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We would like to be able to predict how genomes are folded in the cell from the primary DNA sequence. A model for the three-dimensional structure of all genomes is presented; it is based on the structure of the bacterial nucleoid, where RNA polymerases cluster and loop the DNA. Loops appear and disappear as polymerases initiate and terminate, but the microscopic structure is 'self-organizing' and, to some extent, predictable. At the macroscopic level, transcriptional activity drives pairing between homologous sequences, inactivity allows genome compaction, and the segregation machinery orients whole chromosomes.
