Eukaryotic genomes have distinct higher-order chromatin structures that are closely packaged functional relates to gene expression. Chromatin compresses the genome to fit into the cell nucleus, while still ensuring that the gene can be accessed when needed, such as during gene transcription, replication, and DNA repair.  The entirety of genome function is based on the underlying relationship between nuclear organization and the mechanisms involved in genome organization, in which there are a number of complex mechanisms and biochemical pathways which can affect the expression of individual genes within the genome. The remaining mitochondrial proteins, metabolic enzymes, DNA and RNA polymerases, ribosomal proteins, and mtDNA regulatory factors are all encoded by nuclear genes. Because nuclear genes constitute the genetic foundation of all eukaryotic organisms, anything that might change their genetic expression has a direct impact on the organism's cellular genotypes and phenotypes. The nucleus also contains a number of distinct subnuclear foci known as nuclear bodies, which are dynamically controlled structures that help numerous nuclear processes run more efficiently. Active genes, for instance, might migrate from chromosomal regions and concentrate into subnuclear foci known as transcription factories.