Using the non-perturbative renormalization technique, we calculate the renormalization factors for quark bilinear operators made of overlap fermions on the lattice. The background gauge field is generated by the JLQCD and TWQCD collaborations including dynamical effects of two or 2+1 flavors of light quarks on a 16$^3times$32 or 16$^3times$48 lattice at lattice spacing around 0.1 fm. By reducing the quark mass close to the chiral limit, where the finite volume system enters the so-called $epsilon$-regime, the unwanted effect of spontaneous chiral symmetry breaking on the renormalization factors is suppressed. On the lattices in the conventional $p$-regime, this effect is precisely subtracted by separately calculating the contributions from the chiral condensate.
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