  Our aim is to predict how often genic and non-genic promoters fire within a
cell. We first review a parsimonious pan-genomic model for genome organization
and gene regulation, where transcription rate is determined by proximity in 3D
space of promoters to clusters containing appropriate factors and RNA
polymerases -- structures variously called transcription factories, hubs, and
condensates. This model allows reconciliation of conflicting results indicating
that regulatory mammalian networks are both simple (as over-expressing just 4
transcription factors switches cell state) and complex (as genome-wide
association studies show phenotypes like cell type are determined by thousands
of loci rarely encoding such factors). It also yields simple explanations of
how mysterious motifs like quantitative trait loci, enhancers, and silencers
work. We then present 3D polymer simulations, and a proximity formula based on
our biological model that enables prediction of transcriptional activities of
all promoters in three human cell types. This simple fitting-free formula
contains just one variable (distance on the genetic map to the nearest active
promoter), and we suggest it can be applied to any organism.
