The Chicken Lysozyme Locus as a Paradigm for the Complex Developmental Regulation of Eukaryotic Gene Loci

Abstract

Gene loci of higher organisms have complex structural features. In some cases their coding regions occupy many, even hundreds, of kilobases of DNA. Additionally, the sequences that contain the information for the correct spatial and temporal regulation of a particular gene locus during development often exceed the extensions of the coding region by severalfold. The question of what type of information is encoded in these vast amounts of DNA has puzzled researchers from the beginning. It is now clear that eukaryotic genes are regulated by a number of different cis-regulatory elements distributed over large distances. A convenient way to assay the number and the distribution of cis-regulatory elements has been the mapping of DHS in chromatin. Such local chromatin perturbations are in most cases caused by the binding of transcription factors to their cognate DNA sequences. The pattern of DHS can undergo dramatic developmental changes, indicating a change in the activity of cis-regulatory elements. In addition, the analysis of protein-DNA interactions at a single-nucleotide resolution level in vivo has demonstrated that, depending on the developmental stage, different combinations of transcription factors can occupy the same cis-regulatory element (1, 2). These experiments indicate that the transcriptional activation of a gene locus is achieved by the cooperation of several different cisregulatory elements, which, in turn, assemble transcription factors in a sequential, developmentally controlled fashion. However, the assembly of active transcription factor complexes on natural genes does not occur on naked DNA but in a chromatin context, where nucleosome-DNA interactions have to be counteracted. Hence, the activation of a gene locus requires at least the following steps: the perturbation of chromatin structure by the binding of transcription factors on cis-regulatory elements, the developmentally controlled reorganization of transcription factor complexes, the assembly of the basal transcription machinery and its interaction with upstream regulatory elements, the onset of mRNA synthesis, and, in many cases, the maintenance of an active transcriptional state during multiple rounds of DNA synthesis. How can the molecular basis of locus activation be experimentally studied? While the basal activities of individual cisregulatory elements of particular gene loci can be analyzed by transient and stable transfection experiments, the molecular mechanism of activation of a gene locus from the transcriptionally silent state can only be studied in a developing system, preferentially in transgenic animals. The ideal model locus should be small, thus facilitating the manipulation of individual cis-regulatory elements within the context of an entire genomic locus, and it should be extensively characterized on the molecular level. In addition, to dissect the role of different cis-regulatory elements in the developmental control of gene locus activation, it should be possible to follow cell differentiation experimentally, thus enabling the linkage of a stage-specific chromatin structure with the transcriptional activity of the gene. Here, we summarize recent studies on the molecular basis of the transcriptional activation of the chicken lysozyme locus, which may serve as a paradigm for other developmentally regulated eukaryotic gene loci.