Each unit of the D4Z4 macrosatellite repeat contains a retrotransposed gene 
encoding the DUX4 double-homeobox transcription factor. Facioscapulohumeral 
dystrophy (FSHD) is caused by deletion of a subset of the D4Z4 units in the 
subtelomeric region of chromosome 4. Although it has been reported that the 
deletion of D4Z4 units induces the pathological expression of DUX4 mRNA, the 
association of DUX4 mRNA expression with FSHD has not been rigorously 
investigated, nor has any human tissue been identified that normally expresses 
DUX4 mRNA or protein. We show that FSHD muscle expresses a different splice form 
of DUX4 mRNA compared to control muscle. Control muscle produces low amounts of 
a splice form of DUX4 encoding only the amino-terminal portion of DUX4. FSHD 
muscle produces low amounts of a DUX4 mRNA that encodes the full-length DUX4 
protein. The low abundance of full-length DUX4 mRNA in FSHD muscle cells 
represents a small subset of nuclei producing a relatively high abundance of 
DUX4 mRNA and protein. In contrast to control skeletal muscle and most other 
somatic tissues, full-length DUX4 transcript and protein is expressed at 
relatively abundant levels in human testis, most likely in the germ-line cells. 
Induced pluripotent (iPS) cells also express full-length DUX4 and 
differentiation of control iPS cells to embryoid bodies suppresses expression of 
full-length DUX4, whereas expression of full-length DUX4 persists in 
differentiated FSHD iPS cells. Together, these findings indicate that 
full-length DUX4 is normally expressed at specific developmental stages and is 
suppressed in most somatic tissues. The contraction of the D4Z4 repeat in FSHD 
results in a less efficient suppression of the full-length DUX4 mRNA in skeletal 
muscle cells. Therefore, FSHD represents the first human disease to be 
associated with the incomplete developmental silencing of a retrogene array 
normally expressed early in development.