Defining the gene expression cascade underlying cell fate determination is a key element in understanding development and diseases that arise due to mis-regulation. The availability of whole genome microarrays and next generation sequencing, coupled with the isolation of nearly pure cell type populations, allows one to begin to define the transcriptome associated with specific cell fates. Muscle cells have been attractive targets for such studies in mature animals due to their ease of isolation and_or culture and their importance in human pathologies. It has been more difficult, however, to determine early in vivo embryonic myogenic gene expression patterns that would give insights into the regulation of muscle development. To this end, we have done both developmental and tissue-specific profiles of gene expression to identify key transcriptional regulators. We continue to study the in vivo target genes activated by the myogenic regulator, HLH-1,a homolog of the vertebrate MyoD family. We have previously shown that ectopic expression of hlh-1 in early C. elegans embryos is sufficient to convert most blastomeres to a body wall muscle like fate. To define the transcriptional targets of HLH-1 that underlie muscle cell fate specification and differentiation, we have use chromatin immunoprecipitation (ChIP) followed by probing whole genome tilling microarrays (chip) and next generation sequencing (seq). The results reveal that the in vivo binding sites for this transcription factor are widespread throughout the genome, similar to what has recently been reported in the mouse. This strongly suggests that these master regulators of myogenesis are acting to control more than just downstream target gene activation, perhaps being also involved in chromatin organization. We have initiated a new focus on somatic gonad muscle cells in an attempt to understand their development. One of the key myogenic transcription factors discovered previously, UNC-120, is also expressed and is required for proper development of this tissue. We seek to identify other transcription regulators that work in combination with UNC-120 to specify this muscle tissue and have approached this by isolation of dissected gonads and RNA-seq profiling.