Exploring function of conserved non-coding DNA in its chromosomal context

There is renewed interest in understanding expression of vertebrate genes in their chromosomal context because regulatory sequences that confer tissue-specific expression are often distributed over large distances along the DNA from the gene. One approach inserts a universal sensor/reporter-gene into the mouse or zebrafish genome to identify regulatory sequences in highly conserved non-coding DNA in the vicinity of the integrated reporter-gene. However detailed mechanisms of interaction of these regulatory elements among themselves and/or with the genes they influence remain elusive with the strategy. The inability to associate distant regulatory elements with the genes they regulate makes it difficult to examine the contribution of sequence changes in regulatory DNA to human disease. Such associations have been obtained in favorable circumstances by testing the regulatory potential of highly conserved non-coding DNA individually in small reporter-gene-containing plasmids. Alternative approaches use tiny fragments of chromosomes in Bacterial Artificial Chromosomes, BACs, where the gene of interest is tagged <em>in vitro</em> with a reporter/sensor gene and integrated into the germ-line of animals for expression. Mutational analysis of the BAC DNA identifies regulatory sequences. A recent approach inserts a sensor/reporter-gene into a BAC that is also truncated progressively from an end of genomic insert, and the end-deleted BAC carrying the sensor is then integrated into the genome of a developing animal for expression. The approach allows mechanisms of tissue-specific gene expression to be explored in much greater detail, although the chromosomal context of such mechanisms is limited to the length of the BAC. Here we discuss the relative strengths of the various approaches and explore how the integrated-sensor in the BACs method applied to a contig of BACs spanning a chromosomal region is likely to address mechanistic questions on interactions between gene and regulatory DNA in greater molecular detail