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Abstract
A layer of dense heterochromatin is found at the periphery of the nucleus. Because
this peripheral heterochromatin functions as a repressive phase, mechanisms that relocate
genes to the periphery play an important role in regulating transcription. Using Monte
Carlo simulations, we show that an interaction that attracts euchromatin and heterochromatin
equally to the nuclear envelope will still preferentially locate heterochromatin to
the nuclear periphery. This observation considerably broadens the class of possible
interactions that result in peripheral positioning to include boundary interactions
that either weakly attract all chromatin or strongly bind to a randomly chosen 0.05%
of nucleosomes. The key distinguishing feature of heterochromatin is its high chromatin
density with respect to euchromatin. In our model, this densification is caused by
heterochromatin protein 1’s preferential binding to histone H3 tails with a methylated
lysine at the ninth residue, a hallmark of heterochromatin. We find that a global
rearrangement of chromatin to place heterochromatin at the nuclear periphery can be
accomplished by attaching a small subset of loci, even if these loci are uncorrelated
with heterochromatin. Hence, factors that densify chromatin determine which genomic
regions condense to form peripheral heterochromatin.