Bending and Looping of long DNA by Polycomb repressive complex 2 revealed by AFM imaging in liquid

Polycomb repressive complex 2 (PRC2) is a histone methyltransferase that
methylates histone H3 at Lysine 27. PRC2 is critical for epigenetic gene
silencing, cellular differentiation, and the formation of facultative
heterochromatin. It can also promote or inhibit oncogenesis. Despite this
importance, the molecular mechanisms by which PRC2 compacts chromatin are
relatively understudied. Here, we visualized the binding of PRC2 to naked
DNA in liquid at the single-molecule level using atomic force microscopy.
Analysis of the resulting images showed PRC2, consisting of 5 subunits
(EZH2, EED, SUZ12, AEBP2, and RBBP4), bound to a 2.5-kbp DNA with an
apparent dissociation constant (KdApp) of 150 ± 12 nM. PRC2 did not show
sequence-specific binding to a region of high GC content (76%) derived
from a CpG island embedded in such a long DNA substrate. At higher
concentrations, PRC2 compacted DNA by forming DNA loops typically anchored
by two or more PRC2 molecules. Additionally, PRC2 binding led to a 3-fold
increase in the local bending of DNA’s helical backbone and no evidence of
DNA wrapping around the protein. We suggest that the bending and looping
of DNA by PRC2, independent of PRC2’s methylation activity, may contribute
to heterochromatin formation and therefore epigenetic gene silencing.