental material is available at http://www.genesdev.org.

Loci-specific histone acetylation profiles associated with transcriptional coactivator p300 during early myoblast differentiation

“…While maintaining a high correlation with transcriptional programs of primary myoblasts, C2C12 myoblasts are less prone to spontaneous differentiation [4,35], and thus they are a system of choice for genome-wide studies of histone modification and associated transcriptional regulators, including p300 in myotubes and proliferating myoblasts [16]. To study the role of p300 in the early steps of differentiation, we performed p300 ChIP-seq analysis in C2C12 myoblasts differentiated for 24 hours in comparison to proliferating myoblasts.…”

“…Previous studies have examined the role of p300 in myotube formation by comparing global p300 occupancy and histone modification of mature myotubes generated from C2C12 myoblasts [16]. Although an in vitro system, it mirrors the molecular processes of primary myoblasts; however, C2C12 myoblast are more synchronized to differentiate and fuse into post-mitotic myotubes [4,35]. Comprehensive gene expression analyses have also shown that myogenic differentiation ensues in a stepwise fashion, where sequential activation of a specific set of genes restructures the cells one step at a time toward the differentiated phenotype [48].…”

DNA microarray technologies for measuring protein–DNA interactions

“…Early ChIP-chip studies in mammalian genomes utilized various types of PCR amplicon arrays, including arrays tiling a specific genomic region of interest [28], CpG island arrays [29], and promoter arrays [30]. Promoter arrays covering roughly −750 bp to +250 bp relative to transcription start sites have been used to analyze binding of HNF1α, HNF4α, and HNF6 in post-mortem human liver and pancreas [31] and muscle regulatory TFs MyoD, myogenin, and MEF2 in differentiating murine C2C12 skeletal muscle cells [32].…”

Intron retention generates ANKRD1 splice variants that are co-regulated with the main transcript in normal and failing myocardium

“…The robust increase in ankrd1 expression after various physiological stimuli or pathological insults suggests the gene appears to be involved in responding to muscle-specific stresses, such as biomechanical stretch, hypertrophic remodeling and sarcomeric dysfunction (Miller et al, 2003;Blais et al, 2005). Although a high stress-induced level of the ankrd1 mRNA results from a rapid burst of gene transcription (Kanai et al, 2001), it is increasingly more recognized that posttranscriptional regulation can also be an important mechanism in terms of controlling ankrd1 transcript and protein abundance (Zolk et al, 2003;Samaras et al, 2007;Witt et al, 2008).…”