Research interests

Because a chromosome’s primary sequence is carefully folded into the densely packed cell nucleus, its 3-D higher-order structure is likely to play important roles in regulating and coordinating gene expression. Dramatic genome reorganization within the nucleus is a hallmark of normal developing cells and tumors, as are changes in gene expression programs. In addition, a need for 3-D organization is implied by evidence for regulatory mechanisms that extend beyond the sequence of the gene and its local promoter. Co-expressed genes are preferentially clustered together along the linear sequence, and thus may share regulatory sequences within a sub-chromosomal region. Moreover, gene expression can be genetically linked to or controlled by distant sequences. However, an understanding of higher-order chromosome structure has remained elusive, as has its effects on gene expression at this larger scale.

We have addressed whether the ensemble of genes along a stretch of chromosome several Mb in length is spatially coordinated. As a model system, we selected a region of mouse Chromosome 14, defined by the piebald deletion complex. Its central five Mb had been extensively characterized and annotated in a collaboration between Jackson Laboratory Staff Scientist Carol Bult and Dr. Tim O'Brien of Cornell University. This region contains 20 genes, many of which are involved in common pathways and the regulation of multiple developmental processes. Importantly, these genes are grouped in five clusters that are separated by large (500 kb) “gene deserts.” This clear segmentation of genetic information in the primary sequence readily lends itself to cytological examination. In addition, the genetic relationships in this region enable studies of the relationship between 3-D chromosome architecture and mechanisms that coordinate gene expression.

We have directly compared the nuclear locations of all the gene clusters and deserts within this five-Mb model region. Fluorescence in situ hybridization and high-resolution microscopy revealed 3-D organization beyond the linear arrangement of these different sequence segments. Most significantly, multiple gene clusters are further organized into three-dimensionally associated nuclear “hubs.” This discovery has provided a long-sought structural framework for communication between distant genes along the chromosome. The relationship between gene coordination and “hub” formation is now being further defined in deletion mutants and engineered chromosomes. To identify specific sequence elements affecting 3-D chromosome architecture, we are collaborating with Dr. Bult to further query the underlying sequence in light of quantitatively defined structural features. Plans are under way to examine these features at the highest resolution possible, using the new 4Pi confocal laser scanning fluorescence microscope in the Institute for Molecular Biophysics (see External Scientific Collaborations report in this volume). Finally, the nuclear structure of this chromosome region is also being investigated in a variety of developing mouse tissues, with different gene expression programs, to gain further insights into the dynamics and function of 3-D genome architecture.

Publications

• Moen PT, Johnson CV, Byron M, Shopland LS, de la Serna I, Imbalzano A, Lawrence JB. 2004. Repositioning of muscle-specific genes to the periphery of SC-35 domains during skeletal myogenesis. Mol Biol Cell 15:197-206.
• Shopland LS, Johnson CV, Byron M, McNeil J, Lawrence JB. 2003. Clustering of multiple specific genes and gene-rich R-bands around SC-35 domains: Evidence for local euchromatic neighborhoods. J Cell Biol 162:981-990.
• Laboratory for Surface Science and Technology, University of Maine: “Coordinating Operations in Command Central: Nuclear Structure and Function,” Orono, Maine, January 2003.
• Advances in Nanostructural Genomics III Workshop, The Jackson Laboratory: “Linking Primary Sequence with Three-Dimensional Structure: Nuclear Organization of Gene Clusters and Deserts,” Bar Harbor, Maine, October 2003.