Stern-Ginossar et al. investigated regulation of protein expression in human cytomegalovirus (HCMV). They analysed patterns of mRNA and protein expression at four time points after infection using transcript analysis and ribosome profiling. Many previously unannotated open reading frames (ORFs), including short ORFs of 21–80 codons, were identified and confirmed by mass spectrometry. Analysis of gene expression through the time course revealed that protein expression was regulated at the level of transcription by the use of alternative transcription start sites that allow many proteins to be produced from one transcript.