Overview
Genes function within the physical context of the cell nucleus. Changes to gene positions within the nucleus occur during normal development and in some genetic diseases, particularly in cancers. To better understand how gene function and nuclear structure are related, we are carefully mapping the nuclear locations of several genes that control normal mammalian development. These include genes in a region of mouse chromosome 14, known as the "piebald deletion complex," which shows great similarity to human chromosome 13. The mouse piebald region is organized near the nuclear periphery, a nuclear compartment implicated in gene regulation. We are investigating how gene positioning at the nuclear periphery is related to gene regulation during development. In addition, we are also testing the role of the nuclear periphery in the formation chromosome rearrangements in cancer (lymphoma) cells. These studies will help to elucidate the ways in which genes work together during normal development as well as how gene regulation can go wrong in cancer.
Research details
Three-Dimensional Organization of Chromosomes During Development and Tumorigenesis
Gene organization in the nucleus
We investigate the relationships between mammalian gene expression, chromosome sequence organization, and chromosome structure in the nucleus. We are particularly interested in chromosome architecture as gene expression programs change during normal development and in tumorigenesis. The expression status of a gene correlates with its three-dimensional (3D) organization in the nucleus. Positioning of a gene near functional nuclear "compartments", or near another sequence, can affect its epigenetic markings and its activity. While these structure-function relationships are known to exist for certain genes, the molecular mechanisms controlling them, and the extent of structural networking between many genes across the genome, are poorly understood.
We have recently found that chromosome 3D architecture and spatial associations between genes are related to the gene distribution pattern in the underlying DNA sequence. We focused on a 5 Mb region on distal mouse Chromosome 14 (Mmu14), which is genetically defined by the piebald deletion complex and contains several genes expressed during mouse embryogenesis. These genes are organized in the primary sequence into four clusters separated by gene-poor stretches of ~ 500 kb called "gene deserts". In nuclei where the gene clusters are expressed, this region folds into multiple but non-random 3D structures. These structures are based on the underlying gene cluster-desert sequence pattern. Remarkably, we found that these structures contain multiple gene clusters aggregated together from across the 5 Mb chromosomal region. These findings suggest dynamic 3-D folding states that support a variety of nuclear interactions for diverse developmental genes. We are currently investigating the formation of nuclear gene "hubs" in differentiating cells and developing embryonic tissues where different subsets of the Mmu14 region genes are active.
Gene-gene associations at the nuclear periphery
One key feature of genome organization within the nucleus is that different sequences associate with distinct nuclear "compartments". Nuclear compartments are non-membrane bound regions in the nucleus that accumulate specific proteins and RNAs, and foster certain biochemical activities. We have found that the Mmu14 piebald region is organized near one such compartment, the outermost region of the nucleus containing the nuclear lamina and nuclear envelope. We are now investigating whether components of the nuclear lamina mediate the 3D folding of this region and the spatial associations between its gene clusters. For example, we are collaborating with Dr. Leonard Shultz (The Jackson Laboratory) to test the effects of a lamin B receptor mutation in the icthyosis mouse, a model for Pelger-Huet anomaly with altered heterochromatin distribution in the nucleus.
The nuclear periphery is implicated in gene regulation, by association with transcription factors (e.g., SMADs) and by promoting heterochromatin formation. Interestingly, we have found that the Mmu14 gene deserts preferentially align with the nuclear periphery when gene clusters form hubs. Gene deserts also contain sequences that regulate tissue specific gene expression. Thus, gene deserts may mediate gene expression by a structural mechanism, bridging gene clusters and the nuclear periphery. To identify sequence elements that mediate association with the nuclear periphery, we are collaborating with Dr. Carol Bult (The Jackson Laboratory) to analyze gene desert sequences based on conservation and functional annotation. We also are mapping gene desert sequences in situ relative to the genes they regulate to determine whether they spatially interact, and how these interactions change as a function of gene activity.
Chromosome architecture in lymphoma cells
Our finding that chromosome 3D structure is closely linked to primary sequence organization is particularly relevant to cancer. Virtually all tumor cells harbor chromosome sequence rearrangements, which thus have the potential for long-range "position effects" on multiple genes. We are testing the larger-scale effects of chromosome rearrangements in a mouse model of progenitor B cell lymphoma, in collaboration with Dr. Kevin Mills (The Jackson Laboratory). These lymphoma cells carry a recurrent translocation and a complex amplification of the c-myc locus. Our goal is to determine whether these rearrangements affect the nuclear organization, folding, epigenetic state, and expression of genes beyond those disrupted at chromosomal breakpoints. These studies will provide novel insights into how specific gene expression programs are controlled during tumorigenesis and will point to targets for individualized cancer therapy.
Lab staff
Principal Investigator: Lindsay S. Shopland, Ph.D.
Research Assistant I: Katherine Gassman, B.S., Li Lou, B.S.
Graduate Student: Kathy Snow, B.S.
Postdoctoral Fellow: C. Herbert Pratt, Ph.D.
Research Administrative Assistant: Ashley Stanton
Publication listings
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.
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, Lynch CR, Peterson K, Thornton K, Kepper N, Stein S, Vincent S, Molloy K, Kreth G, Cremer C, Bult CJ, OÍBrien, TP. 2006. Folding and organization of a contiguous chromosome region according to the gene distribution pattern in primary genomic sequence, J. Cell Biol 174: 27-38.
