Models. (A) Targeting to factories. The promoter encoded by the minichromosome in the center can initiate only in a factory containing the appropriate machinery (i.e., one of similar color). As a result, it forms a cluster with two similar minichromosomes by association with the factory on the right. (B) Intron targeting. A newly replicated intron-containing minichromosome is “naïve” (left), and may either bind and initiate (incorrectly) in a nonsplicing (polymerase II) factory (bottom, blue) or a “splicing” factory (top, magenta), where it acquires a mark during splicing (e.g., a histone modification; right) that now targets it to the appropriate (splicing) factory. (C) Chromosome pairing. Just as similar (“homologous”) minichromosomes cluster (“pair”) in A, a similar process may underlie the pairing of homologous chromosomes in both somatic and meiotic cells. For example, during meiosis, homologues seek out and align with their partners before the close synapsis that occurs during recombination. It is now accepted that distinct mechanisms underlie alignment and synapsis, as homologues still align in mutants unable to carry out the later steps (McKee, 2004; Gerton, and Hawley, 2005). During alignment, homologues are transcriptionally active (Cook, 1997) so that each chromosome in the haploid set will possess a unique array of active transcription units running from telomere to telomere. Only the homologue will possess a similar array. Here, only one of the many loops associated with a factory is shown. The yellow promoter on maternal chromosome 2 (2m) is unlikely to bind to the green factory on maternal chromosome 1 (1m). But just as a factory of a particular type nucleates pairing between minichromosomes bearing similar transcription units, correct alignment begins when the yellow (2m) promoter binds to the yellow factory on its homologue (2p). Once transcription of the yellow promoter on 2m begins, 2m and 2p become temporarily tethered together, and this will increase the chances that adjacent promoters bind to homologous factories (i.e, the gray unit on 2m with the gray factory on 2p, etc.). As a result, 2m and 2p eventually become zipped together (arrowhead) and thus aligned.