Research proposed is directed to understanding the interplay between complex nuclear structure, gene expression, and genomic organization. It is increasingly recognized that the mammalian nucleus is more complex than earlier envisioned, with a number of distinct intranuclear compartments or "domains" whose functions are yet to be uncovered. Our focus is on the functional relationship of specific gone loci and mRNAs (or pre-mRNAs) with SC35 domains, regions rich in poly (A) RNA and mRNA metabolic factors. A substantial subset of active protein-coding genes position at the immediate periphery of these domains. This positioning is correlated with cell-type specific gene regulation. In contrast, some inactive genes localize to a heterochromatic compartment. In addition, Cajal Bodies associate with snRNA and histone genes while PML domains are known to associate with DNA viruses. Hence, genes are expressed (or repressed) in different nuclear environments. This concept has far-reaching but unexplored implications for gone expression. In Aim 1 we will investigate what sequences or properties of a gene locus determine association with SC35 domains, which we suggest may be reciprocally related to localization in the heterochromatic compartment. The cause and effect relationships between domain association and gene transcription, and the possible influence of "nuclear neighborhood" will be examined. Aim 2 investigates the hypothesis that passage of some largely spliced mRNAs through an SC35 domain is a previously unrecognized step in early transport from the gene, and can be blocked in conditions that perturb nuclear trafficking. Strategies include the analysis of specific human disease mutations that block transport of mutant transcripts, applied specifically to nuclear RNAs carrying triplet repeats in myotonic dystrophy. Aim 3 proposes development of a novel approach that couples bioinformatic analysis of genomic sequence with molecular cytology to investigate potential inter-relationships between chromosomal linkage, gene expression, and nuclear compartments. Hypotheses tested have potential to elucidate the functional evolution of the karyotype and such features as cytogenetic bands and conserved gene clusters, which may associate with distinct intranuclear compartments.