In 2001, the first nearly complete sequence of a vertebrate genome, the human genome, was published (1, 2). Soon after, several other genomes of vertebrates such as mouse, rat, dog, opossum, and chicken were reported. The tremendous effort put into sequencing and assembling these genome sequences is a prerequisite to furthering our understanding of genetic information and its role in development, disease, and evolution. One of the first insights from comparative genomics was unexpected, namely, that the majority of human genes have a single identifiable ortholog in other vertebrate species (3, 4). Because of the combination of our understanding of the genetic code and comparative genomic sequencing, we know that protein-coding sequences are under strong purifying selection and are, therefore, highly conserved between species (3). However, the vast majority of a vertebrate's genome does not code for proteins, and the evolution and function of those non-coding sequences is poorly understood. Some of the noncoding sequences in the human genome serve regulatory functions, and it was proposed decades ago that regulatory variation may explain many of the phenotypic differences that can be observed between closely related species given the few differences in their protein-coding sequence (5). Exactly how regulatory sequences evolve over evolutionary times remains to be understood and is of particular importance given the frequent involvement of regulatory changes in many human diseases.
A comparison between human and mouse showed that transcription factor binding sites are considerably less conserved than protein-coding sequences (69). My Ph.D. thesis extended these prior analyses by comparing in vivo binding of the tissue-specific transcription factors CEBPA and HNF4A among human, mouse, dog, opossum, and chicken. Although tens of thousands of binding events are found in each individual species and the DNA binding preferences of the transcription factors are highly conserved, most binding is species-specific.
