Fig. 1

Ontogeny as a software program encoded in the genome and running in the epigenome. The developmental software program is encoded in the DNA sequence. As the program runs, numerous subroutines are called and operate in different spatial and temporal contexts. The epigenome, at the level of DNA methylation (shown), histone modifications, chromatin structure and noncoding RNAs (not shown), acts in cells as the software’s data area. Differences in space and time in the running of the developmental software program (represented by different colours in the code) are also embedded in the epigenome/data area that is read and written by the software and dictates when and which subroutines are run—e.g. different gene expression programs, transcription factors, signalling pathways and protein levels (not shown)—and ultimately determines cellular phenotypes